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170  structures 737  species 3  interactions 4243  sequences 455  architectures

Family: RicinB_lectin_2 (PF14200)

Summary: Ricin-type beta-trefoil lectin domain-like

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This is the Wikipedia entry entitled "Ricin". More...

Ricin Edit Wikipedia article

Ricin structure.png
Ricin structure. The A chain is shown in blue and the B chain in orange.
Organism Ricinus communis
Symbol RCOM_2159910
Entrez 8287993
RefSeq (mRNA) XM_002534603.1
RefSeq (Prot) XP_002534649.1
UniProt P02879
Other data
EC number
Chromosome whole genome: 0 - 0.01 Mb
Ribosome inactivating protein (Ricin A chain)
Symbol RIP
Pfam PF00161
InterPro IPR001574
SCOP 1paf
Ricin-type beta-trefoil lectin domain (Ricin B chain)
Symbol N/A
Pfam PF00652
Pfam clan CL0066
SCOP 1abr
CDD cd00161

Ricin (/ˈrsɪn/ RYE-sin) is a highly toxic, naturally occurring lectin (a carbohydrate-binding protein) produced in the seeds of the castor oil plant, Ricinus communis. A dose of purified ricin powder the size of a few grains of table salt can kill an adult human.[1] The median lethal dose (LD50) of ricin is around 22 micrograms per kilogram of body weight if the exposure is from injection or inhalation (1.78 milligrams for an average adult).[2] Oral exposure to ricin is far less toxic as some of the poison is inactivated in the stomach. An estimated lethal oral dose in humans is approximately 1 milligram per kilogram.[2]


Ricin is classified as a type 2 ribosome-inactivating protein (RIP). Whereas type 1 RIPs are composed of a single protein chain that possesses catalytic activity, type 2 RIPs, also known as holotoxins, are composed of two different protein chains that form a heterodimeric complex. Type 2 RIPs consist of an A chain that is functionally equivalent to a type 1 RIP, covalently connected by a single disulfide bond to a B chain that is catalytically inactive, but serves to mediate transport of the A-B protein complex from the cell surface, via vesicle carriers, to the lumen of the endoplasmic reticulum (ER). Both type 1 and type 2 RIPs are functionally active against ribosomes in vitro; however, only type 2 RIPs display cytotoxicity due to the lectin-like properties of the B chain. In order to display its ribosome-inactivating function, the ricin disulfide bond must be reductively cleaved.[3]


Ricin is synthesized in the endosperm of castor oil plant seeds.[4] The ricin precursor protein is 576 amino acid residues in length and contains a signal peptide (residues 1–35), the ricin A chain (36–302), a linker peptide (303–314), and the ricin B chain (315–576).[5] The N-terminal signal sequence delivers the prepropolypeptide to the endoplasmic reticulum (ER) and then the signal peptide is cleaved off. Within the lumen of the ER the propolypeptide is glycosylated and a protein disulfide isomerase catalyzes disulfide bond formation between cysteines 294 and 318. The propolypeptide is further glycosylated within the Golgi apparatus and transported to protein storage bodies. The propolypeptide is cleaved within protein bodies by an endopeptidase to produce the mature ricin protein that is composed of a 267 residue A chain and a 262 residue B chain that are covalently linked by a single disulfide bond.[4]


The quaternary structure of ricin is a globular, glycosylated heterodimer of approximately 60–65 kDa.[6] Ricin toxin A chain and ricin toxin B chain are of similar molecular weights, approximately 32 kDa and 34 kDa, respectively.

  • Ricin toxic A chain (RTA) is an N-glycoside hydrolase composed of 267 amino acids.[7] It has three structural domains with approximately 50% of the polypeptide arranged into alpha-helices and beta-sheets.[8] The three domains form a pronounced cleft that is the active site of RTA.
  • Ricin toxic B chain (RTB) is a lectin composed of 262 amino acids that is able to bind terminal galactose residues on cell surfaces.[9] RTB forms a bilobal, barbell-like structure lacking alpha-helices or beta-sheets where individual lobes contain three subdomains. At least one of these three subdomains in each homologous lobe possesses a sugar-binding pocket that gives RTB its functional character.

