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5  structures 2  species 1  interaction 3  sequences 1  architecture

Family: HDV_ag (PF01517)

Summary: Hepatitis delta virus delta antigen

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This is the Wikipedia entry entitled "Hepatitis D". More...

Hepatitis D Edit Wikipedia article

Hepatitis D
Classification and external resources
Specialty infectious disease
ICD-10 B17.0, B18.0
ICD-9-CM 070.31
DiseasesDB 5792
MeSH D003699

Hepatitis D (hepatitis delta) is a disease caused by the hepatitis D virus (HDV), a small spherical enveloped virusoid. This is one of five known hepatitis viruses: A, B, C, D, and E. HDV is considered to be a subviral satellite because it can propagate only in the presence of the hepatitis B virus (HBV).[1] Transmission of HDV can occur either via simultaneous infection with HBV (coinfection) or superimposed on chronic hepatitis B or hepatitis B carrier state (superinfection).

Both superinfection and coinfection with HDV results in more severe complications compared to infection with HBV alone. These complications include a greater likelihood of experiencing liver failure in acute infections and a rapid progression to liver cirrhosis, with an increased risk of developing liver cancer in chronic infections.[2] In combination with hepatitis B virus, hepatitis D has the highest fatality rate of all the hepatitis infections, at 20%.


Hepatitis D
Schematic representation of the hepatitis delta virus virion.
Virus classification
Group: Group V ((−)ssRNA)
Order: Unassigned
Family: Unassigned
Genus: Deltavirus
Species: Hepatitis delta virus

Structure and genome

Hepatitis delta virus delta antigen
PDB 1a92 EBI.jpg
oligomerization domain of hepatitis delta antigen
Symbol HDV_ag
Pfam PF01517
InterPro IPR002506
SCOP 1a92

The HDV is a small, spherical virus with a 36 nm diameter. It has an outer coat containing three kinds of HBV envelope protein - large, medium, and small hepatitis B surface antigens - and host lipids surrounding an inner nucleocapsid. The nucleocapsid contains single-stranded, circular RNA of 1679 nucleotides and about 200 molecules of hepatitis D antigen (HDAg) for each genome. The central region of HDAg has been shown to bind RNA.[3] Several interactions are also mediated by a coiled-coil region at the N terminus of HDAg.[4] The hepatitis D circular genome is unique to animal viruses because of its high GC nucleotide content. The HDV genome exists as an enveloped, negative sense, single-stranded, closed circular RNA. Its nucleotide sequence is 70% self-complementary, allowing the genome to form a partially double-stranded, rod-like RNA structure.[5] With a genome of approximately 1700 nucleotides, HDV is the smallest "virus" known to infect animals. It has been proposed that HDV may have originated from a class of plant pathogens called viroids, which are much smaller than viruses.[6][7]

Life cycle

Like Hepatitis B, HDV gains entry into liver cells via the NTCP[8] bile transporter. HDV recognizes its receptor via the N-terminal domain of the large hepatitis B surface antigen, HBsAg.[9] Mapping by mutagenesis of this domain has shown that amino acid residues 9–15 make up the receptor binding site.[10] After entering the hepatocyte, the virus is uncoated and the nucleocapsid translocated to the nucleus due to a signal in HDAg[11] Since the nucleocapsid does not contain an RNA polymerase to replicate the virus’ genome, the virus makes use of the cellular RNA polymerases. Initially just RNA pol II,[12][13] now RNA polymerases I and III have also been shown to be involved in HDV replication[14] Normally RNA polymerase II utilizes DNA as a template and produces mRNA. Consequently, if HDV indeed utilizes RNA polymerase II during replication, it would be the only known animal pathogen capable of using a DNA-dependent polymerase as an RNA-dependent polymerase.

