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327  structures 1701  species 0  interactions 16672  sequences 710  architectures

Family: Ricin_B_lectin (PF00652)

Summary: Ricin-type beta-trefoil lectin domain

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Ricin-type beta-trefoil lectin domain Provide feedback

No Pfam abstract.

Internal database links

External 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 23 members:

AbfB Agglutinin Agglutinin_C Botulinum_HA-17 BTD CDtoxinA DUF569 Fascin FGF FRG1 IL1 IL33 Inhibitor_I48 Inhibitor_I66 Ins145_P3_rec Kunitz_legume Lectin_C_term Lipoprotein_11 MIR NTNH_C Ricin_B_lectin RicinB_lectin_2 Toxin_R_bind_C

Alignments

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 and the UniProtKB 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.

  Seed
(85)
Full
(16672)
Representative proteomes UniProt
(40038)
RP15
(1990)
RP35
(6109)
RP55
(15181)
RP75
(22983)
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HTML View             
PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(85)
Full
(16672)
Representative proteomes UniProt
(40038)
RP15
(1990)
RP35
(6109)
RP55
(15181)
RP75
(22983)
Alignment:
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Sequence:
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Download options

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.

  Seed
(85)
Full
(16672)
Representative proteomes UniProt
(40038)
RP15
(1990)
RP35
(6109)
RP55
(15181)
RP75
(22983)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download  

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...

Trees

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: Prosite
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 85
Number in full: 16672
Average length of the domain: 120.70 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 20.64 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 29.0 29.0
Trusted cut-off 29.0 29.0
Noise cut-off 28.9 28.9
Model length: 127
Family (HMM) version: 24
Download: download the raw HMM for this family

Species distribution

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Selections

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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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Structures

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 Ricin_B_lectin domain has been found. There are 327 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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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0G2JG52 View 3D Structure Click here
A0A0G2JU25 View 3D Structure Click here
A0A0G2K2W0 View 3D Structure Click here
A0A0G2KK98 View 3D Structure Click here
A0A0G2L6V9 View 3D Structure Click here
A0A0R4IGF6 View 3D Structure Click here
A0A0R4IRC9 View 3D Structure Click here
A0A1D6EN25 View 3D Structure Click here
A0A1D6EN25 View 3D Structure Click here
A0A286Y879 View 3D Structure Click here
A0A286Y8F2 View 3D Structure Click here
A0A286YBK3 View 3D Structure Click here
A0A2R8QSL1 View 3D Structure Click here
A1A5P1 View 3D Structure Click here
B0V0U4 View 3D Structure Click here
B8A6C4 View 3D Structure Click here
D3ZD31 View 3D Structure Click here
D3ZD79 View 3D Structure Click here
D3ZQA1 View 3D Structure Click here
D3ZTT8 View 3D Structure Click here
D4A3A9 View 3D Structure Click here
D4A864 View 3D Structure Click here
E5D8G1 View 3D Structure Click here
E7EZL6 View 3D Structure Click here
E7F4H6 View 3D Structure Click here
E7FDA0 View 3D Structure Click here
F1LQN1 View 3D Structure Click here
F1M8T4 View 3D Structure Click here
F1Q6D3 View 3D Structure Click here
F1R0I8 View 3D Structure Click here
F1R7M5 View 3D Structure Click here
F1R913 View 3D Structure Click here
G3X942 View 3D Structure Click here
O08832 View 3D Structure Click here
O08912 View 3D Structure Click here
O45947 View 3D Structure Click here
O61394 View 3D Structure Click here
O61397 View 3D Structure Click here
O88422 View 3D Structure Click here
P22897 View 3D Structure Click here
P34678 View 3D Structure Click here
P70419 View 3D Structure Click here
P9WLX9 View 3D Structure Click here
Q10471 View 3D Structure Click here
Q10472 View 3D Structure Click here
Q10473 View 3D Structure Click here
Q14435 View 3D Structure Click here
Q1LVP1 View 3D Structure Click here
Q1LVP2 View 3D Structure Click here
Q3T1J4 View 3D Structure Click here
Q49A17 View 3D Structure Click here
Q54BF5 View 3D Structure Click here
Q54FW5 View 3D Structure Click here
Q55FW5 View 3D Structure Click here
Q5RFV2 View 3D Structure Click here
Q61830 View 3D Structure Click here
Q6AYA4 View 3D Structure Click here
Q6IS24 View 3D Structure Click here
Q6NX01 View 3D Structure Click here
Q6P6V1 View 3D Structure Click here
Q6P9A2 View 3D Structure Click here
Q6P9S7 View 3D Structure Click here
Q6PB93 View 3D Structure Click here
Q6UE39 View 3D Structure Click here
Q6WV16 View 3D Structure Click here
Q6WV17 View 3D Structure Click here
Q6WV19 View 3D Structure Click here
Q6WV20 View 3D Structure Click here
Q75JP7 View 3D Structure Click here
Q7K755 View 3D Structure Click here
Q7TT15 View 3D Structure Click here
Q7Z1I0 View 3D Structure Click here
Q7Z1Z9 View 3D Structure Click here
Q7Z202 View 3D Structure Click here
Q7Z203 View 3D Structure Click here
Q7Z7M9 View 3D Structure Click here
Q80VA0 View 3D Structure Click here
Q80W49 View 3D Structure Click here
Q86SF2 View 3D Structure Click here
Q86SR1 View 3D Structure Click here
Q8BGT9 View 3D Structure Click here
Q8BVG5 View 3D Structure Click here
Q8C102 View 3D Structure Click here
Q8C7U7 View 3D Structure Click here
Q8CF93 View 3D Structure Click here
Q8I136 View 3D Structure Click here
Q8IA41 View 3D Structure Click here
Q8IA42 View 3D Structure Click here
Q8IA43 View 3D Structure Click here
Q8IA44 View 3D Structure Click here
Q8IUC8 View 3D Structure Click here
Q8IXK2 View 3D Structure Click here
Q8K1B9 View 3D Structure Click here
Q8MRC9 View 3D Structure Click here
Q8MV48 View 3D Structure Click here
Q8MVS5 View 3D Structure Click here
Q8MYY6 View 3D Structure Click here
Q8N3T1 View 3D Structure Click here
Q8N428 View 3D Structure Click here
Q8N4A0 View 3D Structure Click here
Q8NCL4 View 3D Structure Click here
Q8NCW6 View 3D Structure Click here
Q921L8 View 3D Structure Click here
Q925R7 View 3D Structure Click here
Q95ZJ1 View 3D Structure Click here
Q96FL9 View 3D Structure Click here
Q9D2N8 View 3D Structure Click here
Q9HCQ5 View 3D Structure Click here
Q9JJ61 View 3D Structure Click here
Q9NY28 View 3D Structure Click here
Q9R0C5 View 3D Structure Click here
Q9U2C4 View 3D Structure Click here
Q9VUT6 View 3D Structure Click here
Q9Y117 View 3D Structure Click here
Q9Y4K1 View 3D Structure Click here
X1WFC6 View 3D Structure Click here
X1WGF8 View 3D Structure Click here