While other plants contain the protein chains found in ricin, both protein chains must be present in order to produce toxic effects. For example, plants that contain only protein chain A, such as barley, are not toxic because without the link to protein chain B, protein chain A cannot enter the cell and do damage to ribosomes.[10]

Entry into the cytoplasm

Ricin B chain binds complex carbohydrates on the surface of eukaryotic cells containing either terminal N-acetylgalactosamine or beta-1,4-linked galactose residues. In addition, the mannose-type glycans of ricin are able to bind cells that express mannose receptors.[11] RTB has been shown to bind to the cell surface on the order of 106-108 ricin molecules per cell surface.[12]

The profuse binding of ricin to surface membranes allows internalization with all types of membrane invaginations. The holotoxin can be taken up by clathrin-coated pits, as well as by clathrin-independent pathways including caveolae and macropinocytosis.[13][14] Intracellular vesicles shuttle ricin to endosomes that are delivered to the Golgi apparatus. The active acidification of endosomes is thought to have little effect on the functional properties of ricin. Because ricin is stable over a wide pH range, degradation in endosomes or lysosomes offers little or no protection against ricin.[15] Ricin molecules are thought to follow retrograde transport via early endosomes, the trans-Golgi network, and the Golgi to enter the lumen of the endoplasmic reticulum (ER).[16]

For ricin to function cytotoxically, RTA must be reductively cleaved from RTB in order to release a steric block of the RTA active site. This process is catalysed by the protein PDI (protein disulphide isomerase) that resides in the lumen of the ER.[17][18] Free RTA in the ER lumen then partially unfolds and partially buries into the ER membrane, where it is thought to mimic a misfolded membrane-associated protein.[19] Roles for the ER chaperones GRP94,[20] EDEM[21] and BiP[22] have been proposed prior to the 'dislocation' of RTA from the ER lumen to the cytosol in a manner that utilizes components of the endoplasmic reticulum-associated protein degradation (ERAD) pathway. ERAD normally removes misfolded ER proteins to the cytosol for their destruction by cytosolic proteasomes. Dislocation of RTA requires ER membrane-integral E3 ubiquitin ligase complexes,[23] but RTA avoids the ubiquitination that usually occurs with ERAD substrates because of its low content of lysine residues, which are the usual attachment sites for ubiquitin.[24] Thus, RTA avoids the usual fate of dislocated proteins (destruction that is mediated by targeting ubiquitinylated proteins to the cytosolic proteasomes). In the mammalian cell cytosol, RTA then undergoes triage by the cytosolic molecular chaperones Hsc70 and Hsp90 and their co-chaperones, as well as by one subunit (RPT5) of the proteasome itself, that results in its folding to a catalytic conformation,[20][25] which de-purinates ribosomes, thus halting protein synthesis.

Ribosome inactivation

RTA has rRNA N-glycosylase activity that is responsible for the cleavage of a glycosidic bond within the large rRNA of the 60S subunit of eukaryotic ribosomes.[26] RTA specifically and irreversibly hydrolyses the N-glycosidic bond of the adenine residue at position 4324 (A4324) within the 28S rRNA, but leaves the phosphodiester backbone of the RNA intact.[27] The ricin targets A4324 that is contained in a highly conserved sequence of 12 nucleotides universally found in eukaryotic ribosomes. The sequence, 5’-AGUACGAGAGGA-3’, termed the sarcin-ricin loop, is important in binding elongation factors during protein synthesis.[28] The depurination event rapidly and completely inactivates the ribosome, resulting in toxicity from inhibited protein synthesis. A single RTA molecule in the cytosol is capable of depurinating approximately 1500 ribosomes per minute.