The RNA polymerases treat the RNA genome as double stranded DNA due to the folded rod-like structure it is in. Three forms of RNA are made; circular genomic RNA, circular complementary antigenomic RNA, and a linear polyadenylated antigenomic RNA, which is the mRNA containing the open reading frame for the HDAg. Synthesis of antigenomic RNA occurs in the nucleolus, mediated by RNA Pol I, whereas synthesis of genomic RNA takes place in the nucleoplasm, mediated by RNA Pol II.[15] HDV RNA is synthesized first as linear RNA that contains many copies of the genome. The genomic and antigenomic RNA contain a sequence of 85 nucleotides, the Hepatitis delta virus ribozyme, that acts as a ribozyme, which self-cleaves the linear RNA into monomers. These monomers are then ligated to form circular RNA.[16][17]

There are eight reported genotypes of HDV with unexplained variations in their geographical distribution and pathogenicity.

Delta antigens

A significant difference between viroids and HDV is that, while viroids produce no proteins, HDV is known to produce one protein, namely HDAg. It comes in two forms; a 27kDa large-HDAg, and a small-HDAg of 24kDa. The N-terminals of the two forms are identical, they differ by 19 more amino acids in the C-terminal of the large HDAg.[18] Both isoforms are produced from the same reading frame which contains an UAG stop codon at codon 196, which normally produces only the small-HDAg. However, editing by cellular enzyme adenosine deaminase-1 changes the stop codon to UGG, allowing the large-HDAg to be produced.[18][19] Despite having 90% identical sequences, these two proteins play diverging roles during the course of an infection. HDAg-S is produced in the early stages of an infection and enters the nucleus and supports viral replication. HDAg-L, in contrast, is produced during the later stages of an infection, acts as an inhibitor of viral replication, and is required for assembly of viral particles.[20][21][22] Thus RNA editing by the cellular enzymes is critical to the virus’ life cycle because it regulates the balance between viral replication and virion assembly.

Antigenic Loop Infectivity

The HDV envelope protein has three of the HBV surface proteins anchored to it. The S region of the genome is most commonly expressed and its main function is to assemble subviral particles. HDV antigen proteins can combine with the viral genome to form a ribonucleoprotein (RNP) which when enveloped with the subviral particles can form viral-like particles that are almost identical to mature HDV, but they are not infectious. Researchers had concluded that the determinant of infectivity of HDV was within the N-terminal pre-S1 domain of the large protein (L). It was found to be a mediator in binding to the cellular receptor. Recently, researchers Georrges Abou Jaoudé and Camille Sureau published an article that studied the role of the antigenic loop, found in HDV envelope proteins, in the infectivity of the virus. The antigenic loop, like the N-terminal pre-S1 domain of the large protein, is exposed at the virion surface. Jaoudé and Sureau’s study provided evidence that the antigenic loop may be an important factor in HDV entry into the host cell and by mutating parts of the antigenic loop, the infectivity of HDV may be minimized.[23]


The routes of transmission of hepatitis D are similar to those for hepatitis B. Infection is largely restricted to persons at high risk of hepatitis B infection, particularly injecting drug users and persons receiving clotting factor concentrates. Worldwide more than 15 million people are co-infected. HDV is rare in most developed countries, and is mostly associated with intravenous drug use. However, HDV is much more common in the immediate Mediterranean region, sub-Saharan Africa, the Middle East, and the northern part of South America.[24] In all, about 20 million people may be infected with HDV.[25]

Treatment and prevention

The vaccine for hepatitis B protects against hepatitis D virus because of the latter's dependence on the presence of hepatitis B virus for it to replicate.[26][27]

Latest evidence suggests that Pegylated interferon alpha is effective in reducing the viral load and the effect of the disease during the time the drug is given, but the benefit generally stops if the drug is discontinued.[28] The efficiency of the pegylated interferon treatment does not usually exceed ~20%.[29]


Hepatitis D virus was first reported in the mid-1977 as a nuclear antigen in patients infected with HBV who had severe liver disease.[30] This nuclear antigen was then thought to be a hepatitis B antigen and was called the delta antigen. Subsequent experiments in chimpanzees showed that the hepatitis delta antigen (HDAg) was a structural part of a pathogen that required HBV infection to replicate.[31] The entire genome was cloned and sequenced in 1986. It was subsequently placed in its own genus: Deltavirus.[32][33]


Three genotypes (I–III) were originally described. Genotype I has been isolated in Europe, North America, Africa and some Asia. Genotype II has been found in Japan, Taiwan, and Yakutia (Russia). Genotype III has been found exclusively in South America (Peru, Colombia, and Venezuela). Some genomes from Taiwan and the Okinawa islands have been difficult to type but have been placed in genotype 2. However it is now known that there are at least 8 genotypes of this virus (HDV-1 to HDV-8).[34] Phylogenetic studies suggest an African origin for this pathogen.[24]

An analysis of 36 strains of genotype 3 estimated that the most recent common ancestor of these strains originated around 1930.[35] This genotype spread exponentially from early 1950s to the 1970s in South America. The substitution rate was estimated to be 1.07×10−3 substitutions per site per year.

