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- PDB-2knc: Platelet integrin ALFAIIB-BETA3 transmembrane-cytoplasmic heteroc... -

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Basic information

Entry
Database: PDB / ID: 2knc
TitlePlatelet integrin ALFAIIB-BETA3 transmembrane-cytoplasmic heterocomplex
Components
  • Integrin alpha-IIb
  • Integrin beta-3
KeywordsCELL ADHESION / integrin / transmembrane signaling / protein structure / Cleavage on pair of basic residues / Disease mutation / Disulfide bond / Glycoprotein / Membrane / Pyrrolidone carboxylic acid / Receptor / Transmembrane / Host-virus interaction / Phosphoprotein
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 / positive regulation of leukocyte migration / 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 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / cell-cell adhesion / 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
Similarity search - Function
Bicelle-embedded integrin alpha(iib) transmembrane segment / Cytochrome c1, transmembrane anchor, C-terminal / 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 alpha Ig-like domain 3 ...Bicelle-embedded integrin alpha(iib) transmembrane segment / Cytochrome c1, transmembrane anchor, C-terminal / 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 alpha Ig-like domain 3 / 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 alpha cytoplasmic region / 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 alpha-2 / Integrin alpha Ig-like domain 1 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / : / Integrin alpha Ig-like domain 2 / Integrins alpha chain signature. / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin domain superfamily / Integrin alpha, N-terminal / 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. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Integrin beta-3 / Integrin alpha-IIb
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsYang, J. / Ma, Y. / Page, R.C. / Misra, S. / Plow, E.F. / Qin, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structure of an integrin alphaIIb beta3 transmembrane-cytoplasmic heterocomplex provides insight into integrin activation.
Authors: Yang, J. / Ma, Y.Q. / Page, R.C. / Misra, S. / Plow, E.F. / Qin, J.
History
DepositionAug 20, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 10, 2011Group: Database references
Revision 1.3Feb 26, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4Aug 18, 2021Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Structure summary
Category: database_2 / pdbx_nmr_exptl ...database_2 / pdbx_nmr_exptl / pdbx_nmr_exptl_sample / pdbx_nmr_representative / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / struct
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_representative.selection_criteria / _pdbx_nmr_software.authors / _pdbx_nmr_software.classification / _pdbx_nmr_spectrometer.manufacturer / _pdbx_nmr_spectrometer.model / _struct.pdbx_model_details
Revision 1.5Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.6May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integrin alpha-IIb
B: Integrin beta-3


Theoretical massNumber of molelcules
Total (without water)14,8322
Polymers14,8322
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 / 98structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Integrin alpha-IIb / Platelet membrane glycoprotein IIb / GPalpha IIb / GPIIb / Integrin alpha-IIb heavy chain / ...Platelet membrane glycoprotein IIb / GPalpha IIb / GPIIb / Integrin alpha-IIb heavy chain / Integrin alpha-IIb light chain / form 1 / Integrin alpha-IIb light chain / form 2


Mass: 6057.068 Da / Num. of mol.: 1
Fragment: transmembrane and cytoplasmic domains, residues 991-1039
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGA2B, GP2B, ITGAB / Plasmid: pMAL-C2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: P08514
#2: Protein Integrin beta-3 / Platelet membrane glycoprotein IIIa / GPIIIa


Mass: 8775.271 Da / Num. of mol.: 1
Fragment: transmembrane and cytoplasmic domains, residues 715-788
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB3, GP3A / Plasmid: pMAL-C2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: P05106

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCO
1213D HNCA
1313D HN(CA)CB
1413D CBCA(CO)NH
1513D H(CCO)NH
1613D C(CO)NH
1733D 13C-15N NOESY
1833D 1H-15N NOESY
1943D 13C-15N NOESY
11023D HNCO
11123D HNCA
11223D HN(CA)CB
11323D CBCA(CO)NH
11423D H(CCO)NH
11523D C(CO)NH
11643D 1H-15N NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.2 MM [U-100% 13C U-100% 15N] AIIBTMCD, 0.6 MM B3TMCD, 50% CD3CN/50% H2O, 0.1% TFAsample_150% CD3CN/50% H2O
solution20.2 MM [U-100% 13C U-100% 15N] B3TMCD, 0.6 MM AIIBTMCD, 50% CD3CN/50% H2O, 0.1% TFAsample_250% CD3CN/50% H2O
solution30.4 MM [U-100% 2H U-100% 15N] B3TMCD, 1.2 MM AIIBTMCD, 50% CD3CN/50% H2O, 0.1% TFAsample_350% CD3CN/50% H2O
solution40.4 MM [U-100% 2H U-100% 15N] AIIBTMCD, 1.2 MM B3TMCD, 50% CD3CN/50% H2O, 0.1% TFAsample_450% CD3CN/50% H2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.2 mMAIIbTMCD-1[U-100% 13C; U-100% 15N]1
0.6 mMB3TMCD-2natural abundance1
0.2 mMB3TMCD-3[U-100% 13C; U-100% 15N]2
0.6 mMAIIbTMCD-4natural abundance2
0.4 mMB3TMCD-5[U-100% 2H; U-100% 15N]3
1.2 mMAIIbTMCD-6natural abundance3
0.4 mMAIIbTMCD-7[U-100% 2H; U-100% 15N]4
1.2 mMB3TMCD-8natural abundance4
0.1 %TFAnatural abundance1
0.1 %TFAnatural abundance2
0.1 %TFAnatural abundance3
0.1 %TFAnatural abundance4
Sample conditionsIonic strength: 0 / Pressure: AMBIENT / Temperature: 25 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE8002
Bruker AVANCEBrukerAVANCE9003

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.15.0Schwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIH2.15.0Schwieters, Kuszewski, Tjandra and Clorestructure solution
NMRPipe2.4Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PASAXu, Wang, Yang, Vaynberg, Qinchemical shift assignment
PROCHECKLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thodata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 2100 / NOE intraresidue total count: 665 / NOE long range total count: 83 / NOE medium range total count: 688 / NOE sequential total count: 664 / Hydrogen bond constraints total count: 213 / Protein phi angle constraints total count: 74 / Protein psi angle constraints total count: 74
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 98 / Conformers submitted total number: 20

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