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- PDB-1s4w: NMR structure of the cytoplasmic domain of integrin AIIb in DPC m... -

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Basic information

Entry
Database: PDB / ID: 1s4w
TitleNMR structure of the cytoplasmic domain of integrin AIIb in DPC micelles
ComponentsIntegrin alpha-IIb
KeywordsCELL ADHESION
Function / homology
Function and homology information


integrin alphaIIb-beta3 complex / platelet alpha granule membrane / fibrinogen binding / extracellular matrix binding / positive regulation of leukocyte migration / integrin complex / cell adhesion mediated by integrin / p130Cas linkage to MAPK signaling for integrins / GRB2:SOS provides linkage to MAPK signaling for Integrins / ECM proteoglycans ...integrin alphaIIb-beta3 complex / platelet alpha granule membrane / fibrinogen binding / extracellular matrix binding / positive regulation of leukocyte migration / integrin complex / cell adhesion mediated by integrin / p130Cas linkage to MAPK signaling for integrins / GRB2:SOS provides linkage to MAPK signaling for Integrins / ECM proteoglycans / Integrin cell surface interactions / Integrin signaling / cell-matrix adhesion / Signal transduction by L1 / integrin-mediated signaling pathway / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / cell-cell adhesion / 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 / Signaling by BRAF and RAF1 fusions / integrin binding / Platelet degranulation / angiogenesis / molecular adaptor activity / blood microparticle / external side of plasma membrane / focal adhesion / cell surface / extracellular exosome / metal ion binding / identical protein binding / plasma membrane
Similarity search - Function
: / Integrin alpha Ig-like domain 3 / Integrin alpha cytoplasmic 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 ...: / Integrin alpha Ig-like domain 3 / Integrin alpha cytoplasmic 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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / hybrid distance geometry, dynamic simulated annealing
AuthorsVinogradova, O. / Vaynberg, J. / Kong, X. / Haas, T.A. / Plow, E.F. / Qin, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Membrane-mediated structural transitions at the cytoplasmic face during integrin activation.
Authors: Vinogradova, O. / Vaynberg, J. / Kong, X. / Haas, T.A. / Plow, E.F. / Qin, J.
History
DepositionJan 19, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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


Theoretical massNumber of molelcules
Total (without water)2,3961
Polymers2,3961
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 / 99structures with the least restraint violations
RepresentativeModel #2closest to the average

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Components

#1: Protein/peptide Integrin alpha-IIb / Platelet membrane glycoprotein IIb / GPalpha IIb / GPIIb / CD41 antigen


Mass: 2395.579 Da / Num. of mol.: 1 / Fragment: cytoplasmic domain (residues 1020-1039)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGA2B, ITGAB, GP2B / Plasmid: pET31b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P08514

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY

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Sample preparation

DetailsContents: 300 mM dDPC, 95/5% H2O/D2O / Solvent system: 95/5% H2O/D2O
Sample conditionspH: 6.3 / Temperature: 313 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 spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

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Processing

NMR software
NameClassification
VNMRcollection
NMRPipeprocessing
PIPPdata analysis
X-PLORstructure solution
X-PLORrefinement
RefinementMethod: hybrid distance geometry, dynamic simulated annealing
Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 99 / Conformers submitted total number: 20

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