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- PDB-1kup: Solution Structure of the Membrane Proximal Regions of alpha-IIb ... -

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Basic information

Entry
Database: PDB / ID: 1kup
TitleSolution Structure of the Membrane Proximal Regions of alpha-IIb and beta-3 Integrins
Components
  • integrin alpha-IIb
  • integrin beta-3
KeywordsCELL ADHESION / coiled-coil
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 / 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 ...regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / tube development / 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 / platelet alpha granule membrane / positive regulation of glomerular mesangial cell proliferation / integrin alphav-beta3 complex / negative regulation of lipoprotein metabolic process / 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 / cell-cell adhesion mediated by integrin / angiogenesis involved in wound healing / positive regulation of vascular endothelial growth factor signaling pathway / cell-substrate junction assembly / regulation of release of sequestered calcium ion into cytosol / positive regulation of bone resorption / mesodermal cell differentiation / Elastic fibre formation / alphav-beta3 integrin-IGF-1-IGF1R complex / platelet-derived growth factor receptor binding / 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 / smooth muscle cell migration / 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 / platelet-derived growth factor receptor signaling pathway / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / positive regulation of cell-matrix adhesion / Syndecan interactions / p130Cas linkage to MAPK signaling for integrins / cellular response to insulin-like growth factor stimulus / 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 / TGF-beta receptor signaling activates SMADs / lamellipodium membrane / fibronectin binding / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / blood coagulation, fibrin clot formation / negative regulation of endothelial cell apoptotic process / ECM proteoglycans / Integrin cell surface interactions / positive regulation of T cell migration / cellular response to platelet-derived growth factor stimulus / embryo implantation / coreceptor activity / substrate adhesion-dependent cell spreading / Integrin signaling / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of endothelial cell proliferation / cell-matrix adhesion / positive regulation of smooth muscle cell proliferation / cell adhesion molecule binding / positive regulation of endothelial cell migration / 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 / Signal transduction by L1 / wound healing / regulation of actin cytoskeleton organization / cellular response to xenobiotic stimulus / cell-cell adhesion / cellular response to mechanical stimulus / platelet activation / Signaling by high-kinase activity BRAF mutants / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / MAP2K and MAPK activation / platelet aggregation / VEGFA-VEGFR2 Pathway / integrin binding / positive regulation of fibroblast proliferation
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 tail domain / Integrin beta cytoplasmic domain / Integrin alpha Ig-like domain 3 / Integrin_b_cyt / : / Integrin EGF domain ...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 / EGF-like domain signature 1. / von Willebrand factor A-like domain superfamily / EGF-like domain signature 2.
Similarity search - Domain/homology
Integrin beta-3 / Integrin alpha-IIb
Similarity search - Component
MethodSOLUTION NMR / simulated annealing, molecular dynamics, matrix relaxation, torsion angle dynamics
AuthorsWeljie, A.M. / Hwang, P.M. / Vogel, H.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Solution structures of the cytoplasmic tail complex from platelet integrin alpha IIb- and beta 3-subunits.
Authors: Weljie, A.M. / Hwang, P.M. / Vogel, H.J.
History
DepositionJan 22, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)4,6112
Polymers4,6112
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 / 100structures with acceptable covalent geometry,structures with the least restraint violations,structures with the lowest energy
Representative

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Components

#1: Protein/peptide integrin alpha-IIb


Mass: 1472.801 Da / Num. of mol.: 1 / Fragment: Membrane proximal region / Source method: obtained synthetically
Details: This protein was Custom synthesized. It is naturally found in Homo sapiens (human).
References: UniProt: P08514
#2: Protein/peptide integrin beta-3


Mass: 3138.619 Da / Num. of mol.: 1 / Fragment: Membrane proximal region / Source method: obtained synthetically
Details: This protein was Custom synthesized. It is naturally found in Homo sapiens (human).
References: UniProt: P05106

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1222D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
12 mM aIIb/b3 peptides; pH 5.2 (unbuffered), 90% H2O 10% D2O90% H2O/10% D2O
22 mM aIIb/b3 peptides; pH 5.2 (unbuffered), 100% D2O100% D2O
Sample conditionspH: 5.2 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipeVersion 1.8 Rev 2000.243.12.42Bax, A et al.processing
CNS1.1Brunger, A.T. et al.refinement
ARIA1.1Nilges, M. et al.refinement
NMRView5.03Johnson, B.A. et al.data analysis
RefinementMethod: simulated annealing, molecular dynamics, matrix relaxation, torsion angle dynamics
Software ordinal: 1
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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