Another study[36] found an overall evolution rate of 3.18 x 10×10−3 substitutions per site per year. The mutation rate varied with position : the hypervariable region evolved faster (4.55 x 10×10−3 substitutions per site per year) than the hepatitis delta antigen coding region (2.60 x 10×10−3 substitutions per site per year) and the autocatalytic region (1.11 x 10×10−3 substitutions per site per year).

A third study suggested a mutation rate between 9.5x10×10−3 to 1.2x10×10−3 substitutions/site/year.[37]

Genotype 8 has also been isolated from South America. This genotype is usually only found in Africa and may have been imported into South America during the slave trade.[38]

Genotypes, with the exception of type 1, appear to be restricted to certain geographical areas: HDV-2 (previously HDV-IIa) is found in Japan, Taiwan and Yakoutia, Russia; HDV-4 (previously HDV-IIb) in Japan and Taiwan; HDV-3 in the Amazonian region; HDV-5, HDV-6, HDV-7 and HDV-8 in Africa.[39]

See also


  1. ^ Makino S, Chang MF, Shieh CK, Kamahora T, Vannier DM, Govindarajan S, Lai MM (1987). "Molecular cloning and sequencing of a human hepatitis delta (delta) virus RNA". Nature. 329 (6137): 343–6. doi:10.1038/329343a0. PMID 3627276. 
  2. ^ Fattovich G, Giustina G, Christensen E, Pantalena M, Zagni I, Realdi G, Schalm SW (March 2000). "Influence of hepatitis delta virus infection on morbidity and mortality in compensated cirrhosis type B. The European Concerted Action on Viral Hepatitis (Eurohep)". Gut. 46 (3): 420–6. doi:10.1136/gut.46.3.420. PMC 1727859Freely accessible. PMID 10673308. 
  3. ^ Poisson F, Roingeard P, Baillou A, Dubois F, Bonelli F, Calogero RA, Goudeau A (November 1993). "Characterization of RNA-binding domains of hepatitis delta antigen". The Journal of General Virology. 74 (Pt 11): 2473–8. doi:10.1099/0022-1317-74-11-2473. PMID 8245865. 
  4. ^ Zuccola HJ, Rozzelle JE, Lemon SM, Erickson BW, Hogle JM (July 1998). "Structural basis of the oligomerization of hepatitis delta antigen". Structure. 6 (7): 821–30. doi:10.1016/S0969-2126(98)00084-7. PMID 9687364. 
  5. ^ Saldanha JA, Thomas HC, Monjardino JP (July 1990). "Cloning and sequencing of RNA of hepatitis delta virus isolated from human serum". The Journal of General Virology. 71 (7): 1603–6. doi:10.1099/0022-1317-71-7-1603. PMID 2374010. 
  6. ^ Elena SF, Dopazo J, Flores R, Diener TO, Moya A (July 1991). "Phylogeny of viroids, viroidlike satellite RNAs, and the viroidlike domain of hepatitis delta virus RNA". Proceedings of the National Academy of Sciences of the United States of America. 88 (13): 5631–4. doi:10.1073/pnas.88.13.5631. PMC 51931Freely accessible. PMID 1712103. 
  7. ^ Sureau C (2006). "The role of the HBV envelope proteins in the HDV replication cycle". Current Topics in Microbiology and Immunology. Current Topics in Microbiology and Immunology. 307: 113–31. doi:10.1007/3-540-29802-9_6. ISBN 978-3-540-29801-4. PMID 16903223. 
  8. ^ Yan H, Zhong G, Xu G, He W, Jing Z, Gao Z, Huang Y, Qi Y, Peng B, Wang H, Fu L, Song M, Chen P, Gao W, Ren B, Sun Y, Cai T, Feng X, Sui J, Li W (November 2012). "Sodium taurocholate cotransporting polypeptide is a functional receptor for human hepatitis B and D virus". eLife. 1: e00049. doi:10.7554/eLife.00049. PMC 3485615Freely accessible. PMID 23150796. 
  9. ^ Engelke M, Mills K, Seitz S, Simon P, Gripon P, Schnölzer M, Urban S (April 2006). "Characterization of a hepatitis B and hepatitis delta virus receptor binding site". Hepatology. 43 (4): 750–60. doi:10.1002/hep.21112. PMID 16557545. 
  10. ^ Schulze A, Schieck A, Ni Y, Mier W, Urban S (February 2010). "Fine mapping of pre-S sequence requirements for hepatitis B virus large envelope protein-mediated receptor interaction". Journal of Virology. 84 (4): 1989–2000. doi:10.1128/JVI.01902-09. PMC 2812397Freely accessible. PMID 20007265. 
