6CGR

CryoEM structure of herpes simplex virus 1 capsid with associated tegument protein complexes.

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
EA [auth 4]	Herpes_MCP	e6cgr41	A: a+b complex topology	X: Major capsid protein VP5 (From Topology)	H: Major capsid protein VP5 (From Topology)	T: Major capsid protein VP5	F: Herpes_MCP	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E, A, B, C, D, E, EA [auth 4], F, M, N, O, S, T, U, V, W, X	PF01802	Herpesvirus VP23 like capsid protein (Herpes_V23)	Herpesvirus VP23 like capsid protein	-	Family
A, B, C, D, E, A, B, C, D, E, EA [auth 4], F, M, N, O, S, T, U, V, W, X	PF03122	Herpes virus major capsid protein (Herpes_MCP)	Herpes virus major capsid protein	-	Family
A, B, C, D, E, A, B, C, D, E, EA [auth 4], F, M, N, O, S, T, U, V, W, X	PF01499	Herpesvirus UL25 family (Herpes_UL25)	Herpesvirus UL25 family	-	Family
A, B, C, D, E, A, B, C, D, E, EA [auth 4], F, M, N, O, S, T, U, V, W, X	PF03327	Herpesvirus capsid shell protein VP19C (Herpes_VP19C)	Herpesvirus capsid shell protein VP19C	-	Family
AA [auth 0], BA [auth 1], CA [auth 2], DA [auth 3], G, AA [auth 0], BA [auth 1], CA [auth 2], DA [auth 3], G, H, I, J, K, L, P, Q, R, Y, Z	PF01802	Herpesvirus VP23 like capsid protein (Herpes_V23)	Herpesvirus VP23 like capsid protein	-	Family
AA [auth 0], BA [auth 1], CA [auth 2], DA [auth 3], G, AA [auth 0], BA [auth 1], CA [auth 2], DA [auth 3], G, H, I, J, K, L, P, Q, R, Y, Z	PF04496	Herpesvirus UL35 family (Herpes_UL35)	Herpesvirus UL35 family	-	Family
AA [auth 0], BA [auth 1], CA [auth 2], DA [auth 3], G, AA [auth 0], BA [auth 1], CA [auth 2], DA [auth 3], G, H, I, J, K, L, P, Q, R, Y, Z	PF01499	Herpesvirus UL25 family (Herpes_UL25)	Herpesvirus UL25 family	-	Family
AA [auth 0], BA [auth 1], CA [auth 2], DA [auth 3], G, AA [auth 0], BA [auth 1], CA [auth 2], DA [auth 3], G, H, I, J, K, L, P, Q, R, Y, Z	PF04559	Herpesvirus UL17 protein (Herpes_UL17)	Herpesvirus UL17 protein	-	Family
FA [auth 5], IA [auth 8], LA [auth b], OA [auth e], RA [auth h]	PF03327	Herpesvirus capsid shell protein VP19C (Herpes_VP19C)	Herpesvirus capsid shell protein VP19C	-	Family
GA [auth 6], HA [auth 7], JA [auth 9], KA [auth a], MA [auth c], GA [auth 6], HA [auth 7], JA [auth 9], KA [auth a], MA [auth c], NA [auth d], PA [auth f], QA [auth g], SA [auth i], TA [auth j]	PF01802	Herpesvirus VP23 like capsid protein (Herpes_V23)	Herpesvirus VP23 like capsid protein	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E, A, B, C, D, E, EA [auth 4], F, M, N, O, S, T, U, V, W, X	Major capsid protein	structural molecule activity	-	viral capsid icosahedral viral capsid virion component T=16 icosahedral viral capsid
AA [auth 0], BA [auth 1], CA [auth 2], DA [auth 3], G, AA [auth 0], BA [auth 1], CA [auth 2], DA [auth 3], G, H, I, J, K, L, P, Q, R, Y, Z	Small capsomere-interacting protein	-	viral process	viral capsid virion component host intracellular membrane-bounded organelle host cellular component host intracellular part host cell part host intracellular region cellular anatomical entity host cell nucleus host intracellular organelle
FA [auth 5], IA [auth 8], LA [auth b], OA [auth e], RA [auth h]	Triplex capsid protein 1	DNA binding binding organic cyclic compound binding nucleic acid binding	virion assembly viral process viral capsid assembly viral life cycle	-
GA [auth 6], HA [auth 7], JA [auth 9], KA [auth a], MA [auth c], GA [auth 6], HA [auth 7], JA [auth 9], KA [auth a], MA [auth c], NA [auth d], PA [auth f], QA [auth g], SA [auth i], TA [auth j]	Triplex capsid protein 2	structural molecule activity	-	viral capsid virion component
