5VKU | pdb_00005vku

An atomic structure of the human cytomegalovirus (HCMV) capsid with its securing layer of pp150 tegument protein

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)
L [auth B]	Herpes_MCP	e5vkuB1	A: beta barrels	X: Trefoil/Plexin domain-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Herpes_MCP	ECOD (v294.2)
M [auth C]	MIF4G	e5vkuC1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: MIF4G	ECOD (v294.2)
O [auth E]	MIF4G	e5vkuE1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: MIF4G	ECOD (v294.2)
P [auth F]	MIF4G	e5vkuF1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: MIF4G	ECOD (v294.2)
R [auth H]	MIF4G	e5vkuH1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: MIF4G	ECOD (v294.2)
S [auth I]	MIF4G	e5vkuI1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: MIF4G	ECOD (v294.2)
T [auth J]	MIF4G	e5vkuJ1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: MIF4G	ECOD (v294.2)
U [auth K]	MIF4G	e5vkuK1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: MIF4G	ECOD (v294.2)
V [auth L]	MIF4G	e5vkuL1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: MIF4G	ECOD (v294.2)
W [auth M]	MIF4G	e5vkuM1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: MIF4G	ECOD (v294.2)
Y [auth O]	MIF4G	e5vkuO1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: MIF4G	ECOD (v294.2)
Z [auth P]	MIF4G	e5vkuP1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: MIF4G	ECOD (v294.2)
X [auth N]	MIF4G	e5vkuN1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: MIF4G	ECOD (v294.2)
Q [auth G]	MIF4G	e5vkuG1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: MIF4G	ECOD (v294.2)
N [auth D]	MIF4G	e5vkuD1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: MIF4G	ECOD (v294.2)
K [auth A]	MIF4G	e5vkuA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: MIF4G	ECOD (v294.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
AA [auth Q], BA [auth R], CA [auth S], DA [auth T], EA [auth U], AA [auth Q], BA [auth R], CA [auth S], DA [auth T], EA [auth U], FA [auth V], GA [auth W], HA [auth X], IA [auth Y], JA [auth Z], KA [auth a], LA [auth b], MA [auth c], NA [auth d], OA [auth e], PA [auth f]	PF01802	Herpesvirus VP23 like capsid protein (Herpes_V23)	Herpesvirus VP23 like capsid protein	-	Family
AA [auth Q], BA [auth R], CA [auth S], DA [auth T], EA [auth U], AA [auth Q], BA [auth R], CA [auth S], DA [auth T], EA [auth U], FA [auth V], GA [auth W], HA [auth X], IA [auth Y], JA [auth Z], KA [auth a], LA [auth b], MA [auth c], NA [auth d], OA [auth e], PA [auth f]	PF03327	Herpesvirus capsid shell protein VP19C (Herpes_VP19C)	Herpesvirus capsid shell protein VP19C	-	Family
K [auth A], L [auth B], M [auth C], N [auth D], O [auth E], K [auth A], L [auth B], M [auth C], N [auth D], O [auth E], P [auth F], Q [auth G], R [auth H], S [auth I], T [auth J], U [auth K], V [auth L], W [auth M], X [auth N], Y [auth O], Z [auth P]	PF01802	Herpesvirus VP23 like capsid protein (Herpes_V23)	Herpesvirus VP23 like capsid protein	-	Family
K [auth A], L [auth B], M [auth C], N [auth D], O [auth E], K [auth A], L [auth B], M [auth C], N [auth D], O [auth E], P [auth F], Q [auth G], R [auth H], S [auth I], T [auth J], U [auth K], V [auth L], W [auth M], X [auth N], Y [auth O], Z [auth P]	PF03122	Herpes virus major capsid protein (Herpes_MCP)	Herpes virus major capsid protein	-	Family
K [auth A], L [auth B], M [auth C], N [auth D], O [auth E], K [auth A], L [auth B], M [auth C], N [auth D], O [auth E], P [auth F], Q [auth G], R [auth H], S [auth I], T [auth J], U [auth K], V [auth L], W [auth M], X [auth N], Y [auth O], Z [auth P]	PF03327	Herpesvirus capsid shell protein VP19C (Herpes_VP19C)	Herpesvirus capsid shell protein VP19C	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
AB [auth q], BB [auth r], DB [auth t], EB [auth u], RA [auth h], AB [auth q], BB [auth r], DB [auth t], EB [auth u], RA [auth h], SA [auth i], UA [auth k], VA [auth l], XA [auth n], YA [auth o]	Triplex capsid protein 2	structural molecule activity	-	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
CB [auth s], QA [auth g], TA [auth j], WA [auth m], ZA [auth p]	Triplex capsid protein 1	DNA binding binding nucleic acid binding	virion assembly viral process viral capsid assembly viral life cycle	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
AA [auth Q], BA [auth R], CA [auth S], DA [auth T], EA [auth U], AA [auth Q], BA [auth R], CA [auth S], DA [auth T], EA [auth U], FA [auth V], GA [auth W], HA [auth X], IA [auth Y], JA [auth Z], KA [auth a], LA [auth b], MA [auth c], NA [auth d], OA [auth e], PA [auth f]	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
K [auth A], L [auth B], M [auth C], N [auth D], O [auth E], K [auth A], L [auth B], M [auth C], N [auth D], O [auth E], P [auth F], Q [auth G], R [auth H], S [auth I], T [auth J], U [auth K], V [auth L], W [auth M], X [auth N], Y [auth O], Z [auth P]	Major capsid protein	structural molecule activity	-	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 viral capsid icosahedral viral capsid virion component T=16 icosahedral viral capsid
A [auth 0], B [auth 1], C [auth 2], D [auth 3], E [auth 4], A [auth 0], B [auth 1], C [auth 2], D [auth 3], E [auth 4], F [auth 5], FB [auth v], G [auth 6], GB [auth w], H [auth 7], HB [auth x], I [auth 8], IB [auth y], J [auth 9], JB [auth z]	Tegument protein pp150	structural molecule activity	-	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 host cell perinuclear region of cytoplasm host cell cytoplasm host cell cytoplasm part cytoplasmic viral factory host cell viral assembly compartment 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 host cell perinuclear region of cytoplasm host cell cytoplasm host cell cytoplasm part cytoplasmic viral factory host cell viral assembly compartment viral factory host cell cytoplasmic vesicle virion component viral tegument