  11. ^ Xia YP, Yeh CT, Ou JH, Lai MM (February 1992). "Characterization of nuclear targeting signal of hepatitis delta antigen: nuclear transport as a protein complex". Journal of Virology. 66 (2): 914–21. PMC 240792Freely accessible. PMID 1731113. 
  12. ^ Lehmann E, Brueckner F, Cramer P (November 2007). "Molecular basis of RNA-dependent RNA polymerase II activity". Nature. 450 (7168): 445–9. doi:10.1038/nature06290. PMID 18004386. 
  13. ^ Filipovska J, Konarska MM (January 2000). "Specific HDV RNA-templated transcription by pol II in vitro". RNA. 6 (1): 41–54. doi:10.1017/S1355838200991167. PMC 1369892Freely accessible. PMID 10668797. 
  14. ^ Greco-Stewart VS, Schissel E, Pelchat M (March 2009). "The hepatitis delta virus RNA genome interacts with the human RNA polymerases I and III". Virology. 386 (1): 12–5. doi:10.1016/j.virol.2009.02.007. PMID 19246067. 
  15. ^ Li YJ, Macnaughton T, Gao L, Lai MM (July 2006). "RNA-templated replication of hepatitis delta virus: genomic and antigenomic RNAs associate with different nuclear bodies". Journal of Virology. 80 (13): 6478–86. doi:10.1128/JVI.02650-05. PMC 1488965Freely accessible. PMID 16775335. 
  16. ^ Branch AD, Benenfeld BJ, Baroudy BM, Wells FV, Gerin JL, Robertson HD (February 1989). "An ultraviolet-sensitive RNA structural element in a viroid-like domain of the hepatitis delta virus". Science. 243 (4891): 649–52. doi:10.1126/science.2492676. PMID 2492676. 
  17. ^ Wu HN, Lin YJ, Lin FP, Makino S, Chang MF, Lai MM (March 1989). "Human hepatitis delta virus RNA subfragments contain an autocleavage activity". Proceedings of the National Academy of Sciences of the United States of America. 86 (6): 1831–5. doi:10.1073/pnas.86.6.1831. PMC 286798Freely accessible. PMID 2648383. 
  18. ^ a b Weiner AJ, Choo QL, Wang KS, Govindarajan S, Redeker AG, Gerin JL, Houghton M (February 1988). "A single antigenomic open reading frame of the hepatitis delta virus encodes the epitope(s) of both hepatitis delta antigen polypeptides p24 delta and p27 delta". Journal of Virology. 62 (2): 594–9. PMC 250573Freely accessible. PMID 2447291. 
  19. ^ Jayan GC, Casey JL (December 2002). "Inhibition of hepatitis delta virus RNA editing by short inhibitory RNA-mediated knockdown of ADAR1 but not ADAR2 expression". Journal of Virology. 76 (23): 12399–404. doi:10.1128/JVI.76.23.12399-12404.2002. PMC 136899Freely accessible. PMID 12414985. 
  20. ^ Sato S, Cornillez-Ty C, Lazinski DW (August 2004). "By inhibiting replication, the large hepatitis delta antigen can indirectly regulate amber/W editing and its own expression". Journal of Virology. 78 (15): 8120–34. doi:10.1128/JVI.78.15.8120-8134.2004. PMC 446097Freely accessible. PMID 15254184. 
  21. ^ Taylor JM (2006). "Structure and replication of hepatitis delta virus RNA". Current Topics in Microbiology and Immunology. Current Topics in Microbiology and Immunology. 307: 1–23. doi:10.1007/3-540-29802-9_1. ISBN 978-3-540-29801-4. PMID 16903218. 
  22. ^ Chang MF, Chen CJ, Chang SC (February 1994). "Mutational analysis of delta antigen: effect on assembly and replication of hepatitis delta virus". Journal of Virology. 68 (2): 646–53. PMC 236498Freely accessible. PMID 8289368. 
  23. ^ Jaoude GA, Sureau C (2005). "Role of the Antigenic Loop of the Hepatitis B Virus Envelope Proteins in Infectivity of Hepatitis Delta Virus". Journal of Virology. 79 (16): 10460–10466. CiteSeerX accessible. doi:10.1128/jvi.79.16.10460-10466.2005. 
  24. ^ a b Radjef N, Gordien E, Ivaniushina V, Gault E, Anaïs P, Drugan T, Trinchet JC, Roulot D, Tamby M, Milinkovitch MC, Dény P (March 2004). "Molecular phylogenetic analyses indicate a wide and ancient radiation of African hepatitis delta virus, suggesting a deltavirus genus of at least seven major clades". Journal of Virology. 78 (5): 2537–44. doi:10.1128/JVI.78.5.2537-2544.2004. PMC 369207Freely accessible. PMID 14963156. 
