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Yorodumi- PDB-2w0p: Crystal structure of the filamin A repeat 21 complexed with the m... -
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-Basic information
Entry | Database: PDB / ID: 2w0p | ||||||
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Title | Crystal structure of the filamin A repeat 21 complexed with the migfilin peptide | ||||||
Components |
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Keywords | CELL ADHESION / ALTERNATIVE SPLICING / CYTOSKELETON-COMPLEX / PHOSPHOPROTEIN / DISEASE MUTATION / IMMUNOGLOBULIN LIKE / ZINC / FILAMIN / COMPLEX / INTEGRIN / MIGFILIN / RECEPTOR / POLYMORPHISM / CYTOSKELETON / ACTIN-BINDING / CELL JUNCTION / METAL-BINDING / CYTOPLASM / LIM DOMAIN / CELL SHAPE / ACETYLATION | ||||||
Function / homology | Function and homology information regulation of integrin activation / regulation of membrane repolarization during atrial cardiac muscle cell action potential / regulation of membrane repolarization during cardiac muscle cell action potential / filamin binding / 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 ...regulation of integrin activation / regulation of membrane repolarization during atrial cardiac muscle cell action potential / regulation of membrane repolarization during cardiac muscle cell action potential / filamin binding / 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 / cytoplasmic sequestering of protein / 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 / early endosome to late endosome transport / 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 / RHO GTPases activate PAKs / actin filament bundle / brush border / 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 / stress fiber / positive regulation of substrate adhesion-dependent cell spreading / release of sequestered calcium ion into cytosol / regulation of cell migration / dendritic shaft / cell periphery / protein localization to plasma membrane / G protein-coupled receptor binding / actin filament / protein kinase C binding / synapse organization / mRNA transcription by RNA polymerase II / establishment of protein localization / trans-Golgi network / negative regulation of protein catabolic process / negative regulation of DNA-binding transcription factor activity / cerebral cortex development / fibrillar center / small GTPase binding / kinase binding / platelet aggregation / Z disc / cell-cell adhesion / positive regulation of protein import into nucleus / cell-cell junction / actin filament binding / actin cytoskeleton / Platelet degranulation / GTPase binding / cell junction / negative regulation of neuron projection development / regulation of cell shape / actin cytoskeleton organization / postsynapse / perikaryon / angiogenesis / DNA-binding transcription factor binding / positive regulation of canonical NF-kappaB signal transduction / transmembrane transporter binding / protein stabilization / cadherin binding / focal adhesion / glutamatergic synapse / nucleolus / negative regulation of apoptotic process / perinuclear region of cytoplasm / protein homodimerization activity / RNA binding / extracellular exosome / extracellular region / membrane / nucleus / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Ruskamo, S. / Ylanne, J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Structural Basis of the Migfilin-Filamin Interaction and Competition with Integrin {Beta} Tails. Authors: Lad, Y. / Jiang, P. / Ruskamo, S. / Harburger, D.S. / Ylanne, J. / Campbell, I.D. / Calderwood, D.A. | ||||||
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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2w0p.cif.gz | 51.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w0p.ent.gz | 36.9 KB | Display | PDB format |
PDBx/mmJSON format | 2w0p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2w0p_validation.pdf.gz | 447.4 KB | Display | wwPDB validaton report |
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Full document | 2w0p_full_validation.pdf.gz | 449 KB | Display | |
Data in XML | 2w0p_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | 2w0p_validation.cif.gz | 13.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w0/2w0p ftp://data.pdbj.org/pub/pdb/validation_reports/w0/2w0p | HTTPS FTP |
-Related structure data
Related structure data | 2brqS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 4 / Auth seq-ID: 2237 - 2328 / Label seq-ID: 2 - 93
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-Components
#1: Protein | Mass: 9705.669 Da / Num. of mol.: 2 / Fragment: IG-21, RESIDUES 2236-2329 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-4T-3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P21333 #2: Protein/peptide | | Mass: 1616.898 Da / Num. of mol.: 1 / Fragment: RESIDUES 5-19 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q8WUP2 #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.6 % / Description: NONE |
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Crystal grow | Details: 1.7M (NH4)2SO4, 5% 2-PROPANOL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 17, 2008 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: DIAMOND (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→32.48 Å / Num. obs: 17625 / % possible obs: 99.9 % / Redundancy: 2.54 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.35 / % possible all: 97.7 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BRQ, CHAIN A Resolution: 1.9→32.48 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.046 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SOME OF THE SIDE CHAIN ATOMS OF RESIDUES A 2262 TRP, A 2287 ASP, A 2289 LYS, B 2252 GLU, B 2265 GLU, B 2268 ALA, B 2289 LYS, B 2313 GLU, B ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SOME OF THE SIDE CHAIN ATOMS OF RESIDUES A 2262 TRP, A 2287 ASP, A 2289 LYS, B 2252 GLU, B 2265 GLU, B 2268 ALA, B 2289 LYS, B 2313 GLU, B 2314 GLU HAVE NO ELECTRON DENSITY BUT THEY WERE MODELED. SOME OF THE SIDE CHAIN ATOMS OF RESIDUES A 2239 HIS, A 2240 LYS, A 2242 ARG, A 2250 ARG, A 2252 GLU, A 2268 ALA, A 2286 GLU, A 2314 GLU, B 2240 LYS, B 2250 ARG, B 2286 GLU, B 2306 GLU HAVE A POORLY DEFINED DENSITY.
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.88 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→32.48 Å
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Refine LS restraints |
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