8T2U | pdb_00008t2u

Cryo-EM Structures of Full-length Integrin alphaIIbbeta3 in Native Lipids complexed with Eptifibatide

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Membrane Protein Annotation: mpstruc
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Integrin domains	8055552	3002062	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	vWA-like	8055554	3000832	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Integrin alpha N-terminal domain	8042728	3000314	SCOP2B (2022-06-29)

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 (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF00362	Integrin beta chain VWA domain (Integrin_beta)	Integrin beta chain VWA domain	Integrins have been found in animals and their homologues have also been found in cyanobacteria, probably due to horizontal gene transfer [1]. This domain corresponds to the integrin beta VWA domain.	Domain
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
C	Eptifibatide	-	-	-
B	Integrin beta-3	protein binding binding signaling receptor binding platelet-derived growth factor receptor binding growth factor receptor binding protein-containing complex binding fibrinogen binding cation binding ion binding metal ion binding small molecule binding cell adhesion molecule binding enzyme binding protease binding protein binding binding signaling receptor binding platelet-derived growth factor receptor binding growth factor receptor binding protein-containing complex binding fibrinogen binding cation binding ion binding metal ion binding small molecule binding cell adhesion molecule binding enzyme binding protease binding cytokine receptor binding vascular endothelial growth factor receptor binding vascular endothelial growth factor receptor 2 binding molecular transducer activity coreceptor activity signaling receptor activity isomerase activity intramolecular oxidoreductase activity catalytic activity, acting on a protein intramolecular oxidoreductase activity, transposing S-S bonds catalytic activity protein disulfide isomerase activity fibronectin binding identical protein binding virus receptor activity exogenous protein binding extracellular matrix binding integrin binding kinase binding protein kinase C binding protein kinase binding	cellular response to stimulus cellular response to nitrogen compound response to stimulus response to endogenous stimulus response to peptide hormone cellular response to peptide hormone stimulus response to oxygen-containing compound response to nitrogen compound cellular response to oxygen-containing compound cellular response to endogenous stimulus cellular response to chemical stimulus response to hormone response to chemical cellular process cellular response to stimulus cellular response to nitrogen compound response to stimulus response to endogenous stimulus response to peptide hormone cellular response to peptide hormone stimulus response to oxygen-containing compound response to nitrogen compound cellular response to oxygen-containing compound cellular response to endogenous stimulus cellular response to chemical stimulus response to hormone response to chemical cellular process cellular response to insulin-like growth factor stimulus cellular response to hormone stimulus regulation of biological process regulation of cellular process regulation of cell-substrate adhesion positive regulation of cell adhesion regulation of cell adhesion biological regulation positive regulation of biological process cell-substrate adhesion positive regulation of cell-matrix adhesion cell adhesion cell-matrix adhesion positive regulation of cell-substrate adhesion regulation of cell-matrix adhesion positive regulation of cellular process biological process involved in interspecies interaction between organisms symbiont entry into host cell viral process symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction regulation of localization negative regulation of lipid transport transport regulation of transport negative regulation of biological process lipid localization lipid transport negative regulation of transport regulation of lipid transport establishment of localization negative regulation of lipid localization localization regulation of lipid localization macromolecule localization substrate adhesion-dependent cell spreading positive regulation of cell communication cellular response to growth factor stimulus positive regulation of signal transduction signaling regulation of signal transduction cell surface receptor protein tyrosine kinase signaling pathway cell communication positive regulation of response to stimulus signal transduction regulation of vascular endothelial growth factor signaling pathway enzyme-linked receptor protein signaling pathway regulation of signaling regulation of cellular response to vascular endothelial growth factor stimulus cell surface receptor signaling pathway regulation of cellular response to growth factor stimulus positive regulation of vascular endothelial growth