  25. ^ Taylor JM (January 2006). "Hepatitis delta virus". Virology. 344 (1): 71–6. doi:10.1016/j.virol.2005.09.033. PMID 16364738. 
  26. ^ U.S. National Library of Medicine "Delta Agent (hepatitis D)"
  27. ^ Tayor JM (2009). Desk Encyclopedia of Human and Medical Virology. Boston: Academic Press. p. 121. ISBN 0-12-375147-0. 
  28. ^ Abbas Z, Khan MA, Salih M, Jafri W (December 2011). Abbas Z, ed. "Interferon alpha for chronic hepatitis D". The Cochrane Database of Systematic Reviews (12): CD006002. doi:10.1002/14651858.CD006002.pub2. PMID 22161394. 
  29. ^ Pascarella S, Negro F (January 2011). "Hepatitis D virus: an update". Liver International. 31 (1): 7–21. doi:10.1111/j.1478-3231.2010.02320.x. PMID 20880077. 
  30. ^ Rizzetto M, Canese MG, Aricò S, Crivelli O, Trepo C, Bonino F, Verme G (December 1977). "Immunofluorescence detection of new antigen-antibody system (delta/anti-delta) associated to hepatitis B virus in liver and in serum of HBsAg carriers". Gut. 18 (12): 997–1003. doi:10.1136/gut.18.12.997. PMC 1411847Freely accessible. PMID 75123. 
  31. ^ Rizzetto M, Canese MG, Purcell RH, London WT, Sly LD, Gerin JL (Nov–Dec 1981). "Experimental HBV and delta infections of chimpanzees: occurrence and significance of intrahepatic immune complexes of HBcAg and delta antigen". Hepatology. 1 (6): 567–74. doi:10.1002/hep.1840010602. PMID 7030907. 
  32. ^ Wang KS, Choo QL, Weiner AJ, Ou JH, Najarian RC, Thayer RM, Mullenbach GT, Denniston KJ, Gerin JL, Houghton M (Oct 9–15, 1986). "Structure, sequence and expression of the hepatitis delta (delta) viral genome". Nature. 323 (6088): 508–14. doi:10.1038/323508a0. PMID 3762705. 
  33. ^ Fauquet, CM; Mayo MA; Maniloff J; Desselberger U; Ball LA (2005). "Deltavirus". Eight Report of the International Committee on Taxonomy of Viruses. London: 735–8. 
  34. ^ Celik I, Karatayli E, Cevik E, Kabakçi SG, Karatayli SC, Dinç B, Cinar K, Yalçin K, Idilman R, Yurdaydin C, Bozdayi AM, et al. (December 2011). "Complete genome sequences and phylogenetic analysis of hepatitis delta viruses isolated from nine Turkish patients". Archives of Virology. 156 (12): 2215–20. doi:10.1007/s00705-011-1120-y. PMID 21984217. 
  35. ^ Alvarado-Mora MV, Romano CM, Gomes-Gouvêa MS, Gutierrez MF, Carrilho FJ, Pinho JR (August 2011). "Dynamics of hepatitis D (delta) virus genotype 3 in the Amazon region of South America". Infection, Genetics and Evolution. Elsevier. 11 (6): 1462–8. doi:10.1016/j.meegid.2011.05.020. PMID 21645647. 
  36. ^ Chao YC, Tang HS, Hsu CT (August 1994). "Evolution rate of hepatitis delta virus RNA isolated in Taiwan". Journal of Medical Virology. 43 (4): 397–403. doi:10.1002/jmv.1890430414. PMID 7964650. 
  37. ^ Homs M, Rodriguez-Frias F, Gregori J, Ruiz A, Reimundo P, Casillas R, Tabernero D, Godoy C, Barakat S, Quer J, Riveiro-Barciela M, Roggendorf M, Esteban R, Buti M (2016). "Evidence of an Exponential Decay Pattern of the Hepatitis Delta Virus Evolution Rate and Fluctuations in Quasispecies Complexity in Long-Term Studies of Chronic Delta Infection". PLOS One. 11 (6): e0158557. doi:10.1371/journal.pone.0158557. PMC 4928832Freely accessible. PMID 27362848. 
  38. ^ Barros LM, Gomes-Gouvêa MS, Pinho JR, Alvarado-Mora MV, Dos Santos A, Mendes-Corrêa MC, Caldas AJ, Sousa MT, Santos MD, Ferreira AS (September 2011). "Hepatitis Delta virus genotype 8 infection in Northeast Brazil: inheritance from African slaves?". Virus Research. 160 (1–2): 333–9. doi:10.1016/j.virusres.2011.07.006. PMID 21798297. 
  39. ^ Le Gal F, Gault E, Ripault MP, Serpaggi J, Trinchet JC, Gordien E, Dény P (September 2006). "Eighth major clade for hepatitis delta virus". Emerging Infectious Diseases. 12 (9): 1447–50. doi:10.3201/eid1209.060112. PMC 3294742Freely accessible. PMID 17073101. 

