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- PDB-2bp3: Crystal structure of Filamin A domain 17 and GPIb alpha cytoplasm... -
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Basic information
Entry | Database: PDB / ID: 2bp3 | ||||||
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Title | Crystal structure of Filamin A domain 17 and GPIb alpha cytoplasmic domain complex | ||||||
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![]() | STRUCTURAL PROTEIN / CYTOSKELETON-COMPLEX / ACTIN BINDING PROTEIN / CYTOSKELETON / COMPLEX | ||||||
Function / homology | ![]() thrombin-activated receptor activity / regulation of membrane repolarization during atrial cardiac muscle cell action potential / regulation of membrane repolarization during cardiac muscle cell action potential / establishment of Sertoli cell barrier / Myb complex / glycoprotein Ib-IX-V complex / adenylate cyclase-inhibiting dopamine receptor signaling pathway / formation of radial glial scaffolds / positive regulation of integrin-mediated signaling pathway / Enhanced binding of GP1BA variant to VWF multimer:collagen ...thrombin-activated receptor activity / regulation of membrane repolarization during atrial cardiac muscle cell action potential / regulation of membrane repolarization during cardiac muscle cell action potential / establishment of Sertoli cell barrier / Myb complex / glycoprotein Ib-IX-V complex / adenylate cyclase-inhibiting dopamine receptor signaling pathway / formation of radial glial scaffolds / positive regulation of integrin-mediated signaling pathway / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / cytoplasmic sequestering of protein / positive regulation of leukocyte tethering or rolling / tubulin deacetylation / actin crosslink formation / blood coagulation, intrinsic pathway / protein localization to bicellular tight junction / OAS antiviral response / positive regulation of actin filament bundle assembly / positive regulation of neuron migration / positive regulation of potassium ion transmembrane transport / Cell-extracellular matrix interactions / Defective F9 activation / early endosome to late endosome transport / Platelet Adhesion to exposed collagen / apical dendrite / Fc-gamma receptor I complex binding / cell-cell junction organization / positive regulation of neural precursor cell proliferation / positive regulation of platelet activation / protein localization to cell surface / wound healing, spreading of cells / negative regulation of transcription by RNA polymerase I / megakaryocyte development / GP1b-IX-V activation signalling / cortical cytoskeleton / positive regulation of axon regeneration / receptor clustering / SMAD binding / regulation of blood coagulation / RHO GTPases activate PAKs / actin filament bundle / brush border / Platelet Aggregation (Plug Formation) / semaphorin-plexin signaling pathway / mitotic spindle assembly / cilium assembly / potassium channel regulator activity / epithelial to mesenchymal transition / blood vessel remodeling / axonal growth cone / heart morphogenesis / positive regulation of substrate adhesion-dependent cell spreading / release of sequestered calcium ion into cytosol / regulation of cell migration / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / extracellular matrix / dendritic shaft / protein localization to plasma membrane / G protein-coupled receptor binding / actin filament / protein kinase C binding / synapse organization / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / mRNA transcription by RNA polymerase II / establishment of protein localization / cell morphogenesis / trans-Golgi network / negative regulation of protein catabolic process / negative regulation of DNA-binding transcription factor activity / platelet activation / cerebral cortex development / small GTPase binding / kinase binding / platelet aggregation / Z disc / positive regulation of protein import into nucleus / cell-cell junction / actin filament binding / blood coagulation / actin cytoskeleton / Platelet degranulation / GTPase binding / negative regulation of neuron projection development / actin cytoskeleton organization / postsynapse / perikaryon / angiogenesis / DNA-binding transcription factor binding / positive regulation of canonical NF-kappaB signal transduction / transmembrane transporter binding / cell surface receptor signaling pathway / protein stabilization / cell adhesion / cadherin binding / external side of plasma membrane / focal adhesion / glutamatergic synapse / nucleolus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pudas, R. / Ylanne, J. | ||||||
![]() | ![]() Title: The Structure of the Gpib-Filamin a Complex. Authors: Nakamura, F. / Pudas, R. / Heikkinen, O. / Permi, P. / Kilpelainen, I. / Munday, A.D. / Hartwig, J.H. / Stossel, T.P. / Ylanne, J. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 54.2 KB | Display | ![]() |
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PDB format | ![]() | 38.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 358.7 KB | Display | ![]() |
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Full document | ![]() | 415.8 KB | Display | |
Data in XML | ![]() | 6 KB | Display | |
Data in CIF | ![]() | 922 B | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2aavC ![]() 1v05S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 9976.017 Da / Num. of mol.: 2 / Fragment: ROD DOMAIN, RESIDUES 1863-1956 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 2563.014 Da / Num. of mol.: 2 / Fragment: CYTOPLASMIC DOMAIN, RESIDUES 572-593 / Source method: obtained synthetically / Source: (synth.) ![]() #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | THE THREE N-TERMINAL RESIDUES OF CHAINS A AND B ARE FROM THE EXPRESSION | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.62 Å3/Da / Density % sol: 65.78 % |
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Crystal grow | pH: 8.2 Details: 1.75M AMMONIUM PHOSPHATE, PH 8.2, AFTER MICROSEEDING: 1.25M AMMONIUM SULFATE PH 8.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 5, 2004 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: SILICON (1 1 1) CHANNEL-CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.32→19.88 Å / Num. obs: 12876 / % possible obs: 86.9 % / Redundancy: 6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2.31→2.45 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3.13 / % possible all: 56.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1V05 Resolution: 2.32→19.88 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.92 / SU B: 5.978 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R: 0.263 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. FLEXIBLE SIDE CHAINS OF SOME RESIDUES LOCATED IN THE LOOP REGIONS COULD NOT BE BUILD USING AVAILABLE DENSITY AND THESE RESIDUES WERE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. FLEXIBLE SIDE CHAINS OF SOME RESIDUES LOCATED IN THE LOOP REGIONS COULD NOT BE BUILD USING AVAILABLE DENSITY AND THESE RESIDUES WERE MODELED: A 1881 ASN, A 1882 LYS, A 1892 ASP, A 1916 GLN, B 1891 LYS, B 1892 ASP, B 1909 GLU, B 1916 GLN, B 1917 ASP
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.94 Å2
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Refinement step | Cycle: LAST / Resolution: 2.32→19.88 Å
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Refine LS restraints |
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