factor signaling pathway vascular endothelial growth factor signaling pathway regulation of response to stimulus regulation of cell communication cellular response to vascular endothelial growth factor stimulus response to growth factor positive regulation of signaling positive regulation of substrate adhesion-dependent cell spreading regulation of substrate adhesion-dependent cell spreading positive regulation of locomotion regulation of cell motility positive regulation of smooth muscle cell migration regulation of smooth muscle cell migration positive regulation of cell migration smooth muscle cell migration muscle cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration cell migration cell motility locomotion platelet-derived growth factor receptor signaling pathway multicellular organismal process regulation of body fluid levels wound healing cell activation hemostasis blood coagulation response to stress coagulation regulation of biological quality response to wounding platelet activation cell population proliferation positive regulation of cell population proliferation positive regulation of osteoblast proliferation osteoblast proliferation regulation of cell population proliferation regulation of osteoblast proliferation developmental process epithelium development morphogenesis of an epithelium epiboly involved in wound healing tissue development morphogenesis of an epithelial sheet wound healing, spreading of epidermal cells tissue morphogenesis anatomical structure morphogenesis anatomical structure development epiboly wound healing, spreading of cells chemotaxis negative chemotaxis taxis response to external stimulus regulation of smooth muscle cell proliferation smooth muscle cell proliferation positive regulation of smooth muscle cell proliferation muscle cell proliferation cellular localization regulation of postsynaptic neurotransmitter receptor diffusion trapping localization within membrane neurotransmitter receptor diffusion trapping regulation of postsynaptic membrane neurotransmitter receptor levels regulation of cellular localization receptor diffusion trapping receptor localization to synapse postsynaptic neurotransmitter receptor diffusion trapping regulation of receptor localization to synapse cellular response to xenobiotic stimulus response to xenobiotic stimulus negative regulation of lipoprotein metabolic process regulation of protein metabolic process lipoprotein metabolic process negative regulation of metabolic process primary metabolic process regulation of macromolecule metabolic process regulation of primary metabolic process negative regulation of cellular process regulation of lipoprotein metabolic process metabolic process protein metabolic process macromolecule metabolic process regulation of metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process import into cell phagocytosis apoptotic cell clearance endocytosis vesicle-mediated transport multicellular organism development tube development intracellular signal transduction positive regulation of ERK1 and ERK2 cascade 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 ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade monoamine transport nitrogen compound transport regulation of neurotransmitter transport serotonin uptake regulation of serotonin uptake serotonin transport organic hydroxy compound transport neurotransmitter transport establishment of localization in cell neurotransmitter uptake neurotransmitter reuptake regulation of neurotransmitter uptake trophoblast cell migration multi-multicellular organism process regulation of trophoblast cell migration reproductive process ameboidal-type cell migration female pregnancy embryo implantation multi-organism reproductive process regulation of cytoskeleton organization regulation of cellular component organization regulation of actin filament-based process actin cytoskeleton organization regulation of organelle organization cellular component organization organelle organization regulation of actin cytoskeleton organization actin filament-based process cellular component organization or biogenesis cytoskeleton organization response to activity protein activation cascade gene expression macromolecule biosynthetic process protein maturation biosynthetic process blood coagulation, fibrin clot formation cell adhesion mediated by integrin extracellular matrix organization regulation of extracellular matrix organization extracellular structure organization external encapsulating structure organization cellular component biogenesis cell junction organization cellular component assembly cell junction assembly cell-substrate junction assembly cell-substrate junction organization response to mechanical stimulus response to abiotic stimulus cellular response to mechanical stimulus cellular response to abiotic stimulus cellular response to external stimulus cellular response to environmental stimulus regulation of protein localization intracellular protein localization