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- PDB-2kv9: Integrin beta3 subunit in a disulfide linked alphaIIb-beta3 cytos... -

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Basic information

Entry
Database: PDB / ID: 2kv9
TitleIntegrin beta3 subunit in a disulfide linked alphaIIb-beta3 cytosolic domain
ComponentsIntegrin beta-3
KeywordsCELL ADHESION / integrin beta3 / beta3 / platelet glycoprotein IIIa / GPIIIa / CD61
Function / homology
Function and homology information


tube development / regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / alpha9-beta1 integrin-ADAM8 complex / regulation of trophoblast cell migration / integrin alphaIIb-beta3 complex / regulation of postsynaptic neurotransmitter receptor diffusion trapping / maintenance of postsynaptic specialization structure / alphav-beta3 integrin-vitronectin complex / regulation of extracellular matrix organization ...tube development / regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / alpha9-beta1 integrin-ADAM8 complex / regulation of trophoblast cell migration / integrin alphaIIb-beta3 complex / regulation of postsynaptic neurotransmitter receptor diffusion trapping / maintenance of postsynaptic specialization structure / alphav-beta3 integrin-vitronectin complex / regulation of extracellular matrix organization / positive regulation of glomerular mesangial cell proliferation / platelet alpha granule membrane / negative regulation of lipoprotein metabolic process / integrin alphav-beta3 complex / alphav-beta3 integrin-PKCalpha complex / fibrinogen binding / alphav-beta3 integrin-HMGB1 complex / blood coagulation, fibrin clot formation / glycinergic synapse / vascular endothelial growth factor receptor 2 binding / negative regulation of lipid transport / positive regulation of vascular endothelial growth factor signaling pathway / : / regulation of release of sequestered calcium ion into cytosol / Elastic fibre formation / mesodermal cell differentiation / cell-substrate junction assembly / alphav-beta3 integrin-IGF-1-IGF1R complex / platelet-derived growth factor receptor binding / angiogenesis involved in wound healing / filopodium membrane / extracellular matrix binding / positive regulation of fibroblast migration / positive regulation of vascular endothelial growth factor receptor signaling pathway / regulation of bone resorption / apolipoprotein A-I-mediated signaling pathway / positive regulation of cell adhesion mediated by integrin / apoptotic cell clearance / wound healing, spreading of epidermal cells / integrin complex / heterotypic cell-cell adhesion / smooth muscle cell migration / Molecules associated with elastic fibres / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / positive regulation of cell-matrix adhesion / negative chemotaxis / cell adhesion mediated by integrin / cellular response to insulin-like growth factor stimulus / Syndecan interactions / microvillus membrane / p130Cas linkage to MAPK signaling for integrins / positive regulation of smooth muscle cell migration / regulation of postsynaptic neurotransmitter receptor internalization / protein disulfide isomerase activity / cell-substrate adhesion / positive regulation of osteoblast proliferation / PECAM1 interactions / TGF-beta receptor signaling activates SMADs / GRB2:SOS provides linkage to MAPK signaling for Integrins / lamellipodium membrane / platelet-derived growth factor receptor signaling pathway / fibronectin binding / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / ECM proteoglycans / Integrin cell surface interactions / positive regulation of bone resorption / positive regulation of T cell migration / negative regulation of endothelial cell apoptotic process / coreceptor activity / cell adhesion molecule binding / cellular response to platelet-derived growth factor stimulus / positive regulation of endothelial cell proliferation / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of endothelial cell migration / Integrin signaling / embryo implantation / substrate adhesion-dependent cell spreading / protein kinase C binding / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / cell-matrix adhesion / Signal transduction by L1 / response to activity / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / positive regulation of smooth muscle cell proliferation / wound healing / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / platelet activation / VEGFA-VEGFR2 Pathway / platelet aggregation / ruffle membrane / cellular response to mechanical stimulus / positive regulation of fibroblast proliferation / positive regulation of angiogenesis / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants
Similarity search - Function
Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / Integrin beta tail domain / Integrin EGF domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail ...Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / Integrin beta tail domain / Integrin EGF domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / EGF-like domain, extracellular / EGF-like domain / Integrins beta chain EGF (I-EGF) domain profile. / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain EGF (I-EGF) domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / Integrin domain superfamily / PSI domain / domain found in Plexins, Semaphorins and Integrins / von Willebrand factor A-like domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2.
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsMetcalf, D.G. / Kielec, J.M. / Valentine, K.G. / Wand, A. / Bennett, J.S. / William, D.F. / Moore, D.T. / Molnar, K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: NMR analysis of the {alpha}IIb{beta}3 cytoplasmic interaction suggests a mechanism for integrin regulation.
Authors: Metcalf, D.G. / Moore, D.T. / Wu, Y. / Kielec, J.M. / Molnar, K. / Valentine, K.G. / Wand, A.J. / Bennett, J.S. / Degrado, W.F.
History
DepositionMar 10, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2020Group: Data collection / Database references / Other
Category: pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Integrin beta-3


