6TYB

Isolation and Structure of an Antibody that Fully Neutralizes Isolate SIVmac239 Reveals Functional Similarity of SIV and HIV Glycan Shields

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)
C [auth H]	d6tybh_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Rhesus (Macaca mulatta ) [TaxId: 9544 ],	SCOPe (2.08)
D [auth L]	d6tybl2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	Rhesus (Macaca mulatta ) [TaxId: 9544 ],	SCOPe (2.08)
D [auth L]	d6tybl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Rhesus (Macaca mulatta ) [TaxId: 9544 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth G]	PF00516	e6tybG1	A: a+b two layers	X: Ribosomal protein L31e-like	H: Ribosomal protein L31e/gp120 outer domain (From Topology)	T: Ribosomal protein L31e/gp120 outer domain	F: PF00516	ECOD (1.6)
A [auth G]	PF00516	e6tybG2	A: a+b two layers	X: gp120 inner domain (From Topology)	H: gp120 inner domain (From Topology)	T: gp120 inner domain	F: PF00516	ECOD (1.6)
B [auth C]	PF00047	e6tybC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF00047	ECOD (1.6)
B [auth C]	PF05790	e6tybC2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF05790	ECOD (1.6)
C [auth H]	PF07654	e6tybH2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
C [auth H]	PF07686	e6tybH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
D [auth L]	PF07654	e6tybL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
D [auth L]	PF07686	e6tybL2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth G]	2.170.40.20	Mainly Beta	Beta Complex	HIV Envelope Protein Gp120	Chain G	CATH (utative)
B [auth C]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
C [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
D [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	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
C [auth H]	Fab ITS90.03, broadly neutralizing	VH-CH1	Chimeric (chimeric)	IGHJ401, IGHG103, IGHG108, IGHG106	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202416-0)
D [auth L]	Fab ITS90.03, broadly neutralizing	L-KAPPA	Chimeric (chimeric)	IGKV1-2001, IGKJ101, IGKJ201, IGKC01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202416-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C [auth H]	Heavy Chain	IGHV5	-	envelope glycoprotein gp160	SAbDab (2024-04-26)
D [auth L]	Light Chain	IGKV1	Kappa	envelope glycoprotein gp160	SAbDab (2024-04-26)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth G]	PF00516	Envelope glycoprotein GP120 (GP120)	Envelope glycoprotein GP120	-	Family
B [auth C]	PF05790	Immunoglobulin C2-set domain (C2-set)	Immunoglobulin C2-set domain	-	Domain
B [auth C]	PF00047	Immunoglobulin domain (ig)	Immunoglobulin domain	Members of the immunoglobulin superfamily are found in hundreds of proteins of different functions. Examples include antibodies, the giant muscle kinase titin and receptor tyrosine kinases. Immunoglobulin-like domains may be involved in protein-prot ...	Members of the immunoglobulin superfamily are found in hundreds of proteins of different functions. Examples include antibodies, the giant muscle kinase titin and receptor tyrosine kinases. Immunoglobulin-like domains may be involved in protein-protein and protein-ligand interactions.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth G]	Envelope glycoprotein gp160	structural molecule activity	viral process membrane fusion involved in viral entry into host cell biological process involved in interspecies interaction between organisms symbiont entry into host cell symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host	cell periphery plasma membrane membrane cellular anatomical entity virion component viral membrane viral envelope host cell plasma membrane host cellular component host cell part host cell membrane virion membrane host intracellular membrane-bounded organelle host intracellular part cell periphery plasma membrane membrane cellular anatomical entity virion component viral membrane viral envelope host cell plasma membrane host cellular component host cell part host cell membrane virion membrane host intracellular membrane-bounded organelle host intracellular part host cell cytoplasm part host intracellular organelle host cell endosome membrane host cell cytoplasm host cell endosome host intracellular region
B [auth C]	T-cell surface glycoprotein CD4	molecular transducer activity coreceptor activity signaling receptor activity protein binding binding signaling receptor binding MHC class II protein binding MHC protein binding protein-containing complex binding MHC protein complex binding MHC class II protein complex binding protein tyrosine kinase binding kinase binding enzyme binding molecular transducer activity coreceptor activity signaling receptor activity protein binding binding signaling receptor binding MHC class II protein binding MHC protein binding protein-containing complex binding MHC protein complex binding MHC class II protein complex binding protein tyrosine kinase binding kinase binding enzyme binding protein kinase binding	interleukin-15-mediated signaling pathway cellular response to stimulus response to organic substance regulation of biological process regulation of cellular process response to stimulus cell surface receptor signaling pathway signaling biological regulation response to cytokine cellular response to interleukin-15 cytokine-mediated signaling pathway cell communication cellular response to chemical stimulus response to chemical interleukin-15-mediated signaling pathway cellular response to stimulus response to organic substance regulation of biological process regulation of cellular process response to stimulus cell surface receptor signaling pathway signaling biological regulation response to cytokine cellular response to interleukin-15 cytokine-mediated signaling pathway cell communication cellular response to chemical stimulus response to chemical cellular response to cytokine stimulus cellular process cellular response to organic substance signal transduction response to interleukin-15 multicellular organismal process T cell activation immune system process cell activation lymphocyte activation leukocyte activation immune response adaptive immune response positive regulation of cell communication positive regulation of signal transduction positive regulation of biological process regulation of signal transduction intracellular signal transduction positive regulation of response to stimulus positive regulation of ERK1 and ERK2 cascade regulation of intracellular signal transduction intracellular signaling cassette positive regulation of cellular process regulation of signaling positive regulation of MAPK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade regulation of response to stimulus MAPK cascade regulation of cell communication ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade positive regulation of signaling cell adhesion developmental process cellular developmental process hemopoiesis cell development mononuclear cell differentiation lymphocyte differentiation cell differentiation anatomical structure development T cell differentiation T cell selection leukocyte differentiation	cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane membrane microdomain membrane raft
C [auth H]	NEUTRALIZING ANTIBODY ITS90.03 FAB HEAVY CHAIN	-	-	-
D [auth L]	NEUTRALIZING ANTIBODY ITS90.03 FAB LIGHT CHAIN	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth G]	IPR000777	Human immunodeficiency virus 1, envelope glycoprotein Gp120	Domain
A [auth G]	IPR036377	Gp120 core superfamily	Homologous Superfamily
A [auth G]	IPR000328	Retroviral envelope protein GP41-like	Domain
B [auth C]	IPR008424	Immunoglobulin C2-set	Domain
B [auth C]	IPR021963	T cell CD4 receptor C-terminal region	Domain
B [auth C]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B [auth C]	IPR003599	Immunoglobulin subtype	Domain
B [auth C]	IPR015274	CD4, extracellular	Domain
B [auth C]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B [auth C]	IPR013106	Immunoglobulin V-set domain	Domain
B [auth C]	IPR000973	T-cell surface antigen CD4	Family
B [auth C]	IPR013151	Immunoglobulin	Domain
B [auth C]	IPR007110	Immunoglobulin-like domain	Domain

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.