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Yorodumi- PDB-1s4w: NMR structure of the cytoplasmic domain of integrin AIIb in DPC m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1s4w | ||||||
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Title | NMR structure of the cytoplasmic domain of integrin AIIb in DPC micelles | ||||||
Components | Integrin alpha-IIb | ||||||
Keywords | CELL ADHESION | ||||||
Function / homology | Function and homology information platelet alpha granule membrane / fibrinogen binding / extracellular matrix binding / integrin complex / positive regulation of leukocyte migration / 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 ...platelet alpha granule membrane / fibrinogen binding / extracellular matrix binding / integrin complex / positive regulation of leukocyte migration / 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 / Signaling by high-kinase activity BRAF mutants / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / 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 / identical protein binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / hybrid distance geometry, dynamic simulated annealing | ||||||
Authors | Vinogradova, O. / Vaynberg, J. / Kong, X. / Haas, T.A. / Plow, E.F. / Qin, J. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1s4w.cif.gz | 120 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1s4w.ent.gz | 83.4 KB | Display | PDB format |
PDBx/mmJSON format | 1s4w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1s4w_validation.pdf.gz | 346.7 KB | Display | wwPDB validaton report |
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Full document | 1s4w_full_validation.pdf.gz | 465.2 KB | Display | |
Data in XML | 1s4w_validation.xml.gz | 11.3 KB | Display | |
Data in CIF | 1s4w_validation.cif.gz | 17 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s4/1s4w ftp://data.pdbj.org/pub/pdb/validation_reports/s4/1s4w | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | 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
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: 2D NOESY |
-Sample preparation
Details | Contents: 300 mM dDPC, 95/5% H2O/D2O / Solvent system: 95/5% H2O/D2O |
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Sample conditions | pH: 6.3 / Temperature: 313 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz |
-Processing
NMR software |
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Refinement | Method: hybrid distance geometry, dynamic simulated annealing Software ordinal: 1 | ||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 99 / Conformers submitted total number: 20 |