formation of primary germ layer mesodermal cell differentiation cellular developmental process mesoderm morphogenesis embryonic morphogenesis embryo development gastrulation cell differentiation anatomical structure formation involved in morphogenesis mesoderm formation mesoderm development negative regulation of endothelial cell apoptotic process negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death negative regulation of apoptotic process endothelial cell apoptotic process apoptotic process programmed cell death regulation of endothelial cell apoptotic process endothelial cell proliferation positive regulation of epithelial cell proliferation regulation of endothelial cell proliferation positive regulation of endothelial cell proliferation regulation of epithelial cell proliferation epithelial cell proliferation maintenance of synapse structure postsynapse organization cellular component maintenance cell junction maintenance maintenance of postsynaptic specialization structure postsynaptic density organization synapse organization postsynaptic specialization organization regulation of biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process positive regulation of macromolecule metabolic process regulation of vascular endothelial growth factor receptor signaling pathway vascular endothelial growth factor receptor signaling pathway positive regulation of vascular endothelial growth factor receptor signaling pathway homotypic cell-cell adhesion platelet aggregation cell-cell adhesion homeostatic process regulation of bone remodeling tissue homeostasis regulation of tissue remodeling regulation of bone resorption bone resorption multicellular organismal-level homeostasis tissue remodeling bone remodeling anatomical structure homeostasis regulation of multicellular organismal process lipid storage regulation of lipid storage negative regulation of lipid storage nutrient storage regulation of plasma lipoprotein particle levels regulation of low-density lipoprotein particle clearance negative regulation of low-density lipoprotein particle clearance plasma lipoprotein particle clearance negative regulation of lipoprotein particle clearance regulation of lipoprotein particle clearance low-density lipoprotein particle clearance negative regulation of multicellular organismal process regulation of lymphocyte migration positive regulation of mononuclear cell migration regulation of immune system process regulation of mononuclear cell migration positive regulation of immune system process positive regulation of lymphocyte migration regulation of leukocyte migration positive regulation of T cell migration lymphocyte migration positive regulation of leukocyte migration leukocyte migration immune system process regulation of T cell migration mononuclear cell migration T cell migration positive regulation of multicellular organismal process positive regulation of bone resorption heterotypic cell-cell adhesion regulation of calcium ion transport inorganic ion homeostasis intracellular calcium ion homeostasis monoatomic ion transmembrane transport calcium ion homeostasis regulation of monoatomic ion transmembrane transport negative regulation of sequestering of calcium ion calcium ion transport metal ion transport maintenance of location in cell regulation of calcium ion transmembrane transport monoatomic cation transmembrane transport intracellular monoatomic cation homeostasis monoatomic ion homeostasis monoatomic ion transport intracellular chemical homeostasis monoatomic cation homeostasis monoatomic cation transport regulation of metal ion transport regulation of sequestering of calcium ion intracellular monoatomic ion homeostasis calcium ion transmembrane import into cytosol regulation of release of sequestered calcium ion into cytosol sequestering of calcium ion regulation of monoatomic ion transport maintenance of location transmembrane transport release of sequestered calcium ion into cytosol regulation of transmembrane transport cellular homeostasis chemical homeostasis regulation of monoatomic cation transmembrane transport calcium ion transmembrane transport blood vessel morphogenesis angiogenesis involved in wound healing angiogenesis vasculature development circulatory system development tube morphogenesis blood vessel development system development receptor internalization postsynaptic neurotransmitter receptor internalization regulation of receptor internalization vesicle-mediated transport in synapse regulation of postsynaptic neurotransmitter receptor internalization regulation of endocytosis regulation of receptor-mediated endocytosis regulation of vesicle-mediated transport neurotransmitter receptor internalization postsynaptic endocytosis receptor-mediated endocytosis regulation of developmental process negative regulation of developmental process macrophage derived foam cell differentiation regulation of cell differentiation negative regulation of macrophage derived foam cell differentiation foam cell