SUPERFAMILY 1.75 HMM library and genome assignments server

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Viral protein domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   Viral protein domain [ 49817]
Superfamily:   Viral protein domain [ 49818] (3)
Families:   Top domain of virus capsid protein [ 49819] (3)
  Influenza hemagglutinin headpiece [ 49823]
  Hemagglutinin domain of haemagglutinin-esterase-fusion glycoprotein HEF1 [ 49826]

Superfamily statistics
Genomes (1) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 1 124,213 28
Proteins 1 124,185 28

Functional annotation
General category Other
Detailed category Viral proteins

Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) multi-organism process 0.0005406 Moderately Informative Direct
Biological Process (BP) interspecies interaction between organisms 0.00000001476 Informative Direct
Biological Process (BP) viral process 0.000000000002995 Highly Informative Direct
Molecular Function (MF) hydrolase activity 0 Least Informative Direct
Molecular Function (MF) hydrolase activity, acting on ester bonds 0 Moderately Informative Direct
Molecular Function (MF) carboxylic ester hydrolase activity 0.00000000000001678 Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Acting on ester bonds0Least InformativeDirect
Enzyme Commission (EC)Carboxylic ester hydrolases0Moderately InformativeDirect
Enzyme Commission (EC)Sialate O-acetylesterase0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processHost-virus interaction0Moderately InformativeDirect
Biological processVirus entry into host cell0InformativeDirect
Biological processFusion of virus membrane with host endosomal membrane0Highly InformativeDirect
Biological processClathrin-mediated endocytosis of virus by host0.0000000004053Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentVirion0Moderately InformativeDirect
Cellular componentHost membrane0InformativeDirect
Cellular componentCapsid protein1InformativeInherited
Cellular componentViral envelope protein0Highly InformativeDirect
DomainTransmembrane0Least InformativeDirect
DomainSignal0Least InformativeDirect
Post-translational modificationHemagglutinin0Highly InformativeDirect
Post-translational modificationDisulfide bond0Least InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationPalmitate0Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR008980 SSF49818 Protein matches

Representatives of this viral protein domain are found in the vp7 capsid protein of bluetongue virus [PubMed7816101], and African horse sickness virus [PubMed8648715], the vp6 capsid protein of bovine rotavirus [PubMed11285213], and in the haemagglutinin protein of influenza virus [PubMed11867515, PubMed9817207].

The vp7 and vp6 capsid proteins each consist of two domains, one a beta sandwich, and the other an alpha helical bundle. The beta sandwich domain described here is structurally very similar in vp6 and vp7, and may be involved in the attachment of the virus to the cell. In influenza A and B viruses, the haemagglutinin membrane glycoprotein serves to recognise the cell surface receptor sialic acid, and this domain forms the head region. In influenza C virus, a single multifunctional glycoprotein, the haemagglutinin-esterase-fusion protein, possesses a haemagglutinin domain, which recognises the cell surface receptor 9-O-acetylsialic acid, and bears strong structural resemblance to the haemagglutinin protein of influenza A and B viruses, as well as to the vp6 and vp7 capsid proteins. In each case, the domain consists of a beta-sandwich, in which the strands making up the sheets exhibit a jellyroll fold. The resultant proteins form trimers.

More information about these protein can be found at Protein of the Month: Bird Flu, Haemagglutinin.

InterPro database

PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.

Alignments of sequences to 14 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.

Browse and view proteins in genomes which have different domain combinations including a Viral protein domain domain.

Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.

Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 14 hidden Markov models representing the Viral protein domain superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]