Depurination reaction

Within the active site of RTA, there exist several invariant amino acid residues involved in the depurination of ribosomal RNA.[15] Although the exact mechanism of the event is unknown, key amino acid residues identified include tyrosine at positions 80 and 123, glutamic acid at position 177, and arginine at position 180. In particular, Arg180 and Glu177 have been shown to be involved in the catalytic mechanism, and not substrate binding, with enzyme kinetic studies involving RTA mutants. The model proposed by Mozingo and Robertus,[8] based on X-ray structures, is as follows:

  1. Sarcin-ricin loop substrate binds RTA active site with target adenine stacking against tyr80 and tyr123.
  2. Arg180 is positioned such that it can protonate N-3 of adenine and break the bond between N-9 of the adenine ring and C-1’ of the ribose.
  3. Bond cleavage results in an oxycarbonium ion on the ribose, stabilized by Glu177.
  4. N-3 protonation of adenine by Arg180 allows deprotonation of a nearby water molecule.
  5. Resulting hydroxyl attacks ribose carbonium ion.
  6. Depurination of adenine results in a neutral ribose on an intact phosphodiester RNA backbone.


Castor beans

Ricin is very toxic if inhaled, injected, or ingested. It can also be toxic if dust contacts the eyes or if it is absorbed through damaged skin. It acts as a toxin by inhibiting protein synthesis.[29][30] It prevents cells from assembling various amino acids into proteins according to the messages it receives from messenger RNA in a process conducted by the cell's ribosome (the protein-making machinery)—that is, the most basic level of cell metabolism, essential to all living cells and thus to life itself. Ricin is resistant, but not impervious, to digestion by peptidases. By ingestion, the pathology of ricin is largely restricted to the gastrointestinal tract, where it may cause mucosal injuries. With appropriate treatment, most patients will make a decent recovery.[31][32]

Because the symptoms are caused by failure to make protein, they may take anywhere from hours to days to appear, depending on the route of exposure and the dose. When ingested, gastrointestinal symptoms can manifest within 6 hours; these symptoms do not always become apparent. Within 2 to 5 days of exposure to ricin, effects of ricin on the central nervous system, adrenal glands, kidneys, and liver appear.[30]

Ingestion of ricin causes pain, inflammation, and hemorrhage in the mucous membranes of the gastrointestinal system. Gastrointestinal symptoms quickly progress to severe nausea, vomiting, diarrhea, and difficulty swallowing (dysphagia). Hemorrhage causes bloody feces (melena) and vomiting blood (hematemesis). The low blood volume (hypovolemia) caused by gastrointestinal fluid loss can lead to organ failure in the pancreas, kidney, liver, and GI tract and progress to shock. Shock and organ failure are indicated by disorientation, stupor, weakness, drowsiness, excessive thirst (polydipsia), low urine production (oliguria), and bloody urine (hematuria).[30]

Symptoms of ricin inhalation are different from those caused by ingestion. Early symptoms include a cough and fever.[30]

When skin or inhalation exposure occur, ricin can cause an allergy to develop. This is indicated by edema of the eyes and lips; asthma; bronchial irritation; dry, sore throat; congestion; skin redness (erythema); skin blisters (vesication); wheezing; itchy, watery eyes; chest tightness; and skin irritation.[30]

An antidote has been developed by the UK military, although it has not yet been tested on humans.[33][34] Another antidote developed by the U.S. military has been shown to be safe and effective in lab mice injected with antibody-rich blood mixed with ricin, and has had some human testing.[35]

Symptomatic and supportive treatments are available for ricin poisoning, but there is no commonly available antidote for ricin available. Existing treatments emphasize minimizing the effects of the poison. Possible treatments include intravenous fluids or electrolytes, airway management, assisted ventilation, or giving medications to remedy seizures and low blood pressure. If the ricin has been ingested recently, the stomach can be flushed by ingesting activated charcoal or by performing gastric lavage. Survivors often develop long-term organ damage. Ricin causes severe diarrhea and vomiting, and victims can die of circulatory shock or organ failure; inhaled ricin can cause fatal pulmonary edema or respiratory failure. Death typically occurs within 3–5 days of exposure.[30]

