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Yorodumi- PDB-1bkr: CALPONIN HOMOLOGY (CH) DOMAIN FROM HUMAN BETA-SPECTRIN AT 1.1 ANG... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bkr | ||||||
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Title | CALPONIN HOMOLOGY (CH) DOMAIN FROM HUMAN BETA-SPECTRIN AT 1.1 ANGSTROM RESOLUTION | ||||||
Components | SPECTRIN BETA CHAIN | ||||||
Keywords | ACTIN-BINDING / FILAMENTOUS ACTIN-BINDING DOMAIN / CYTOSKELETON | ||||||
Function / homology | Function and homology information regulation of SMAD protein signal transduction / membrane assembly / central nervous system formation / cuticular plate / spectrin / spectrin-associated cytoskeleton / plasma membrane organization / Golgi to plasma membrane protein transport / actin filament capping / M band ...regulation of SMAD protein signal transduction / membrane assembly / central nervous system formation / cuticular plate / spectrin / spectrin-associated cytoskeleton / plasma membrane organization / Golgi to plasma membrane protein transport / actin filament capping / M band / Sensory processing of sound by outer hair cells of the cochlea / Interaction between L1 and Ankyrins / Sensory processing of sound by inner hair cells of the cochlea / Nephrin family interactions / ankyrin binding / RHOV GTPase cycle / cortical actin cytoskeleton / mitotic cytokinesis / RHOU GTPase cycle / axolemma / regulation of protein localization to plasma membrane / COPI-mediated anterograde transport / Signaling by FLT3 fusion proteins / positive regulation of interleukin-2 production / NCAM signaling for neurite out-growth / central nervous system development / cell projection / protein localization to plasma membrane / positive regulation of protein localization to plasma membrane / phospholipid binding / structural constituent of cytoskeleton / actin filament binding / cell junction / GTPase binding / actin binding / actin cytoskeleton organization / RAF/MAP kinase cascade / postsynaptic density / calmodulin binding / cadherin binding / glutamatergic synapse / nucleolus / RNA binding / extracellular exosome / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.1 Å | ||||||
Authors | Djinovic Carugo, K. / Banuelos, S. / Saraste, M. | ||||||
Citation | Journal: Structure / Year: 1998 Title: Structural comparisons of calponin homology domains: implications for actin binding. Authors: Banuelos, S. / Saraste, M. / Carugo, K.D. #1: Journal: Nat.Struct.Biol. / Year: 1997 Title: Crystal Structure of a Calponin Homology Domain Authors: Carugo, K.D. / Banuelos, S. / Saraste, M. #2: Journal: Nat.Struct.Biol. / Year: 1997 Title: The Structure of an Actin-Crosslinking Domain from Human Fimbrin Authors: Goldsmith, S.C. / Pokala, N. / Shen, W. / Fedorov, A.A. / Matsudaira, P. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bkr.cif.gz | 67.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bkr.ent.gz | 48.4 KB | Display | PDB format |
PDBx/mmJSON format | 1bkr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bk/1bkr ftp://data.pdbj.org/pub/pdb/validation_reports/bk/1bkr | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | SPECTRIN IS A HETEROTETRAMER CONSISTING OF 2 ALPHA AND 2 BETA CHAINS. CALPONIN HOMOLOGY DOMAIN IS AT THE N-TERMINAL PART OF THE BETA CHAIN. |
-Components
#1: Protein | Mass: 12715.499 Da / Num. of mol.: 1 / Fragment: F-ACTIN BINDING DOMAIN RESIDUES 173 - 281 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell: NON-ERYTHROCYTE / Cellular location: CYTOSKELETAL PROTEINCytoskeleton / Plasmid: PBAT4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q01082 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.8 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.6 Details: PROTEIN WAS CRYSTALLIZED FROM 0.2 M SODIUM ACETATE 0.1 M SODIUM CACODYLATE PH 6.6 PEG8K 30% (W/V) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion / Details: Djinovic, C., (1997) Nat. Struct. Biol., 4, 175. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8883 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8883 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→55 Å / Num. obs: 42236 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.1→1.11 Å / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 2.1 / % possible all: 99.7 |
Reflection | *PLUS Num. measured all: 199306 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO / Resolution: 1.1→10 Å / Num. parameters: 9858 / Num. restraintsaints: 11588 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) FROM 0.225 TO 0.187. ESTIMATED OVERALL COORDINATE ERROR (FROM LUZZATTI PLOT): 0.05 (ASSUMING PERFECT DATA).
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1081.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→10 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.141 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |