6VN1 | pdb_00006vn1

A 2.8 Angstrom Cryo-EM Structure of a Glycoprotein B-Neutralizing Antibody Complex Reveals a Critical Domain for Herpesvirus Fusion Initiation

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A [auth L]	d6vn1l_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth M]	d6vn1m_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G [auth N]	d6vn1n_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth H]	d6vn1h_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth I]	d6vn1i_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H [auth J]	d6vn1j_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth A]	d6vn1a_	Multi-domain proteins (alpha and beta)	Viral glycoprotein ectodomain-like	Viral glycoprotein ectodomain-like	automated matches	automated matches	(Human alphaherpesvirus 3 ) [TaxId: 10335 ],	SCOPe (2.08)
F [auth B]	d6vn1b_	Multi-domain proteins (alpha and beta)	Viral glycoprotein ectodomain-like	Viral glycoprotein ectodomain-like	automated matches	automated matches	(Human alphaherpesvirus 3 ) [TaxId: 10335 ],	SCOPe (2.08)
I [auth C]	d6vn1c_	Multi-domain proteins (alpha and beta)	Viral glycoprotein ectodomain-like	Viral glycoprotein ectodomain-like	automated matches	automated matches	(Human alphaherpesvirus 3 ) [TaxId: 10335 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth A]	SCOP2 Family	Glycoprotein B-like	8096417	4002622	SCOP2 (2022-06-29)
C [auth A]	SCOP2 Superfamily	Viral glycoprotein ectodomain-like	8096418	3001498	SCOP2 (2022-06-29)
F [auth B]	SCOP2B Superfamily	Viral glycoprotein ectodomain-like	8096418	3001498	SCOP2B (2022-06-29)
I [auth C]	SCOP2B Superfamily	Viral glycoprotein ectodomain-like	8096418	3001498	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)
A [auth L]	V-set	e6vn1L1	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)
D [auth M]	V-set	e6vn1M1	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)
G [auth N]	V-set	e6vn1N1	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)
B [auth H]	V-set_8	e6vn1H1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
E [auth I]	V-set_8	e6vn1I1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
H [auth J]	V-set_8	e6vn1J1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
C [auth A]	Glycoprot_B_PH1	e6vn1A3	A: beta barrels	X: PH domain-like	H: first barrel domain in viral glycoproteins (From Topology)	T: first barrel domain in viral glycoproteins	F: Glycoprot_B_PH1	ECOD (1.6)
C [auth A]	Glycoprot_B_PH2	e6vn1A2	A: beta barrels	X: PH domain-like	H: second barrel domain in viral glycoproteins (From Topology)	T: second barrel domain in viral glycoproteins	F: Glycoprot_B_PH2	ECOD (1.6)
C [auth A]	Glycoprotein_B	e6vn1A1	A: beta complex topology	X: Viral glycoprotein ectodomain-like (From Topology)	H: Viral glycoprotein ectodomain-like (From Topology)	T: Viral glycoprotein ectodomain-like	F: Glycoprotein_B	ECOD (1.6)
F [auth B]	Glycoprot_B_PH1	e6vn1B2	A: beta barrels	X: PH domain-like	H: first barrel domain in viral glycoproteins (From Topology)	T: first barrel domain in viral glycoproteins	F: Glycoprot_B_PH1	ECOD (1.6)
F [auth B]	Glycoprot_B_PH2	e6vn1B1	A: beta barrels	X: PH domain-like	H: second barrel domain in viral glycoproteins (From Topology)	T: second barrel domain in viral glycoproteins	F: Glycoprot_B_PH2	ECOD (1.6)
F [auth B]	Glycoprotein_B	e6vn1B3	A: beta complex topology	X: Viral glycoprotein ectodomain-like (From Topology)	H: Viral glycoprotein ectodomain-like (From Topology)	T: Viral glycoprotein ectodomain-like	F: Glycoprotein_B	ECOD (1.6)
I [auth C]	Glycoprot_B_PH1	e6vn1C3	A: beta barrels	X: PH domain-like	H: first barrel domain in viral glycoproteins (From Topology)	T: first barrel domain in viral glycoproteins	F: Glycoprot_B_PH1	ECOD (1.6)
I [auth C]	Glycoprot_B_PH2	e6vn1C2	A: beta barrels	X: PH domain-like	H: second barrel domain in viral glycoproteins (From Topology)	T: second barrel domain in viral glycoproteins	F: Glycoprot_B_PH2	ECOD (1.6)
I [auth C]	Glycoprotein_B	e6vn1C1	A: beta complex topology	X: Viral glycoprotein ectodomain-like (From Topology)	H: Viral glycoprotein ectodomain-like (From Topology)	T: Viral glycoprotein ectodomain-like	F: Glycoprotein_B	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth A]	2.30.30.1230	Mainly Beta	Roll	SH3 type barrels.		CATH (utative)
C [auth A]	2.30.29.100	Mainly Beta	Roll	PH-domain like		CATH (utative)
C [auth A]	6.10.250.3280	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (utative)
F [auth B]	2.30.30.1230	Mainly Beta	Roll	SH3 type barrels.		CATH (utative)
F [auth B]	2.30.29.100	Mainly Beta	Roll	PH-domain like		CATH (utative)
F [auth B]	6.10.250.3280	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (utative)
I [auth C]	2.30.30.1230	Mainly Beta	Roll	SH3 type barrels.		CATH (utative)
I [auth C]	2.30.29.100	Mainly Beta	Roll	PH-domain like		CATH (utative)
I [auth C]	6.10.250.3280	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (utative)