Although there is no antidote currently available for ricin poisoning, vaccination is possible by injecting an inactive form of protein chain A.[10] This vaccination is effective for several months due to the body's production of antibodies to the foreign protein. In 1978 Bulgarian defector Vladimir Kostov survived a ricin attack similar to the one on Georgi Markov, probably due to his body's production of antibodies. When a ricin-laced pellet was removed from the small of his back it was found that some of the original wax coating was still attached. For this reason only small amounts of ricin had leaked out of the pellet, producing some symptoms but allowing his body to develop immunity to further poisoning.[10]

The seeds of Ricinus communis are commonly crushed to extract castor oil. As ricin is not oil-soluble, little is found in the extracted castor oil.[10] The extracted oil is also heated to more than 80 °C to denature any ricin that may be present.[10] The remaining spent crushed seeds, called variously the “cake”, “oil cake”, and “press cake”, can contain up to 5% ricin.[36] While the oil cake from coconut, peanuts, and sometimes cotton seeds can be used as either cattle feed and/or fertilizer, the toxic nature of castor beans precludes their oil cake from being used as feed unless the ricin is first deactivated by autoclaving.[37] Accidental ingestion of Ricinus communis cake intended for fertilizer has been reported to be responsible for fatal ricin poisoning in animals.[29][38]

Deaths from ingesting castor plant seeds are rare, partly because of their indigestible seed coat, and because the body can, although only with difficulty, digest ricin.[6] The pulp from eight beans is considered dangerous to an adult.[39] Rauber and Heard have written that close examination of early 20th century case reports indicates that public and professional perceptions of ricin toxicity "do not accurately reflect the capabilities of modern medical management".[40]


Most acute poisoning episodes in humans are the result of oral ingestion of castor beans, 5–20 of which could prove fatal to an adult. However, swallowing castor beans rarely proves to be fatal unless the bean is thoroughly chewed. The survival rate of castor bean ingestion is 98%.[10] In 2013 a 37-year-old female in the United States survived after ingesting 30 beans.[41] Victims often manifest nausea, diarrhea, fast heart rate, low blood pressure, and seizures persisting for up to a week.[29] Blood, plasma, or urine ricin or ricinine concentrations may be measured to confirm diagnosis. The laboratory testing usually involves immunoassay or liquid chromatography-mass spectrometry.[42]

Therapeutic applications

Although no approved therapeutics are currently based on ricin, it does have the potential to be used in the treatment of tumors, as a "magic bullet" to destroy targeted cells.[15] Because ricin is a protein, it can be linked to a monoclonal antibody to target cancerous cells recognized by the antibody. The major problem with ricin is that its native internalization sequences are distributed throughout the protein. If any of these native internalization sequences are present in a therapeutic agent, the drug will be internalized by, and kill, untargeted non-tumorous cells as well as targeted cancerous cells.

Modifying ricin may sufficiently lessen the likelihood that the ricin component of these immunotoxins will cause the wrong cells to internalize it, while still retaining its cell-killing activity when it is internalized by the targeted cells. However, bacterial toxins, such as diphtheria toxin, which is used in denileukin diftitox, an FDA-approved treatment for leukemia and lymphoma, have proven to be more practical. A promising approach for ricin is to use the non-toxic B subunit (a lectin) as a vehicle for delivering antigens into cells, thus greatly increasing their immunogenicity. Use of ricin as an adjuvant has potential implications for developing mucosal vaccines.


