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- PDB-2k9j: Integrin alphaIIb-beta3 transmembrane complex -

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Basic information

Entry
Database: PDB / ID: 2k9j
TitleIntegrin alphaIIb-beta3 transmembrane complex
Components
  • Integrin alpha-IIb light chain
  • Integrin beta-3
KeywordsMEMBRANE PROTEIN / integrin / transmembrane complex / Cell adhesion / Cleavage on pair of basic residues / Disease mutation / Glycoprotein / Pyrrolidone carboxylic acid / Receptor / Host-virus interaction / Phosphoprotein
Function / homology
Function and homology information


regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / tube development / alpha9-beta1 integrin-ADAM8 complex / response to platelet-derived growth factor / integrin alphaIIb-beta3 complex / regulation of postsynaptic neurotransmitter receptor diffusion trapping / maintenance of postsynaptic specialization structure / alphav-beta3 integrin-vitronectin complex / platelet alpha granule membrane ...regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / tube development / alpha9-beta1 integrin-ADAM8 complex / response to platelet-derived growth factor / integrin alphaIIb-beta3 complex / regulation of postsynaptic neurotransmitter receptor diffusion trapping / maintenance of postsynaptic specialization structure / alphav-beta3 integrin-vitronectin complex / platelet alpha granule membrane / positive regulation of glomerular mesangial cell proliferation / integrin alphav-beta3 complex / negative regulation of lipoprotein metabolic process / smooth muscle cell migration / alphav-beta3 integrin-PKCalpha complex / fibrinogen binding / positive regulation of leukocyte migration / alphav-beta3 integrin-HMGB1 complex / negative regulation of lipid transport / vascular endothelial growth factor receptor 2 binding / angiogenesis involved in wound healing / positive regulation of vascular endothelial growth factor signaling pathway / regulation of release of sequestered calcium ion into cytosol / Elastic fibre formation / mesodermal cell differentiation / positive regulation of bone resorption / alphav-beta3 integrin-IGF-1-IGF1R complex / platelet-derived growth factor receptor binding / cell-cell adhesion mediated by integrin / filopodium membrane / glycinergic synapse / extracellular matrix binding / positive regulation of fibroblast migration / positive regulation of cell adhesion mediated by integrin / positive regulation of vascular endothelial growth factor receptor signaling pathway / apolipoprotein A-I-mediated signaling pathway / regulation of bone resorption / negative regulation of low-density lipoprotein particle clearance / apoptotic cell clearance / wound healing, spreading of epidermal cells / positive regulation of smooth muscle cell migration / integrin complex / Molecules associated with elastic fibres / heterotypic cell-cell adhesion / cell adhesion mediated by integrin / negative chemotaxis / positive regulation of osteoblast proliferation / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / cellular response to insulin-like growth factor stimulus / Syndecan interactions / p130Cas linkage to MAPK signaling for integrins / regulation of postsynaptic neurotransmitter receptor internalization / cell-substrate adhesion / protein disulfide isomerase activity / microvillus membrane / PECAM1 interactions / GRB2:SOS provides linkage to MAPK signaling for Integrins / negative regulation of endothelial cell apoptotic process / TGF-beta receptor signaling activates SMADs / fibronectin binding / lamellipodium membrane / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / Integrin cell surface interactions / ECM proteoglycans / substrate adhesion-dependent cell spreading / positive regulation of T cell migration / cell-matrix adhesion / embryo implantation / coreceptor activity / Integrin signaling / positive regulation of endothelial cell proliferation / positive regulation of smooth muscle cell proliferation / positive regulation of endothelial cell migration / cell adhesion molecule binding / integrin-mediated signaling pathway / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / response to activity / protein kinase C binding / wound healing / Signal transduction by L1 / cellular response to xenobiotic stimulus / regulation of actin cytoskeleton organization / cell-cell adhesion / cellular response to mechanical stimulus / platelet activation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / platelet aggregation / VEGFA-VEGFR2 Pathway / integrin binding / ruffle membrane / blood coagulation / positive regulation of angiogenesis / Signaling by RAF1 mutants / cell-cell junction / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS 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 tail domain / Integrin beta cytoplasmic domain / Integrin alpha Ig-like domain 3 / Integrin_b_cyt ...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 tail domain / Integrin beta cytoplasmic domain / Integrin alpha Ig-like domain 3 / Integrin_b_cyt / : / Integrin EGF domain / EGF-like domain, extracellular / EGF-like domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / Integrin alpha cytoplasmic region / : / 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 alpha-2 / Integrin alpha Ig-like domain 1 / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / Integrin alpha chain / Integrin alpha beta-propellor / : / Integrin alpha Ig-like domain 2 / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / EGF-like domain signature 1. / von Willebrand factor A-like domain superfamily / EGF-like domain signature 2. / 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
Model type detailsminimized average
AuthorsLau, T. / Kim, C. / Ginsberg, M.H. / Ulmer, T.S.
CitationJournal: Embo J. / Year: 2009
Title: The structure of the integrin alphaIIbbeta3 transmembrane complex explains integrin transmembrane signalling
Authors: Lau, T.L. / Kim, C. / Ginsberg, M.H. / Ulmer, T.S.
History
DepositionOct 15, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Data collection / Database references
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)9,4652
Polymers9,4652
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)21 / 21all calculated structures submitted
RepresentativeModel #1minimized average structure

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Components

#1: Protein/peptide Integrin alpha-IIb light chain


Mass: 4751.833 Da / Num. of mol.: 1 / Fragment: Transmembrane domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGA2B, GP2B, ITGAB / Production host: Escherichia coli (E. coli) / References: UniProt: P08514
#2: Protein/peptide Integrin beta-3 / Platelet membrane glycoprotein IIIa / GPIIIa / CD61 antigen


Mass: 4712.788 Da / Num. of mol.: 1 / Fragment: Transmembrane domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB3, GP3A / Production host: Escherichia coli (E. coli) / References: UniProt: P05106

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111TRIPLE RESONANCE
121NOESY, 13C/15N-edited

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Sample preparation

DetailsContents: 1.2 mM [U-100% 13C; U-100% 15N; 80% 2H] Integrin alpha-IIb light chain, 1.2 mM [U-100% 13C; U-100% 15N; 80% 2H] Integrin beta-3, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMentity_1[U-100% 13C; U-100% 15N; 80% 2H]1
1.2 mMentity_2[U-100% 13C; U-100% 15N; 80% 2H]1
Sample conditionsIonic strength: 0.025 / pH: 7.4 / Pressure: ambient / Temperature: 301.2 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 21 / Conformers submitted total number: 21

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