6B1T | pdb_00006b1t

Improved cryoEM structure of human adenovirus type 5 with atomic details of minor proteins VI and VII

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
L	SCOP2B Superfamily	Group II dsDNA viruses VP	8038153	3001214	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Group II dsDNA viruses VP	8038150	3001214	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Group II dsDNA viruses VP	8038150	3001214	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Group II dsDNA viruses VP	8038153	3001214	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Group II dsDNA viruses VP	8038153	3001214	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Group II dsDNA viruses VP	8038150	3001214	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Group II dsDNA viruses VP	8038150	3001214	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Group II dsDNA viruses VP	8038153	3001214	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Group II dsDNA viruses VP	8038153	3001214	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Group II dsDNA viruses VP	8038150	3001214	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Group II dsDNA viruses VP	8038153	3001214	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Group II dsDNA viruses VP	8038150	3001214	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Group II dsDNA viruses VP	8038150	3001214	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Group II dsDNA viruses VP	8038153	3001214	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Group II dsDNA viruses VP	8038153	3001214	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Group II dsDNA viruses VP	8038150	3001214	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Group II dsDNA viruses VP	8038150	3001214	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Group II dsDNA viruses VP	8038153	3001214	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Group II dsDNA viruses VP	8038150	3001214	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Group II dsDNA viruses VP	8038153	3001214	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Group II dsDNA viruses VP	8038150	3001214	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Group II dsDNA viruses VP	8038153	3001214	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Group II dsDNA viruses VP	8038150	3001214	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Group II dsDNA viruses VP	8038153	3001214	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
N	NADHdh	e6b1tN1	A: alpha bundles	X: Family A G protein-coupled receptor-like	H: Sodium/proton antiporter subunits-like	T: NADH-quinone oxidoreductase subunit 8 (Nqo8)-related	F: NADHdh	ECOD (develop294)
M	Ig_3	e6b1tM1	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Ig_3	ECOD (develop294)
L	Ig_3	e6b1tL1	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Ig_3	ECOD (develop294)
K	Ig_3	e6b1tK1	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Ig_3	ECOD (develop294)
J	Ig_3	e6b1tJ1	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Ig_3	ECOD (develop294)
I	Ig_3	e6b1tI1	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Ig_3	ECOD (develop294)
H	Ig_3	e6b1tH1	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Ig_3	ECOD (develop294)
G	Ig_3	e6b1tG1	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Ig_3	ECOD (develop294)
F	Ig_3	e6b1tF1	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Ig_3	ECOD (develop294)
E	Ig_3	e6b1tE1	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Ig_3	ECOD (develop294)
D	Ig_3	e6b1tD1	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Ig_3	ECOD (develop294)
C	Ig_3	e6b1tC1	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Ig_3	ECOD (develop294)
B	Ig_3	e6b1tB1	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Ig_3	ECOD (develop294)
A	Ig_3	e6b1tA1	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Ig_3	ECOD (develop294)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
Q, R, S, T	PF03955	Adenovirus hexon-associated protein (IX) (Adeno_PIX)	Adenovirus hexon-associated protein (IX)	-	Family
O, P	PF01310	Adenovirus hexon associated protein, protein VIII (Adeno_PVIII)	Adenovirus hexon associated protein, protein VIII	-	Family
N	PF02455	Hexon-associated protein (IIIa) (Hex_IIIa)	Hexon-associated protein (IIIa)	-	Family
M	PF01686	Adenovirus penton base protein (Adeno_Penton_B)	Adenovirus penton base protein	-	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	PF01065	Hexon, adenovirus major coat protein, N-terminal domain (Adeno_hexon)	Hexon, adenovirus major coat protein, N-terminal domain	Hexon is the major coat protein from adenovirus type 2. Hexon forms a homo-trimer. The 240 copies of the hexon trimer are organised so that 12 lie on each of the 20 facets. The central 9 hexons in a facet are cemented together by 12 copies of polype ...	Hexon is the major coat protein from adenovirus type 2. Hexon forms a homo-trimer. The 240 copies of the hexon trimer are organised so that 12 lie on each of the 20 facets. The central 9 hexons in a facet are cemented together by 12 copies of polypeptide IX. The penton complex, formed by the peripentonal hexons and base hexon (holding in place a fibre), lie at each of the 12 vertices [1]. The N and C-terminal domains adopt the same PNGase F-like fold although they are significantly different in length.	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	PF03678	Hexon, adenovirus major coat protein, C-terminal domain (Adeno_hexon_C)	Hexon, adenovirus major coat protein, C-terminal domain	Hexon is the major coat protein from adenovirus type 2. Hexon forms a homo-trimer. The 240 copies of the hexon trimer are organised so that 12 lie on each of the 20 facets. The central 9 hexons in a facet are cemented together by 12 copies of polypep ...	Hexon is the major coat protein from adenovirus type 2. Hexon forms a homo-trimer. The 240 copies of the hexon trimer are organised so that 12 lie on each of the 20 facets. The central 9 hexons in a facet are cemented together by 12 copies of polypeptide IX. The penton complex, formed by the peripentonal hexons and base hexon (holding in place a fibre), lie at each of the 12 vertices [1]. The N and C-terminal domains adopt the same PNGase F-like fold although they are significantly different in length.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