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
AB [auth q], BB [auth r], DB [auth t], EB [auth u], RA [auth h], AB [auth q], BB [auth r], DB [auth t], EB [auth u], RA [auth h], SA [auth i], UA [auth k], VA [auth l], XA [auth n], YA [auth o]	IPR002690	Herpesvirus capsid protein 2	Family
CB [auth s], QA [auth g], TA [auth j], WA [auth m], ZA [auth p]	IPR004999	Herpesvirus capsid shell protein 1	Family
AA [auth Q], BA [auth R], CA [auth S], DA [auth T], EA [auth U], AA [auth Q], BA [auth R], CA [auth S], DA [auth T], EA [auth U], FA [auth V], GA [auth W], HA [auth X], IA [auth Y], JA [auth Z], KA [auth a], LA [auth b], MA [auth c], NA [auth d], OA [auth e], PA [auth f]	IPR031385	Small capsid protein, Herpesviridae	Family
K [auth A], L [auth B], M [auth C], N [auth D], O [auth E], K [auth A], L [auth B], M [auth C], N [auth D], O [auth E], P [auth F], Q [auth G], R [auth H], S [auth I], T [auth J], U [auth K], V [auth L], W [auth M], X [auth N], Y [auth O], Z [auth P]	IPR000912	Herpesvirus major capsid protein	Family
K [auth A], L [auth B], M [auth C], N [auth D], O [auth E], K [auth A], L [auth B], M [auth C], N [auth D], O [auth E], P [auth F], Q [auth G], R [auth H], S [auth I], T [auth J], U [auth K], V [auth L], W [auth M], X [auth N], Y [auth O], Z [auth P]	IPR023233	Herpesvirus major capsid protein, upper domain superfamily	Homologous Superfamily
A [auth 0], B [auth 1], C [auth 2], D [auth 3], E [auth 4], A [auth 0], B [auth 1], C [auth 2], D [auth 3], E [auth 4], F [auth 5], FB [auth v], G [auth 6], GB [auth w], H [auth 7], HB [auth x], I [auth 8], IB [auth y], J [auth 9], JB [auth z]	IPR010340	Herpesvirus UL11/UL32	Family

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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.