differentiation regulation of macrophage derived foam cell differentiation negative regulation of cell differentiation endothelial cell migration positive regulation of endothelial cell migration regulation of endothelial cell migration cellular response to platelet-derived growth factor stimulus response to platelet-derived growth factor apolipoprotein A-I-mediated signaling pathway connective tissue development renal system development kidney vasculature development renal system vasculature development positive regulation of glomerular mesangial cell proliferation regulation of glomerular mesangial cell proliferation nephron development positive regulation of cell proliferation involved in kidney development animal organ development cell proliferation involved in kidney development glomerular mesangium development regulation of cell proliferation involved in kidney development glomerulus development glomerular mesangial cell proliferation glomerulus vasculature development kidney development fibroblast proliferation regulation of fibroblast proliferation positive regulation of fibroblast proliferation regulation of fibroblast migration positive regulation of fibroblast migration fibroblast migration integrin-mediated signaling pathway positive regulation of cell adhesion mediated by integrin regulation of cell adhesion mediated by integrin regulation of vasculature development positive regulation of developmental process regulation of anatomical structure morphogenesis regulation of multicellular organismal development positive regulation of angiogenesis positive regulation of vasculature development regulation of angiogenesis regulation of opioid receptor signaling pathway positive regulation of opioid receptor signaling pathway G protein-coupled opioid receptor signaling pathway regulation of G protein-coupled receptor signaling pathway positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway positive regulation of G protein-coupled receptor signaling pathway adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway adenylate cyclase-inhibiting opioid receptor signaling pathway adenylate cyclase-modulating G protein-coupled receptor signaling pathway G protein-coupled receptor signaling pathway	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 integrin alphaIIb-beta3 complex cell-cell junction anchoring junction 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 integrin alphaIIb-beta3 complex cell-cell junction anchoring junction cell junction alphav-beta3 integrin-HMGB1 complex focal adhesion cell-substrate junction apical part of cell plasma membrane region apical plasma membrane ruffle cell leading edge leading edge membrane plasma membrane bounded cell projection cell projection ruffle membrane cell projection membrane cell surface lamellipodium membrane lamellipodium membrane-bounded organelle intracellular anatomical structure platelet alpha granule membrane intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane cytoplasmic vesicle organelle secretory granule secretory vesicle cytoplasm vesicle organelle membrane platelet alpha granule secretory granule membrane postsynapse postsynaptic membrane synapse synaptic membrane alphav-beta3 integrin-PKCalpha complex external side of plasma membrane side of membrane extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle actin-based cell projection microvillus microvillus membrane glutamatergic synapse alphav-beta3 integrin-IGF-1-IGF1R complex integrin alphav-beta3 complex pigment granule melanosome alphav-beta3 integrin-vitronectin complex glycinergic synapse nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen alpha9-beta1 integrin-ADAM8 complex filopodium membrane filopodium
A	Integrin alpha-IIb	extracellular matrix binding binding cell adhesion molecule binding protein-containing complex binding protein binding integrin binding signaling receptor binding molecular adaptor activity fibrinogen binding cation binding ion binding metal ion binding small molecule binding identical protein binding	cell adhesion cell-matrix adhesion cell-substrate adhesion cellular process developmental process multicellular organismal process blood vessel morphogenesis tube development angiogenesis vasculature development circulatory system development anatomical structure morphogenesis multicellular organism development tube morphogenesis cell adhesion cell-matrix adhesion cell-substrate adhesion cellular process developmental process multicellular organismal process blood vessel morphogenesis tube development angiogenesis vasculature development circulatory system development anatomical structure morphogenesis multicellular organism development tube morphogenesis anatomical structure formation involved in morphogenesis anatomical structure development blood vessel development system development cellular response to stimulus regulation of biological process integrin-mediated signaling pathway regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation