4IRZ

Crystal structure of A4b7 headpiece complexed with Fab Natalizumab

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Thera-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 L]	d4irzl2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth L]	d4irzl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth H]	d4irzh_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	human (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)
A	Integrin_alpha2_1st	e4irzA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Integrin_alpha2_1st	ECOD (1.6)
A	FG-GAP_1st	e4irzA2	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: FG-GAP_1st	ECOD (1.6)
B [auth L]	C1-set_4	e4irzL1	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)
B [auth L]	V-set	e4irzL2	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 [auth H]	V-set_8	e4irzH1	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 H]	C1-set_1	e4irzH2	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.130.10.130	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
A	2.60.40.1460	Mainly Beta	Sandwich	Immunoglobulin-like	Integrin domains. Chain A, domain 2	CATH (4.3.0)
B [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth H]	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 L]	INN name	L-KAPPA	Homo sapiens (human)	IGKV1-3301, IGKV1D-3301, IGKJ101, IGKC01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-4_KAPPA	IMGT (202448-0)
C [auth H]	INN name	VH-CH1	Homo sapiens (human)	IGHV1-301, IGHJ601, IGHJ602, IGHG401, IGHG4*04	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-4_KAPPA	IMGT (202448-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth L]	Light Chain	IGKV1	Kappa	integrin alpha4 subunit	SAbDab (2024-12-06)
C [auth H]	Heavy Chain	IGHV1	-	integrin alpha4 subunit	SAbDab (2024-12-06)

Thera-SAbDab Antibody Annotation Thera-SAbDab Database Homepage

Chain	Name	Target	Provenance Source
B [auth L]	Natalizumab	ITGA4/CD49D	Therapeutic SAbDab (2024-12-06)
C [auth H]	Natalizumab	ITGA4/CD49D	Therapeutic SAbDab (2024-12-06)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01839	FG-GAP repeat (FG-GAP)	FG-GAP repeat	-	Repeat
A	PF08441	Integrin alpha Ig-like domain 1 (Integrin_A_Ig_1)	Integrin alpha Ig-like domain 1	This domain is found in integrin alpha and integrin alpha precursors to the C terminus of a number of Pfam:PF01839 repeats and to the N-terminus of the Pfam:PF00357 cytoplasmic region. This region is composed of an immunoglobulin-like domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Integrin alpha4 subunit	C-X3-C chemokine binding protein binding binding chemokine binding cytokine binding cell adhesion molecule binding protein-containing complex binding integrin binding signaling receptor binding cation binding ion binding metal ion binding small molecule binding	cell adhesion cell-cell adhesion cell-cell adhesion mediated by integrin cell adhesion mediated by integrin cellular process leukocyte tethering or rolling leukocyte cell-cell adhesion leukocyte migration immune system process leukocyte adhesion to vascular endothelial cell cellular extravasation cell migration cell motility cell-matrix adhesion cell adhesion cell-cell adhesion cell-cell adhesion mediated by integrin cell adhesion mediated by integrin cellular process leukocyte tethering or rolling leukocyte cell-cell adhesion leukocyte migration immune system process leukocyte adhesion to vascular endothelial cell cellular extravasation cell migration cell motility cell-matrix adhesion ameboidal-type cell migration cell-substrate adhesion cell-matrix adhesion involved in ameboidal cell migration regulation of protein binding regulation of molecular function negative regulation of protein binding regulation of protein homodimerization activity regulation of binding negative regulation of binding biological regulation negative regulation of molecular function negative regulation of protein homodimerization activity regulation of tube diameter multicellular organismal process regulation of biological process system process regulation of tube size regulation of system process negative regulation of biological process negative regulation of vasoconstriction circulatory system process regulation of blood circulation vascular process in circulatory system regulation of vasoconstriction regulation of multicellular organismal process blood vessel diameter maintenance regulation of biological quality negative regulation of multicellular organismal process vasoconstriction blood circulation regulation of anatomical structure size developmental process formation of primary germ layer cellular developmental process embryonic morphogenesis tissue development embryo development gastrulation anatomical structure morphogenesis multicellular organism development endoderm development cell differentiation anatomical structure development anatomical structure formation involved in morphogenesis endoderm formation endodermal cell differentiation substrate adhesion-dependent cell spreading cellular response to stimulus integrin-mediated signaling pathway regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling cell communication signal transduction cell population proliferation positive regulation of cell population proliferation endothelial cell proliferation positive regulation of epithelial cell proliferation positive regulation of biological process regulation of vascular endothelial cell proliferation regulation of endothelial cell proliferation regulation of cell population proliferation positive regulation of endothelial cell proliferation vascular endothelial cell proliferation regulation of epithelial cell proliferation epithelial cell proliferation positive regulation of vascular endothelial cell proliferation positive regulation of cellular process positive regulation of endothelial cell apoptotic process positive regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death positive regulation of apoptotic process endothelial cell apoptotic process apoptotic process programmed cell death regulation of endothelial cell apoptotic process heterotypic cell-cell adhesion protein localization localization cellular localization receptor clustering cellular macromolecule localization macromolecule localization localization within membrane protein localization to membrane cellular response to nitrogen compound response to oxygen-containing compound response to nitrogen compound cellular response to amyloid-beta cellular response to oxygen-containing compound cellular response to chemical stimulus response to chemical response to amyloid-beta	integrin alpha4-beta1 complex protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex receptor complex cell periphery cellular anatomical structure integrin complex plasma membrane signaling receptor complex protein complex involved in cell adhesion cell surface external side of plasma membrane integrin alpha4-beta1 complex protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex receptor complex cell periphery cellular anatomical structure integrin complex plasma membrane signaling receptor complex protein complex involved in cell adhesion cell surface external side of plasma membrane side of membrane integrin alpha4-beta7 complex
B [auth L]	Fab Natalizumab light chain	-	-	-
C [auth H]	Fab Natalizumab heavy chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR013517	FG-GAP repeat	Repeat
A	IPR013519	Integrin alpha beta-propellor	Repeat
A	IPR000413	Integrin alpha chain	Family
A	IPR048286	Integrin alpha, third immunoglobulin-like domain	Domain
A	IPR013649	Integrin alpha, first immunoglubulin-like domain	Domain
A	IPR028994	Integrin alpha, N-terminal	Homologous Superfamily
A	IPR048285	Integrin alpha, second immunoglobulin-like domain	Domain
A	IPR032695	Integrin domain superfamily	Homologous Superfamily
A	IPR018184	Integrin alpha chain, C-terminal cytoplasmic region, 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.