In the U.S., ricin appears on the select agents list of the Department of Health and Human Services,[43] and scientists must register with HHS to use ricin in their research. However, investigators possessing less than 1000 mg are exempt from regulation.[44]

It is classified as an extremely hazardous substance in the United States as defined in Section 302 of the U.S. Emergency Planning and Community Right-to-Know Act (42 U.S.C. 11002), and is subject to strict reporting requirements by facilities that produce, store, or use it in significant quantities.[45]

Chemical or biological warfare agent

A metal vial containing ricin from the 2003 ricin letters

The United States investigated ricin for its military potential during World War I.[46] At that time it was being considered for use either as a toxic dust or as a coating for bullets and shrapnel. The dust cloud concept could not be adequately developed, and the coated bullet/shrapnel concept would violate the Hague Convention of 1899 (adopted in U.S. law at 32 Stat. 1903), specifically Annex §2, Ch.1, Article 23, stating "... it is especially prohibited ... [t]o employ poison or poisoned arms".[47] World War I ended before the United States weaponized ricin.

During World War II the United States and Canada undertook studying ricin in cluster bombs.[48] Though there were plans for mass production and several field trials with different bomblet concepts, the end conclusion was that it was no more economical than using phosgene. This conclusion was based on comparison of the final weapons, rather than ricin's toxicity (LCt50 ~40 mg·min/m3). Ricin was given the military symbol W or later WA.[citation needed] Interest in it continued for a short period after World War II, but soon subsided when the U.S. Army Chemical Corps began a program to weaponize sarin.

The Soviet Union also possessed weaponized ricin. There were speculations that the KGB used it outside the Soviet bloc; however, this was never proven.

Given ricin's extreme toxicity and utility as an agent of chemical/biological warfare, it is noteworthy that the production of the toxin is rather difficult to limit. The castor bean plant from which ricin is derived is a common ornamental and can be grown at home without any special care.

Under both the 1972 Biological Weapons Convention and the 1997 Chemical Weapons Convention, ricin is listed as a schedule 1 controlled substance. Despite this, more than 1 million metric tons of castor beans are processed each year, and approximately 5% of the total is rendered into a waste containing negligible concentrations of undenatured ricin toxin.[49]

Ricin is several orders of magnitude less toxic than botulinum or tetanus toxin, but the latter are harder to come by. Compared to botulinum or anthrax as biological weapons or chemical weapons, the quantity of ricin required to achieve LD50 over a large geographic area is significantly more than an agent such as anthrax (tons of ricin vs. only kilogram quantities of anthrax).[50] Ricin is easy to produce, but is not as practical or likely to cause as many casualties as other agents.[31] Ricin is easily denatured by temperatures over 80 °C (176 °F) meaning many methods of deploying ricin would generate enough heat to denature it.[36] Once deployed, an area contaminated with ricin remains dangerous until the bonds between chain A or B have been broken, a process that takes two or three days.[10] In contrast, anthrax spores may remain lethal for decades. Jan van Aken, a German expert on biological weapons, explained in a report for The Sunshine Project that Al Qaeda’s experiments with ricin suggest their inability to produce botulinum or anthrax.[51]


A biopharmaceutical company called Soligenix, Inc. has licensed an anti-ricin vaccine called RiVax™ from Vitetta et al. at UT Southwestern. The vaccine is safe and immunogenic in mice, rabbits, and humans. It has completed two successful clinical trials.[52]


Ricin has been involved in a number of incidents. In 1978, the Bulgarian dissident Georgi Markov was assassinated by Bulgarian secret police who surreptitiously shot him on a London street with a modified umbrella using compressed gas to fire a tiny pellet contaminated with ricin into his leg.[31][53] He died in a hospital a few days later and his body was passed to a special poison branch of the British Ministry of Defence (MOD) that discovered the pellet during an autopsy. The prime suspects were the Bulgarian secret police: Georgi Markov had defected from Bulgaria some years previously and had subsequently written books and made radio broadcasts that were highly critical of the Bulgarian communist regime. However, it was believed at the time that Bulgaria would not have been able to produce the pellet, and it was also believed that the KGB had supplied it. The KGB denied any involvement, although high-profile KGB defectors Oleg Kalugin and Oleg Gordievsky have since confirmed the KGB's involvement. Earlier, Soviet dissident Aleksandr Solzhenitsyn also suffered (but survived) ricin-like symptoms after an encounter in 1971 with KGB agents.[54]

