4M8Q

Ontogeny of recognition specificity and functionality for the anti-HIV neutralizing antibody 4E10

External Resource: Annotation

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
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	V-set_8	e4m8qA1	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)
D [auth H]	V-set_8	e4m8qH1	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)
B	V-set	e4m8qB1	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)
E [auth L]	V-set	e4m8qL1	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)
C	PTS_EIIA_2	e4m8qC1	A: a+b three layers	X: Phoshotransferase/anion transport protein (From Topology)	H: Phoshotransferase/anion transport protein (From Topology)	T: Phoshotransferase/anion transport protein	F: PTS_EIIA_2	ECOD (1.6)
F [auth S]	PTS_EIIA_2	e4m8qS1	A: a+b three layers	X: Phoshotransferase/anion transport protein (From Topology)	H: Phoshotransferase/anion transport protein (From Topology)	T: Phoshotransferase/anion transport protein	F: PTS_EIIA_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C	3.40.930.10	Alpha Beta	3-Layer(aba) Sandwich	Mannitol-specific EII	Chain A	CATH (4.3.0)
F [auth S]	3.40.930.10	Alpha Beta	3-Layer(aba) Sandwich	Mannitol-specific EII	Chain A	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
A, D [auth H]	GEP 1	VH	Homo sapiens (human)	IGHV1-6906, IGHV1-6914, IGHJ401, IGHJ402, IGHJ4*03	V-DOMAIN VH	IG	FV-HEAVY_KAPPA	IMGT (202450-0)
B, E [auth L]	GEP 1	V-KAPPA	Homo sapiens (human)	IGKV3-2001, IGKJ101	V-DOMAIN V-KAPPA	IG	FV-HEAVY_KAPPA	IMGT (202450-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A, D [auth H]	Heavy Chain	IGHV1	-	4e10 epitope scaffold t117	SAbDab (2024-12-20)
B, E [auth L]	Light Chain	IGKV3	Kappa	4e10 epitope scaffold t117	SAbDab (2024-12-20)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, E [auth L]	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D [auth H]	GEP1 Fv heavy chain	-	-	-
B, E [auth L]	GEP1 Fv light chain	binding antigen binding	response to stimulus immune response immune system process adaptive immune response humoral immune response biological process involved in interspecies interaction between organisms response to other organism defense response antibacterial humoral response defense response to symbiont response to external stimulus antimicrobial humoral response response to biotic stimulus defense response to bacterium response to stimulus immune response immune system process adaptive immune response humoral immune response biological process involved in interspecies interaction between organisms response to other organism defense response antibacterial humoral response defense response to symbiont response to external stimulus antimicrobial humoral response response to biotic stimulus defense response to bacterium defense response to other organism response to stress response to bacterium response to external biotic stimulus multicellular organismal process renal system process system process glomerular filtration renal filtration	cellular anatomical structure extracellular region extracellular space blood microparticle IgA immunoglobulin complex, circulating protein-containing complex secretory IgA immunoglobulin complex IgA immunoglobulin complex polymeric IgA immunoglobulin complex immunoglobulin complex, circulating immunoglobulin complex extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular region extracellular space blood microparticle IgA immunoglobulin complex, circulating protein-containing complex secretory IgA immunoglobulin complex IgA immunoglobulin complex polymeric IgA immunoglobulin complex immunoglobulin complex, circulating immunoglobulin complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle vesicle extracellular membrane-bounded organelle monomeric IgA immunoglobulin complex IgM immunoglobulin complex IgM immunoglobulin complex, circulating pentameric IgM immunoglobulin complex cell periphery plasma membrane membrane
C, F [auth S]	4E10 epitope scaffold T117	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, E [auth L]	IPR050150	Immunoglobulin Variable Light Chain	Family
B, E [auth L]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B, E [auth L]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B, E [auth L]	IPR013106	Immunoglobulin V-set domain	Domain
B, E [auth L]	IPR003599	Immunoglobulin domain subtype	Domain
B, E [auth L]	IPR007110	Immunoglobulin-like domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, E [auth L]	Pharos: P01619	tuberculosis B-cell chronic lymphocytic leukemia cutaneous lupus erythematosus interstitial cystitis malignant colon neoplasm non-small cell lung carcinoma periodontitis sinusitis ulcerative colitis Bruton-type agammaglobulinemia cystic fibrosis lung adenocarcinoma malignant ependymoma osteosarcoma plasma cell myeloma tuberculosis B-cell chronic lymphocytic leukemia cutaneous lupus erythematosus interstitial cystitis malignant colon neoplasm non-small cell lung carcinoma periodontitis sinusitis ulcerative colitis Bruton-type agammaglobulinemia cystic fibrosis lung adenocarcinoma malignant ependymoma osteosarcoma plasma cell myeloma Sjogren syndrome chronic obstructive pulmonary disease esophageal adenocarcinoma lung cancer malignant pancreatic neoplasm pancreatic ductal adenocarcinoma psoriasis

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.