1MHP

Crystal structure of a chimeric alpha1 integrin I-domain in complex with the Fab fragment of a humanized neutralizing antibody

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	d1mhpa_	Alpha and beta proteins (a/b)	vWA-like	vWA-like	Integrin A (or I) domain	Integrin alpha1-beta1	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
D [auth B]	d1mhpb_	Alpha and beta proteins (a/b)	vWA-like	vWA-like	Integrin A (or I) domain	Integrin alpha1-beta1	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
E [auth X]	d1mhpx_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin heavy chain variable domain, VH	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B [auth H]	d1mhph1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin heavy chain variable domain, VH	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B [auth H]	d1mhph2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C [auth L]	d1mhpl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin light chain kappa variable domain, VL-kappa	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C [auth L]	d1mhpl2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin light chain kappa constant domain, CL-kappa	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
F [auth Y]	d1mhpy_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin light chain kappa variable domain, VL-kappa	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	vWA-like	8032267	3000832	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	vWA-like	8032267	3000832	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	VWA	e1mhpA1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: vWA-like	F: VWA	ECOD (1.6)
D [auth B]	VWA	e1mhpB1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: vWA-like	F: VWA	ECOD (1.6)
E [auth X]	V-set_8	e1mhpX1	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 [auth H]	V-set_8	e1mhpH1	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 [auth H]	C1-set_1	e1mhpH2	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)
C [auth L]	C1-set_4	e1mhpL2	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)
C [auth L]	V-set	e1mhpL1	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)
F [auth Y]	V-set	e1mhpY1	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)
A	3.40.50.410	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	von Willebrand factor, type A domain	CATH (4.3.0)
D [auth B]	3.40.50.410	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	von Willebrand factor, type A domain	CATH (4.3.0)
E [auth X]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F [auth Y]	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
A, D [auth B]	Integrin alpha 1, (residues 169-360)	INTEGRIN-ALPHA-1	Rattus norvegicus (Norway rat)	ALPHA-1	I-LIKE-DOMAIN I-DOMAIN	RPI	(INTEGRIN-ALPHA-1)	IMGT (202446-0)
B [auth H], E [auth X]	huAQC2	VH-CH1	Humanized (humanized)	IGHV3-2304, IGHJ401, IGHJ402, IGHJ403, IGHG101, IGHG102, IGHG104, IGHG105	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202446-0)
C [auth L], F [auth Y]	huAQC2	L-KAPPA	Humanized (humanized)	IGKV1D-1301, IGKV1-1302, IGKV1-3901, IGKV1D-3901, IGKV1-NL101, IGKV1D-1302, IGKJ101, IGKC01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202446-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth H], E [auth X]	Heavy Chain	IGHV3	-	integrin alpha 1, (residues 169-360)	SAbDab (2024-11-15)
C [auth L], F [auth Y]	Light Chain	IGKV1D	Kappa	integrin alpha 1, (residues 169-360)	SAbDab (2024-11-15)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D [auth B]	PF00092	von Willebrand factor type A domain (VWA)	von Willebrand factor type A domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D [auth B]	integrin alpha 1, (RESIDUES 169-360)	protein binding binding signaling receptor binding cell adhesion molecule binding collagen binding protein-containing complex binding collagen binding involved in cell-matrix adhesion cell adhesion mediator activity cell-matrix adhesion mediator activity protein phosphatase binding phosphatase binding enzyme binding integrin binding cation binding protein binding binding signaling receptor binding cell adhesion molecule binding collagen binding protein-containing complex binding collagen binding involved in cell-matrix adhesion cell adhesion mediator activity cell-matrix adhesion mediator activity protein phosphatase binding phosphatase binding enzyme binding integrin binding cation binding ion binding metal ion binding small molecule binding	cell adhesion cell-matrix adhesion cell-substrate adhesion cellular process cell chemotaxis cellular response to stimulus chemotaxis response to stimulus neutrophil chemotaxis response to external stimulus neutrophil migration granulocyte migration leukocyte migration cellular response to chemical stimulus cell adhesion cell-matrix adhesion cell-substrate adhesion