X	Pre-protein VI	-	biological process involved in interspecies interaction between organisms microtubule-dependent intracellular transport of viral material microtubule-dependent intracellular transport of viral material towards nucleus intracellular transport of virus viral process viral life cycle transport of virus transport of viral material towards nucleus biological process involved in symbiotic interaction symbiont entry into host cell symbiont entry into host lysis of host organelle involved in viral entry into host cell biological process involved in interaction with host establishment of protein localization biological process involved in interspecies interaction between organisms microtubule-dependent intracellular transport of viral material microtubule-dependent intracellular transport of viral material towards nucleus intracellular transport of virus viral process viral life cycle transport of virus transport of viral material towards nucleus biological process involved in symbiotic interaction symbiont entry into host cell symbiont entry into host lysis of host organelle involved in viral entry into host cell biological process involved in interaction with host establishment of protein localization cellular localization transport protein transport along microtubule microtubule-based protein transport intracellular transport establishment of localization localization protein transport macromolecule localization establishment of localization in cell microtubule-based transport cellular process transport along microtubule cytoskeleton-dependent intracellular transport microtubule-based movement microtubule-based process intracellular protein localization intracellular protein transport exit from host cell viral release from host cell	host cellular component cellular anatomical structure host cell other organism part viral capsid virion component viral procapsid host intracellular membrane-bounded organelle host intracellular part host cell part host intracellular region host cell nucleus host intracellular organelle host cell cytoplasm
W	Pre-histone-like nucleoprotein	DNA binding binding nucleic acid binding	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	host cellular component cellular anatomical structure host cell other organism part viral capsid virion component host intracellular membrane-bounded organelle host intracellular part host cell nucleus host cell nucleolus host cell nuclear part host intracellular organelle host cell part host intracellular region
U, V, Y	Pre-protein VI	-	biological process involved in interspecies interaction between organisms microtubule-dependent intracellular transport of viral material microtubule-dependent intracellular transport of viral material towards nucleus intracellular transport of virus viral process viral life cycle transport of virus transport of viral material towards nucleus biological process involved in symbiotic interaction symbiont entry into host cell symbiont entry into host lysis of host organelle involved in viral entry into host cell biological process involved in interaction with host establishment of protein localization biological process involved in interspecies interaction between organisms microtubule-dependent intracellular transport of viral material microtubule-dependent intracellular transport of viral material towards nucleus intracellular transport of virus viral process viral life cycle transport of virus transport of viral material towards nucleus biological process involved in symbiotic interaction symbiont entry into host cell symbiont entry into host lysis of host organelle involved in viral entry into host cell biological process involved in interaction with host establishment of protein localization cellular localization transport protein transport along microtubule microtubule-based protein transport intracellular transport establishment of localization localization protein transport macromolecule localization establishment of localization in cell microtubule-based transport cellular process transport along microtubule cytoskeleton-dependent intracellular transport microtubule-based movement microtubule-based process intracellular protein localization intracellular protein transport exit from host cell viral release from host cell	host cellular component cellular anatomical structure host cell other organism part viral capsid virion component viral procapsid host intracellular membrane-bounded organelle host intracellular part host cell part host intracellular region host cell nucleus host intracellular organelle host cell cytoplasm
Q, R, S, T	Hexon-interlacing protein	hexon binding protein binding binding	biological process involved in interspecies interaction between organisms symbiont entry into host cell viral process symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction	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 virion component viral capsid, decoration
O, P	Pre-hexon-linking protein VIII	hexon binding protein binding binding	-	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
N	Pre-hexon-linking protein IIIa	-	-	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 viral capsid, decoration
M	Penton protein	structural molecule activity	import into cell receptor-mediated endocytosis of virus by host cell biological process involved in interspecies interaction between organisms transport viral life cycle establishment of localization vesicle-mediated transport biological process involved in interaction with host biological process involved in symbiotic interaction localization symbiont entry into host cell clathrin-dependent endocytosis viral process symbiont entry into host import into cell receptor-mediated endocytosis of virus by host cell biological process involved in interspecies interaction between organisms transport viral life cycle establishment of localization vesicle-mediated transport biological process involved in interaction with host biological process involved in symbiotic interaction localization symbiont entry into host cell clathrin-dependent endocytosis viral process symbiont entry into host cellular process clathrin-dependent endocytosis of virus by host cell receptor-mediated endocytosis endocytosis endocytosis involved in viral entry into host cell virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host	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 icosahedral viral capsid T=25 icosahedral viral capsid
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	Hexon protein	structural molecule activity	biological process involved in interspecies interaction between organisms microtubule-dependent intracellular transport of viral material microtubule-dependent intracellular transport of viral material towards nucleus intracellular transport of virus viral process viral life cycle transport of virus transport of viral material towards nucleus biological process involved in symbiotic interaction symbiont entry into host cell symbiont entry into host biological process involved in interaction with host	host cellular component cellular anatomical structure host cell other organism part viral capsid virion component host intracellular membrane-bounded organelle host intracellular part host cell part host intracellular region host cell nucleus host intracellular organelle icosahedral viral capsid T=25 icosahedral viral capsid

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
X	IPR004243	Minor capsid protein VI	Family
W	IPR004912	Adenoviral core protein VII	Family
U, V, Y	IPR004243	Minor capsid protein VI	Family
Q, R, S, T	IPR005641	Hexon-associated protein IX	Family
O, P	IPR000646	Pre-hexon-linking protein VIII	Family
N	IPR003479	Pre-hexon-linking protein IIIa	Family
N	IPR043053	Pre-hexon-linking protein IIIa, N-terminal	Homologous Superfamily
M	IPR002605	Adenovirus penton base protein	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR044942	Adenovirus Pll, hexon, subdomain 2	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR016107	Adenovirus Pll, hexon, N-terminal	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR016108	Adenovirus Pll, hexon, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR016112	Group II dsDNA virus coat/capsid protein	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR037542	Adenovirus hexon protein	Family