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This article incorporates text from the public domain Pfam and InterPro IPR002506

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Hepatitis delta virus delta antigen Provide feedback

The hepatitis delta virus (HDV) encodes a single protein, the hepatitis delta antigen (HDAg). The central region of this protein has been shown to bind RNA [1]. Several interactions are also mediated by a coiled-coil region at the N terminus of the protein [2].

Literature references

  1. Poisson F, Roingeard P, Baillou A, Dubois F, Bonelli F, Calogero RA, Goudeau A; , J Gen Virol 1993;74:2473-2478.: Characterization of RNA-binding domains of hepatitis delta antigen. PUBMED:8245865 EPMC:8245865

  2. Zuccola HJ, Rozzelle JE, Lemon SM, Erickson BW, Hogle JM; , Structure 1998;6:821-830.: Structural basis of the oligomerization of hepatitis delta antigen. PUBMED:9687364 EPMC:9687364

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002506

The Hepatitis delta virus (HDV) encodes a single protein, the hepatitis delta antigen (HDAg). The central region of this protein has been shown to bind RNA [PUBMED:8245865]. Several interactions are also mediated by a coiled-coil region at the N terminus of the protein [PUBMED:9687364].

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Seed source: Pfam-B_808 (release 4.0)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A
Number in seed: 1
Number in full: 3
Average length of the domain: 156.30 aa
Average identity of full alignment: 68 %
Average coverage of the sequence by the domain: 86.21 %

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build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 25.2 74.2
Noise cut-off 22.5 20.3
Model length: 195
Family (HMM) version: 18
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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 HDV_ag domain has been found. There are 5 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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