Theoretical massNumber of molelcules
Total (without water)8,7181
Polymers8,7181
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 3148structures with the lowest energy
RepresentativeModel #1

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Components

#1: Protein Integrin beta-3 / Platelet membrane glycoprotein IIIa / GPIIIa


Mass: 8717.811 Da / Num. of mol.: 1 / Fragment: UNP residues 739-788
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB3, GP3A / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P05106
Compound detailsALTHOUGH EACH NMR SAMPLE CONTAINED THE ENTIRE SEQUENCES FOR CHAINS A, B AS LISTED IN SEQRES, ONLY A ...ALTHOUGH EACH NMR SAMPLE CONTAINED THE ENTIRE SEQUENCES FOR CHAINS A, B AS LISTED IN SEQRES, ONLY A PORTION OF THE STRUCTURE CORRESPONDING TO THE BETA SUBUNIT WAS OBSERVED. THE ALPHA SUBUNIT (CHAIN A) DOES NOT HAVE A SINGLE UNIQUE CONFORMATION AND HENCE LACKS STRUCTURE. LIKEWISE, THE POLYHIS TAG IN CHAIN B LACKS STRUCTURE
Sequence detailsTHE INTEGRIN ALPHA-IIB STRUCTURE REPRESENTING CHAIN A WITH UNIPROT REFERENCE ITA2B_HUMAN AND ...THE INTEGRIN ALPHA-IIB STRUCTURE REPRESENTING CHAIN A WITH UNIPROT REFERENCE ITA2B_HUMAN AND SEQUENCE SPECWKVGFFKRNRPPLEEDDEEGE IS NOT OBSERVED IN THE EXPERIMENT

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D CBCA(CO)NH
1213D HNCO
1313D HN(CA)CB
1413D (H)CCH-TOCSY
1513D HNHA
1613D 1H-15N NOESY
1713D 1H-15N TOCSY
1813D 1H-13C NOESY
1912D 1H-15N HSQC
11022D 1H-13C HSQC
11112D 1H-13C HSQC
11214D (13C)HSQC-NOESY-(13C)HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
15 mM sodium phosphate-1, 100 mM [U-99% 2H] DPC-2, 0.02 % sodium azide-3, 25 mM TFA-4, 1 mM [U-99% 13C; U-99% 15N] entity_beta3-5, 1 mM entity_alphaIIb-6, 90% H2O/10% D2O90% H2O/10% D2O
25 mM sodium phosphate-7, 100 mM [U-99% 2H] DPC-8, 0.02 % sodium azide-9, 25 mM TFA-10, 1 mM [U-10% 13C; U-99% 15N] entity_beta3-11, 1 mM entity_alphaIIb-12, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
5 mMsodium phosphate-11
100 mMDPC-2[U-99% 2H]1
0.02 %sodium azide-31
25 mMTFA-41
1 mMentity_beta3-5[U-99% 13C; U-99% 15N]1
1 mMentity_alphaIIb-61
5 mMsodium phosphate-72
100 mMDPC-8[U-99% 2H]2
0.02 %sodium azide-92
25 mMTFA-102
1 mMentity_beta3-11[U-10% 13C; U-99% 15N]2
1 mMentity_alphaIIb-122
Sample conditionsIonic strength: not calculated / pH: 6 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
FelixAccelrys Software Inc.processing
SparkyGoddardpeak picking
SparkyGoddardchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 3148 / Conformers submitted total number: 20

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