cell communication signal transduction cell adhesion mediated by integrin positive regulation of locomotion regulation of cell motility regulation of leukocyte migration positive regulation of biological process positive regulation of leukocyte migration positive regulation of cell migration leukocyte migration immune system process regulation of locomotion positive regulation of cell motility regulation of cell migration cell migration regulation of immune system process cell motility positive regulation of immune system process locomotion positive regulation of cellular process cell-cell adhesion	cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex receptor complex cell periphery integrin complex plasma membrane signaling receptor complex cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex receptor complex cell periphery integrin complex plasma membrane signaling receptor complex protein complex involved in cell adhesion integrin alphaIIb-beta3 complex cell surface external side of plasma membrane side of membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle blood microparticle intracellular anatomical structure platelet alpha granule membrane intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane cytoplasmic vesicle secretory granule secretory vesicle cytoplasm organelle membrane platelet alpha granule secretory granule membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR033760	Integrin beta N-terminal	Domain
B	IPR036465	von Willebrand factor A-like domain superfamily	Homologous Superfamily
B	IPR032695	Integrin domain superfamily	Homologous Superfamily
B	IPR002369	Integrin beta subunit, VWA domain	Domain
B	IPR040622	Integrin beta, epidermal growth factor-like domain 1	Domain
B	IPR036349	Integrin beta tail domain superfamily	Homologous Superfamily
B	IPR014836	Integrin beta subunit, cytoplasmic domain	Domain
B	IPR012896	Integrin beta subunit, tail	Domain
B	IPR013111	Epidermal growth factor-like domain, extracellular	Domain
B	IPR015812	Integrin beta subunit	Family
B	IPR016201	PSI domain	Domain
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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: P05106	Glanzmann thrombasthenia 1 platelet-type bleeding disorder 16 carotid artery thrombosis coronary thrombosis thrombocytopenia acute coronary syndrome intracerebral hemorrhage myocardial infarction prostate cancer Gliosis osteopetrosis neonatal thrombocytopenia schizophrenia Glanzmann thrombasthenia glioblastoma Glanzmann thrombasthenia 1 platelet-type bleeding disorder 16 carotid artery thrombosis coronary thrombosis thrombocytopenia acute coronary syndrome intracerebral hemorrhage myocardial infarction prostate cancer Gliosis osteopetrosis neonatal thrombocytopenia schizophrenia Glanzmann thrombasthenia glioblastoma tuberculosis hip fracture malignant glioma autism ovarian cancer cerebrovascular disorder peripheral neuropathy spondyloarthropathy interstitial cystitis malignant mesothelioma autism spectrum disorder autosomal dominant macrothrombocytopenia pilocytic astrocytoma hypothyroidism malignant colon neoplasm malignant pancreatic neoplasm breast cancer osteosarcoma peripheral nervous system disease congenital anemia exocrine pancreatic carcinoma
A	Pharos: P08514	Glanzmann thrombasthenia 1 thrombocytopenia platelet-type bleeding disorder 16 carotid artery thrombosis juvenile idiopathic arthritis Liver Cirrhosis, Experimental Bernard-Soulier syndrome congenital anemia exocrine pancreatic carcinoma gastric cancer intracerebral hemorrhage malignant pancreatic neoplasm acute coronary syndrome thrombotic disease cerebrovascular disorder Glanzmann thrombasthenia 1 thrombocytopenia platelet-type bleeding disorder 16 carotid artery thrombosis juvenile idiopathic arthritis Liver Cirrhosis, Experimental Bernard-Soulier syndrome congenital anemia exocrine pancreatic carcinoma gastric cancer intracerebral hemorrhage malignant pancreatic neoplasm acute coronary syndrome thrombotic disease cerebrovascular disorder coronary artery disease gastric carcinoma medulloblastoma osteosarcoma autosomal dominant macrothrombocytopenia tuberculosis Glanzmann thrombasthenia

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Integrin Adhesion Receptors	full-length integrin αIIbβ3 in native lipid

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C	HRG	Parent Component: ARG
C	MPT
C	NH2	RESID: AA0081 , AA0083 , AA0084 , AA0086 , AA0087 , AA0088 , AA0090 , AA0091 , AA0092 , AA0093 , AA0095 , AA0096 , AA0097 , AA0098 , AA0099 , AA0100 PSI-MOD : L-alanine amide MOD:00090 , L-asparagine amide MOD:00092 , L-aspartic acid 1-amide MOD:00093 , L-glutamine amide MOD:00095 , L-glutamic acid 1-amide MOD:00096 , glycine amide MOD:00097 , L-isoleucine amide MOD:00099 , L-leucine amide MOD:00100 , L-lysine amide MOD:00101 , L-methionine amide MOD:00102 , L-proline amide MOD:00104 , L-serine amide MOD:00105 , L-threonine amide MOD:00106 , L-tryptophan amide MOD:00107 , L-tyrosine amide MOD:00108 , L-valine amide MOD:00109