6CGR | pdb_00006cgr

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

External Resource: Annotation

Domain Annotation: ECOD Classification
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)
WA [auth m]	AAA_lid_3	e6cgrm1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: AAA_lid_3	ECOD (v295)
VA [auth l]	HATPase_c_5	e6cgrl01	A: alpha arrays	X: Voltage-gated ion channels	H: Voltage-gated ion channels	T: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	F: HATPase_c_5	ECOD (v295)
X	AAA_lid_3	e6cgrX1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: AAA_lid_3	ECOD (v295)
W	AAA_lid_3	e6cgrW1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: AAA_lid_3	ECOD (v295)
V	AAA_lid_3	e6cgrV1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: AAA_lid_3	ECOD (v295)
U	AAA_lid_3	e6cgrU1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: AAA_lid_3	ECOD (v295)
T	AAA_lid_3	e6cgrT1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: AAA_lid_3	ECOD (v295)
S	AAA_lid_3	e6cgrS1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: AAA_lid_3	ECOD (v295)
O	AAA_lid_3	e6cgrO1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: AAA_lid_3	ECOD (v295)
N	AAA_lid_3	e6cgrN1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: AAA_lid_3	ECOD (v295)
M	AAA_lid_3	e6cgrM1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: AAA_lid_3	ECOD (v295)
F	AAA_lid_3	e6cgrF1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: AAA_lid_3	ECOD (v295)
EA [auth 4]	Herpes_MCP	e6cgr41	A: alpha arrays	X: DNA methylase specificity domain	H: Bromodomain	T: Bromodomain	F: Herpes_MCP	ECOD (v295)
E	AAA_lid_3	e6cgrE1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: AAA_lid_3	ECOD (v295)
D	AAA_lid_3	e6cgrD1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: AAA_lid_3	ECOD (v295)
C	AAA_lid_3	e6cgrC1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: AAA_lid_3	ECOD (v295)
B	AAA_lid_3	e6cgrB1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: AAA_lid_3	ECOD (v295)
A	AAA_lid_3	e6cgrA1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: AAA_lid_3	ECOD (v295)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular 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	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 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 proteolysis protein metabolic 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 symbiont-mediated perturbation of host process modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction	virion component
VA [auth l], WA [auth m]	Capsid vertex component 2	-	biological process involved in interspecies interaction between organisms viral penetration into host nucleus intracellular transport of virus viral process viral life cycle transport of virus biological process involved in symbiotic interaction symbiont entry into host cell symbiont entry into host biological process involved in interaction with host virion assembly viral genome packaging	host cellular component cellular anatomical structure host cell other organism part 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
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
FA [auth 5], IA [auth 8], LA [auth b], OA [auth e], RA [auth h]	Triplex capsid protein 1	DNA binding binding nucleic acid binding	virion assembly viral process viral capsid assembly viral life cycle	viral capsid virion component
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 cellular anatomical structure host cell part host intracellular region host cell nucleus other organism part host intracellular organelle
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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
XA [auth n], YA [auth o]	IPR005210	Herpesvirus large tegument protein deneddylase	Domain
XA [auth n], YA [auth o]	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
XA [auth n], YA [auth o]	IPR006928	Herpesvirus large tegument protein, USP domain	Domain
XA [auth n], YA [auth o]	IPR034702	Large tegument protein deneddylase	Family
VA [auth l], WA [auth m]	IPR002493	Capsid vertex component 2	Family
UA [auth k]	IPR007640	Herpesvirus capsid vertex component 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
FA [auth 5], IA [auth 8], LA [auth b], OA [auth e], RA [auth h]	IPR004999	Herpesvirus capsid shell protein 1	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	IPR007584	Herpesvirus UL35	Family
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

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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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.