Ten days before the attack on Georgi Markov another Bulgarian defector, Vladimir Kostov, survived a similar attack. Kostov was standing on an escalator of the Paris metro when he felt a sting in his lower back above the belt of his trousers. He developed a fever, but recovered. After Markov's death the wound on Kostov's back was examined and a ricin-laced pellet identical to the one used against Markov was removed.[10]

Several terrorists and terrorist groups have experimented with ricin and caused several incidents of the poisons being mailed to U.S. politicians. For example, on May 29, 2013 two anonymous letters sent to New York City Mayor Michael Bloomberg contained traces of it.[55] Another was sent to the offices of Mayors Against Illegal Guns in Washington DC. A letter containing ricin was also alleged to have been sent to American President Barack Obama at the same time. An actress, Shannon Richardson, was later charged with the crime, to which she pleaded guilty that December.[56] On July 16, 2014, Richardson was sentenced to 18 years in prison plus a restitution fine of $367,000.[57]

In popular culture

Ricin has often been used as a plot device, such as in the television series Breaking Bad (Season 2, Season 4 and Season 5).[58]

The popularity of Breaking Bad inspired several real-life criminal cases involving ricin or similar substances. Kuntal Patel from London attempted to poison her "controlling and selfish" mother with abrin after the latter interfered with her marriage plans.[59] Daniel Milzman, a 19-year-old former Georgetown University student, was charged with manufacturing ricin in his dorm room, as well as the intent of "[using] the ricin on another undergraduate student with whom he had a relationship".[60] Mohammed Ali from Liverpool, England was convicted after attempting to purchase 500 mg of ricin over the dark web from an undercover FBI agent. He was sentenced, on 18 September 2015, to 8 years' imprisonment.[61]

See also


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  31. ^ a b c Schep LJ, Temple WA, Butt GA, Beasley MD (November 2009). "Ricin as a weapon of mass terror—separating fact from fiction". Environ Int. 35 (8): 1267–71. doi:10.1016/j.envint.2009.08.004. PMID 19767104. 
  32. ^ Kopferschmitt J, Flesch F, Lugnier A, Sauder P, Jaeger A, Mantz JM (April 1983). "Acute voluntary intoxication by ricin". Hum Toxicol. 2 (2): 239–42. doi:10.1177/096032718300200211. PMID 6862467. 
  33. ^ Rincon P (2009-11-11). "Ricin 'antidote' to be produced". BBC News. Retrieved 2010-09-01. 
  34. ^ "Human trial proves ricin vaccine safe, induces neutralizing antibodies; further tests planned". University of Texas Southwestern Medical Center. 2006-01-30. Archived from the original on September 27, 2011. Retrieved 2012-05-07. 
  35. ^ Karen Fleming-Michael (2005-09-01). "Vaccine for ricin toxin developed at Detrick lab". Archived from the original on 2012-05-24. Retrieved 2010-09-01. 
  36. ^ a b Levy, Joey (2011). Poison: An Illustrated History. Guilford, Connecticut: Lyons Press. p. 133. ISBN 978-0-7627-7056-4. 
  37. ^ "Oil cake (chemistry)". Encyclopædia Britannica. 
  38. ^ Soto-Blanco B, Sinhorini IL, Gorniak SL, Schumaher-Henrique B (June 2002). "Ricinus communis cake poisoning in a dog". Vet Hum Toxicol. 44 (3): 155–6. PMID 12046967. 
  39. ^ Wedin GP, Neal JS, Everson GW, Krenzelok EP (May 1986). "Castor bean poisoning". Am J Emerg Med. 4 (3): 259–61. doi:10.1016/0735-6757(86)90080-X. PMID 3964368. 
  40. ^ Rauber A, Heard J (December 1985). "Castor bean toxicity re-examined: a new perspective". Vet Hum Toxicol. 27 (6): 498–502. PMID 4082461. 
  41. ^ "Survived after ingesting 30 castor beans". The Salt Lake Tribune. October 3, 2013. Retrieved 2014-08-03. 
  42. ^ Baselt RC (2011). Disposition of Toxic Drugs and Chemicals in Man (Ninth ed.). Seal Beach, California: Biomedical Publications. pp. 1497–1499. ISBN 978-0-9626523-8-7. 
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  44. ^ "Permissible Toxin Amounts". National Select Agent Registry. Retrieved 28 June 2017. 
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  47. ^ "The Avalon Project — Laws of War : Laws and Customs of War on Land (Hague II); July 29, 1899". Retrieved 2010-09-01. 
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  49. ^ "Cornell University Department of Animal Science". Retrieved 2012-05-07. 
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External links

