3EYQ

Crystal structure of MJ5 Fab, a germline antibody variant of anti-human cytomegalovirus antibody 8f9

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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)
B [auth D]	d3eyqd_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A [auth C]	d3eyqc1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A [auth C]	d3eyqc2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B [auth D]	C1-set_1	e3eyqD2	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 D]	V-set_12	e3eyqD1	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)
A [auth C]	C1-set_4	e3eyqC2	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 C]	V-set	e3eyqC1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth D]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A [auth C]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

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 D]	MJ5, variant of 8F9 neutralizing human cytomegalovirus	VH-CH1	Homo sapiens (human)	IGHV3-3018, IGHJ401, IGHJ402, IGHJ403, IGHG101, IGHG102, IGHG1*04	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202443-0)
A [auth C]	MJ5, variant of 8F9 neutralizing human cytomegalovirus	L-KAPPA	Homo sapiens (human)	IGKV3-1101, IGKJ501, IGKC*01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202443-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth D]	Heavy Chain	IGHV3	-	-	SAbDab (2024-11-01)
A [auth C]	Light Chain	IGKV3	Kappa	-	SAbDab (2024-11-01)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth D]	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain
A [auth C]	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain
A [auth C]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth D]	8f9 Fab	-	response to stimulus immune response immune system process adaptive immune response	cell periphery plasma membrane membrane cellular anatomical entity protein-containing complex immunoglobulin complex extracellular region
A [auth C]	M2J5 Fab	-	-	extracellular region cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth D]	IPR050199	Immunoglobulin Heavy Variable	Family
B [auth D]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B [auth D]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B [auth D]	IPR013106	Immunoglobulin V-set domain	Domain
B [auth D]	IPR003599	Immunoglobulin domain subtype	Domain
B [auth D]	IPR007110	Immunoglobulin-like domain	Domain
A [auth C]	IPR003597	Immunoglobulin C1-set	Domain
A [auth C]	IPR050150	Immunoglobulin Variable Light Chain	Family
A [auth C]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A [auth C]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A [auth C]	IPR013106	Immunoglobulin V-set domain	Domain
A [auth C]	IPR003599	Immunoglobulin domain subtype	Domain
A [auth C]	IPR007110	Immunoglobulin-like domain	Domain
A [auth C]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site

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.