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
A [auth L], D [auth M], G [auth N]	-	V-KAPPA	-	IGKV1-503, IGKJ101	V-DOMAIN V-KAPPA	IG	FV-HEAVY_KAPPA	IMGT (202514-0)
B [auth H], E [auth I], H [auth J]	-	VH	-	IGHV1-6915, IGHJ601	V-DOMAIN VH	IG	FV-HEAVY_KAPPA	IMGT (202514-0)
C [auth A], F [auth B], I [auth C]	HUMAN MONOCLONAL ANTIBODY 93K VARIABLE LIGHT CHAIN,H, I, J	(LINKER-LINKER-LINKER-LINKER-LINKER)	-	-	-	IG	(LINKER-LINKER-LINKER-LINKER-LINKER_LINKER-LINKER-LINKER-LINKER-LI	IMGT (202514-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A [auth L], D [auth M], G [auth N]	Light Chain	IGKV1	Kappa	envelope glycoprotein b	SAbDab (2025-04-18)
B [auth H], E [auth I], H [auth J]	Heavy Chain	IGHV1	-	envelope glycoprotein b	SAbDab (2025-04-18)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth A], F [auth B], I [auth C]	PF00606	Herpesvirus Glycoprotein B ectodomain (Glycoprotein_B)	Herpesvirus Glycoprotein B ectodomain	This domain corresponds to the ectodomain of glycoprotein B according to ECOD.	Domain
C [auth A], F [auth B], I [auth C]	PF17417	Herpesvirus Glycoprotein B PH-like domain (Glycoprot_B_PH2)	Herpesvirus Glycoprotein B PH-like domain	This domain corresponds to the second PH-like domain in herpesvirus glycoprotein B.	Domain
C [auth A], F [auth B], I [auth C]	PF17416	Herpesvirus Glycoprotein B (Glycoprot_B_PH1)	Herpesvirus Glycoprotein B	This domain has a PH-like fold.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth L], D [auth M], G [auth N]	Human monoclonal antibody 93k variable light chain	-	-	-
B [auth H], E [auth I], H [auth J]	Human monoclonal antibody 93k variable heavy chain	-	-	-
C [auth A], F [auth B], I [auth C]	Envelope glycoprotein B	-	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 symbiont entry into host cell symbiont entry into host	virion component viral membrane viral envelope cellular anatomical structure membrane host cell plasma membrane host cellular component host cell part host cell membrane virion membrane host intracellular part host cell Golgi membrane host cell Golgi apparatus host cell cytoplasm part virion component viral membrane viral envelope cellular anatomical structure membrane host cell plasma membrane host cellular component host cell part host cell membrane virion membrane host intracellular part host cell Golgi membrane host cell Golgi apparatus host cell cytoplasm part host cell cytoplasm host cell endomembrane system host intracellular region host intracellular membrane-bounded organelle host intracellular organelle host cell endosome membrane host cell endosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth A], F [auth B], I [auth C]	IPR000234	Herpesvirus Glycoprotein B	Family
C [auth A], F [auth B], I [auth C]	IPR035381	Herpesvirus Glycoprotein B, PH-like domain 2	Domain
C [auth A], F [auth B], I [auth C]	IPR035377	Herpesvirus Glycoprotein B, PH-like domain 1	Domain
C [auth A], F [auth B], I [auth C]	IPR038631	Herpesvirus Glycoprotein B, PH-like domain 2 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 R01GM157729.