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Ricin-type beta-trefoil lectin domain-like Provide feedback

No Pfam abstract.

Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000772

Ricin is a legume lectin from the seeds of the castor bean plant, Ricinus communis. The seeds are poisonous to people, animals and insects and just one milligram of ricin can kill an adult.

Primary structure analysis has shown the presence of a similar domain in many carbohydrate-recognition proteins like plant and bacterial AB-toxins, glycosidases or proteases [PUBMED:9603958, PUBMED:7664090, PUBMED:8844840]. This domain, known as the ricin B lectin domain, can be present in one or more copies and has been shown in some instance to bind simple sugars, such as galactose or lactose.

The ricin B lectin domain is composed of three homologous subdomains of 40 amino acids (alpha, beta and gamma) and a linker peptide of around 15 residues (lambda). It has been proposed that the ricin B lectin domain arose by gene triplication from a primitive 40 residue galactoside-binding peptide [PUBMED:3561502, PUBMED:1881882]. The most characteristic, though not completely conserved, sequence feature is the presence of a Q-W pattern. Consequently, the ricin B lectin domain as also been refered as the (QxW)3 domain and the three homologous regions as the QxW repeats [PUBMED:7664090, PUBMED:8844840]. A disulphide bond is also conserved in some of the QxW repeats [PUBMED:7664090].

The 3D structure of the ricin B chain has shown that the three QxW repeats pack around a pseudo threefold axis that is stabilised by the lambda linker [PUBMED:3561502]. The ricin B lectin domain has no major segments of a helix or beta sheet but each of the QxW repeats contains an omega loop [PUBMED:1881882]. An idealized omega-loop is a compact, contiguous segment of polypeptide that traces a 'loop-shaped' path in three-dimensional space; the main chain resembles a Greek omega.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan Trefoil (CL0066), which has the following description:

This family corresponds to a large set of related beta-trefoil proteins [1]. The beta-trefoil is formed by six two-stranded hairpins [2]. Three of these form a barrel structure and the other three are in a triangular array that caps the barrel. The arrangement of the secondary structures gives the molecules a pseudo 3-fold axis.

The clan contains the following 20 members:

AbfB Agglutinin Botulinum_HA-17 BTD CDtoxinA DUF569 Fascin FGF FRG1 IL1 IL33 Inhibitor_I48 Inhibitor_I66 Ins145_P3_rec Kunitz_legume MIR NTNH_C Ricin_B_lectin RicinB_lectin_2 Toxin_R_bind_C


We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

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Key: ✓ available, x not generated, not available.

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Representative proteomes UniProt

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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...


This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Jackhmmer:Q8X123
Previous IDs: none
Type: Domain
Author: Coggill P
Number in seed: 274
Number in full: 4243
Average length of the domain: 81.90 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 27.69 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.6 25.6
Trusted cut-off 25.6 25.6
Noise cut-off 25.5 25.5
Model length: 89
Family (HMM) version: 5
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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The tree shows the occurrence of this domain across different species. More...


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There are 3 interactions for this family. More...

Crystall Crystall RicinB_lectin_2


For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the RicinB_lectin_2 domain has been found. There are 170 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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