UA [auth k]	Capsid vertex component 1	-	cellular component organization organelle organization chromosome organization cellular process cellular component organization or biogenesis	viral capsid virion component
VA [auth l], WA [auth m]	Capsid vertex component 2	-	viral penetration into host nucleus intracellular transport of virus viral process viral life cycle transport of virus biological process involved in interspecies interaction between organisms symbiont entry into host cell symbiont entry into host biological process involved in interaction with host biological process involved in symbiotic interaction virion assembly viral genome packaging	host cellular component host cell cellular anatomical entity viral capsid virion component
XA [auth n], YA [auth o]	Large tegument protein deneddylase	cysteine-type peptidase activity ubiquitin-like protein peptidase activity peptidase activity cysteine-type deubiquitinase activity catalytic activity, acting on a protein hydrolase activity catalytic activity deubiquitinase activity deNEDDylase activity	cellular biosynthetic process cellular metabolic process viral DNA genome replication primary metabolic process viral life cycle DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process viral genome replication viral process cellular biosynthetic process cellular metabolic process viral DNA genome replication primary metabolic process viral life cycle DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process viral genome replication viral process metabolic process cellular process macromolecule metabolic process DNA biosynthetic process symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host ubiquitin-like protein modification modulation by symbiont of host process modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction organonitrogen compound metabolic process proteolysis protein metabolic process	virion component viral tegument host intracellular membrane-bounded organelle host cellular component host intracellular part host cell part host intracellular region cellular anatomical entity host cell nucleus host intracellular organelle host cell cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E, A, B, C, D, E, EA [auth 4], F, M, N, O, S, T, U, V, W, X	IPR000912	Herpesvirus major capsid protein	Family
A, B, C, D, E, A, B, C, D, E, EA [auth 4], F, M, N, O, S, T, U, V, W, X	IPR023233	Herpesvirus major capsid protein, upper domain superfamily	Homologous Superfamily
AA [auth 0], BA [auth 1], CA [auth 2], DA [auth 3], G, AA [auth 0], BA [auth 1], CA [auth 2], DA [auth 3], G, H, I, J, K, L, P, Q, R, Y, Z	IPR007584	Herpesvirus UL35	Family
FA [auth 5], IA [auth 8], LA [auth b], OA [auth e], RA [auth h]	IPR004999	Herpesvirus capsid shell protein 1	Family
GA [auth 6], HA [auth 7], JA [auth 9], KA [auth a], MA [auth c], GA [auth 6], HA [auth 7], JA [auth 9], KA [auth a], MA [auth c], NA [auth d], PA [auth f], QA [auth g], SA [auth i], TA [auth j]	IPR002690	Herpesvirus capsid protein 2	Family
UA [auth k]	IPR007640	Herpesvirus capsid vertex component 1	Family
VA [auth l], WA [auth m]	IPR002493	Herpesvirus UL25	Family
XA [auth n], YA [auth o]	IPR005210	Herpesvirus large tegument protein deneddylase	Domain
XA [auth n], YA [auth o]	IPR006928	Herpesvirus large tegument protein, USP domain	Domain
XA [auth n], YA [auth o]	IPR051352	Cell Adhesion and Viral Modulation Protein	Family
XA [auth n], YA [auth o]	IPR034702	Large tegument protein deneddylase	Family
XA [auth n], YA [auth o]	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.