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- PDB-1bkr: CALPONIN HOMOLOGY (CH) DOMAIN FROM HUMAN BETA-SPECTRIN AT 1.1 ANG... -
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Open data
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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 | ||||||
![]() | SPECTRIN BETA CHAIN | ||||||
![]() | ACTIN-BINDING / FILAMENTOUS ACTIN-BINDING DOMAIN / CYTOSKELETON | ||||||
Function / homology | ![]() 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 / RHOU GTPase cycle / mitotic cytokinesis / 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 / structural constituent of cytoskeleton / phospholipid binding / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Djinovic Carugo, K. / Banuelos, S. / Saraste, M. | ||||||
![]() | ![]() Title: Structural comparisons of calponin homology domains: implications for actin binding. Authors: Banuelos, S. / Saraste, M. / Carugo, K.D. #1: ![]() Title: Crystal Structure of a Calponin Homology Domain Authors: Carugo, K.D. / Banuelos, S. / Saraste, M. #2: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 67.2 KB | Display | ![]() |
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PDB format | ![]() | 48.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 430.8 KB | Display | ![]() |
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Full document | ![]() | 433.1 KB | Display | |
Data in XML | ![]() | 9.1 KB | Display | |
Data in CIF | ![]() | 13 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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. |
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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.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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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 |