cellular process cell chemotaxis cellular response to stimulus chemotaxis response to stimulus neutrophil chemotaxis response to external stimulus neutrophil migration granulocyte migration leukocyte migration cellular response to chemical stimulus taxis immune system process granulocyte chemotaxis response to chemical myeloid leukocyte migration cell migration cell motility leukocyte chemotaxis locomotion regulation of biological process integrin-mediated signaling pathway regulation of cellular process cell surface receptor signaling pathway signaling biological regulation cell communication signal transduction neuron apoptotic process positive regulation of programmed cell death regulation of apoptotic process positive regulation of biological process regulation of programmed cell death cell death positive regulation of apoptotic process apoptotic process positive regulation of neuron apoptotic process programmed cell death positive regulation of cellular process regulation of neuron apoptotic process negative regulation of signaling negative regulation of ERBB signaling pathway negative regulation of biological process regulation of signal transduction cell surface receptor protein tyrosine kinase signaling pathway negative regulation of cell communication regulation of epidermal growth factor receptor signaling pathway negative regulation of cellular process epidermal growth factor receptor signaling pathway enzyme-linked receptor protein signaling pathway regulation of signaling regulation of ERBB signaling pathway negative regulation of response to stimulus negative regulation of signal transduction regulation of response to stimulus negative regulation of epidermal growth factor receptor signaling pathway ERBB signaling pathway regulation of cell communication cellular extravasation cell adhesion mediated by integrin multicellular organismal process cellular developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis cellular component organization neurogenesis multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation anatomical structure development cellular component organization or biogenesis system development developmental process plasma membrane bounded cell projection organization nervous system development generation of neurons anatomical structure morphogenesis neuron development regulation of tube diameter system process regulation of tube size circulatory system process vascular process in circulatory system blood vessel diameter maintenance regulation of biological quality vasodilation blood circulation regulation of anatomical structure size positive regulation of cell communication positive regulation of signal transduction intracellular signal transduction positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette positive regulation of MAPK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade MAPK cascade positive regulation of signaling negative regulation of cell population proliferation cell population proliferation regulation of cell population proliferation cell-cell adhesion	cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction somatodendritic compartment cell body perikaryon neuronal cell body cell periphery cell surface membrane plasma membrane external side of plasma membrane cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction somatodendritic compartment cell body perikaryon neuronal cell body cell periphery cell surface membrane plasma membrane external side of plasma membrane side of membrane protein-containing complex plasma membrane protein complex membrane protein complex receptor complex integrin complex plasma membrane signaling receptor complex integrin alpha1-beta1 complex protein complex involved in cell adhesion basal part of cell acrosomal vesicle membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle secretory granule secretory vesicle cytoplasm vesicle
B [auth H], E [auth X]	Fab fragment, heavy chain	-	-	-
C [auth L], F [auth Y]	FAB FRAGMENT, light chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D [auth B]	IPR013517	FG-GAP repeat	Repeat
A, D [auth B]	IPR013519	Integrin alpha beta-propellor	Repeat
A, D [auth B]	IPR000413	Integrin alpha chain	Family
A, D [auth B]	IPR048286	Integrin alpha, third immunoglobulin-like domain	Domain
A, D [auth B]	IPR036465	von Willebrand factor A-like domain superfamily	Homologous Superfamily
A, D [auth B]	IPR013649	Integrin alpha, first immunoglubulin-like domain	Domain
A, D [auth B]	IPR028994	Integrin alpha, N-terminal	Homologous Superfamily
A, D [auth B]	IPR002035	von Willebrand factor, type A	Domain
A, D [auth B]	IPR048285	Integrin alpha, second immunoglobulin-like domain	Domain
A, D [auth B]	IPR032695	Integrin domain superfamily	Homologous Superfamily
A, D [auth B]	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.