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Yorodumi- PDB-2brq: Crystal structure of the filamin A repeat 21 complexed with the i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2brq | ||||||
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Title | Crystal structure of the filamin A repeat 21 complexed with the integrin beta7 cytoplasmic tail peptide | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / CYTOSKELETON-COMPLEX / ACTIN-BINDING / CYTOSKELETON / IMMUNOGLOBULIN LIKE / INTEGRIN / CELL ADHESION | ||||||
Function / homology | Function and homology information immune response in gut-associated lymphoid tissue / cell-matrix adhesion involved in ameboidal cell migration / integrin alpha4-beta7 complex / 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 / formation of radial glial scaffolds / glycoprotein Ib-IX-V complex / adenylate cyclase-inhibiting dopamine receptor signaling pathway ...immune response in gut-associated lymphoid tissue / cell-matrix adhesion involved in ameboidal cell migration / integrin alpha4-beta7 complex / 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 / formation of radial glial scaffolds / glycoprotein Ib-IX-V complex / adenylate cyclase-inhibiting dopamine receptor signaling pathway / T cell migration / positive regulation of integrin-mediated signaling pathway / cytoplasmic sequestering of protein / tubulin deacetylation / actin crosslink formation / OAS antiviral response / blood coagulation, intrinsic pathway / protein localization to bicellular tight junction / positive regulation of actin filament bundle assembly / positive regulation of neuron migration / Cell-extracellular matrix interactions / positive regulation of potassium ion transmembrane transport / leukocyte tethering or rolling / early endosome to late endosome transport / apical dendrite / cell-cell junction organization / positive regulation of neural precursor cell proliferation / positive regulation of platelet activation / protein localization to cell surface / heterotypic cell-cell adhesion / integrin complex / negative regulation of transcription by RNA polymerase I / Fc-gamma receptor I complex binding / wound healing, spreading of cells / megakaryocyte development / GP1b-IX-V activation signalling / cortical cytoskeleton / receptor clustering / positive regulation of axon regeneration / actin filament bundle / SMAD binding / RHO GTPases activate PAKs / brush border / semaphorin-plexin signaling pathway / cilium assembly / mitotic spindle assembly / potassium channel regulator activity / epithelial to mesenchymal transition / blood vessel remodeling / Integrin cell surface interactions / axonal growth cone / heart morphogenesis / positive regulation of substrate adhesion-dependent cell spreading / regulation of cell migration / release of sequestered calcium ion into cytosol / cell adhesion molecule binding / substrate adhesion-dependent cell spreading / cell-matrix adhesion / protein kinase C binding / dendritic shaft / G protein-coupled receptor binding / actin filament / integrin-mediated signaling pathway / protein localization to plasma membrane / synapse organization / mRNA transcription by RNA polymerase II / establishment of protein localization / trans-Golgi network / negative regulation of DNA-binding transcription factor activity / negative regulation of protein catabolic process / cerebral cortex development / platelet aggregation / small GTPase binding / Z disc / kinase binding / positive regulation of protein import into nucleus / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / actin filament binding / cell-cell junction / actin cytoskeleton / negative regulation of neuron projection development / integrin binding / Platelet degranulation / virus receptor activity / GTPase binding / perikaryon / actin cytoskeleton organization / postsynapse / angiogenesis / positive regulation of canonical NF-kappaB signal transduction / DNA-binding transcription factor binding / transmembrane transporter binding / protein stabilization / receptor complex / cell adhesion / cadherin binding / focal adhesion / glutamatergic synapse / nucleolus / negative regulation of apoptotic process Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Kiema, T.-R. / Ylanne, J. | ||||||
Citation | Journal: Mol.Cell / Year: 2006 Title: The Molecular Basis of Filamin Binding to Integrins and Competition with Talin. Authors: Kiema, T. / Lad, Y. / Jiang, P. / Oxley, C.L. / Baldassarre, M. / Wegener, K.L. / Campbell, I.D. / Ylanne, J. / 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 | 2brq.cif.gz | 57 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2brq.ent.gz | 40.5 KB | Display | PDB format |
PDBx/mmJSON format | 2brq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/br/2brq ftp://data.pdbj.org/pub/pdb/validation_reports/br/2brq | HTTPS FTP |
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-Related structure data
Related structure data | 1v05S 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 / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 3
NCS ensembles :
NCS oper:
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-Components
#1: Protein | Mass: 9964.994 Da / Num. of mol.: 2 / Fragment: ROD DOMAIN, RESIDUES 2236-2329 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX4T-3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P21333 #2: Protein/peptide | Mass: 3552.918 Da / Num. of mol.: 2 / Fragment: RESIDUES 768-798 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P26010 #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Nonpolymer details | GLUTATHIONE (GTT): GLUTATHIONES X1 AND X2 ARE COVALENTLY ATTACHED TO A 2293 CYS AND B 2293 CYS, ...GLUTATHION | Sequence details | THE FIRST THREE RESIDUES GAM ORIGINATES | |
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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: 2.6 Å3/Da / Density % sol: 52.6 % / Description: FILAMIN C REPEAT 24 |
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Crystal grow | pH: 5.5 / Details: 1.26 M SODIUM CITRATE, 0.1 M CITRIC ACID PH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 |
Detector | Type: MARRESEARCH MAR165 / Detector: CCD / Date: Feb 17, 2005 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 2→37.68 Å / Num. obs: 13748 / % possible obs: 96.9 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.05 / Mean I/σ(I) obs: 5 / % possible all: 96.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1V05 Resolution: 2.1→37.68 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.925 / SU B: 10.227 / SU ML: 0.136 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.228 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SOME OF THE SIDE CHAIN ATOMS OF RESIDUES A 2264 ARG, A 2280 LYS, A 2287 ASP, B 2240 LYS, B 2250 ARG, B 2262 TRP, B 2280 LYS, B 2287 ASP, B ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SOME OF THE SIDE CHAIN ATOMS OF RESIDUES A 2264 ARG, A 2280 LYS, A 2287 ASP, B 2240 LYS, B 2250 ARG, B 2262 TRP, B 2280 LYS, B 2287 ASP, B 2288 ARG, D 785 THR AND D 787 ASN HAVE A POORLY DEFINED DENSITY. THE SIDE CHAIN ATOMS OF RESIDUES A 2289 LYS, B 2239 HIS, B 2264 ARG, B 2286 GLU, B 2289 LYS AND B 2314 GLU HAVE NO ELECTRON DENSITY BUT THEY WERE MODELED. BREAK IN THE MAIN CHAIN ELECTRON DENSITY BETWEEN RESIDUES B 2286 GLU - B 2287 ASP, B 2288 ARG - B 2289 LYS AND D 786 ILE - D 787 ASN.
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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: 36.43 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→37.68 Å
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Refine LS restraints |
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