7DNK

2-fold subparticles refinement of human papillomavirus type 58 pseudovirus in complexed with the Fab fragment of 5G9

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
IMGT Antibody Annotation
SAbDab Antibody Annotation
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)
C [auth B]	SCOP2B Superfamily	Group I dsDNA viruses	8071416	3000939	SCOP2B (2022-06-29)
D [auth A]	SCOP2B Superfamily	Group I dsDNA viruses	8071416	3000939	SCOP2B (2022-06-29)
E [auth C]	SCOP2B Superfamily	Group I dsDNA viruses	8071416	3000939	SCOP2B (2022-06-29)
F [auth D]	SCOP2B Superfamily	Group I dsDNA viruses	8071416	3000939	SCOP2B (2022-06-29)
G [auth E]	SCOP2B Superfamily	Group I dsDNA viruses	8071416	3000939	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)
B [auth H]	C1-set_1	e7dnkH2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
B [auth H]	V-set_12	e7dnkH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
C [auth B]	Late_protein_L1	e7dnkB1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Late_protein_L1	ECOD (1.6)
D [auth A]	Late_protein_L1	e7dnkA1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Late_protein_L1	ECOD (1.6)
E [auth C]	Late_protein_L1	e7dnkC1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Late_protein_L1	ECOD (1.6)
F [auth D]	Late_protein_L1	e7dnkD1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Late_protein_L1	ECOD (1.6)
G [auth E]	Late_protein_L1	e7dnkE1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Late_protein_L1	ECOD (1.6)
A [auth L]	C1-set_4	e7dnkL2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
A [auth L]	V-set	e7dnkL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
B [auth H]	Fab 2H3, anti-HPV58, neutralizing	VH-CH1	Mus musculus (house mouse)	IGHV5-9-101, IGHJ401, IGHG2B*01	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-2B_KAPPA	IMGT (202436-0)
A [auth L]	Fab 2H3, anti-HPV58, neutralizing	L-KAPPA	Mus musculus (house mouse)	IGKV16-10401, IGKJ101, IGKC01, IGKC02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-2B_KAPPA	IMGT (202436-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth H]	Heavy Chain	IGHV5	-	major capsid protein l1 \| major capsid protein l1 \| major capsid protein l1 \| major capsid protein l1	SAbDab (2024-09-13)
A [auth L]	Light Chain	IGKV16	Kappa	major capsid protein l1 \| major capsid protein l1 \| major capsid protein l1 \| major capsid protein l1	SAbDab (2024-09-13)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth B], D [auth A], E [auth C], F [auth D], G [auth E]	PF00500	L1 (late) protein (Late_protein_L1)	L1 (late) protein	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth H]	The heavy chain of 5G9 Fab fragment	-	-	-
C [auth B], D [auth A], E [auth C], F [auth D], G [auth E]	Major capsid protein L1	structural molecule activity	virion attachment to host cell biological process involved in interspecies interaction between organisms adhesion of symbiont to host cell viral process viral life cycle adhesion of symbiont to host biological process involved in interaction with host biological process involved in symbiotic interaction import into cell transport establishment of localization vesicle-mediated transport localization symbiont entry into host cell virion attachment to host cell biological process involved in interspecies interaction between organisms adhesion of symbiont to host cell viral process viral life cycle adhesion of symbiont to host biological process involved in interaction with host biological process involved in symbiotic interaction import into cell transport establishment of localization vesicle-mediated transport localization symbiont entry into host cell symbiont entry into host cellular process endocytosis involved in viral entry into host cell endocytosis transport of virus	viral capsid icosahedral viral capsid T=7 icosahedral 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
A [auth L]	The light chain of 5G9 Fab fragment	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth B], D [auth A], E [auth C], F [auth D], G [auth E]	IPR036973	Major capsid L1 (late) superfamily, Papillomavirus	Homologous Superfamily
C [auth B], D [auth A], E [auth C], F [auth D], G [auth E]	IPR011222	Double-stranded DNA virus, group I, capsid	Homologous Superfamily
C [auth B], D [auth A], E [auth C], F [auth D], G [auth E]	IPR002210	Major capsid L1 (late) protein, Papillomavirus	Family

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.