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Yorodumi- PDB-2wwm: Crystal structure of the Titin M10-Obscurin like 1 Ig complex in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wwm | ||||||
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Title | Crystal structure of the Titin M10-Obscurin like 1 Ig complex in space group P1 | ||||||
Components |
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Keywords | TRANSFERASE/STRUCTURAL PROTEIN / TRANSFERASE-STRUCTURAL PROTEIN COMPLEX / SARCOMERE / TPR REPEAT / IMMUNOGLOBULIN DOMAIN / LIMB-GIRDLE MUSCULAR DYSTROPHY / SERINE/THREONINE-PROTEIN KINASE / TRANSFERASE / CARDIOMYOPATHY / CALMODULIN-BINDING / NUCLEOTIDE-BINDING | ||||||
Function / homology | Function and homology information 3M complex / sarcomerogenesis / structural molecule activity conferring elasticity / telethonin binding / skeletal muscle myosin thick filament assembly / protein localization to Golgi apparatus / cardiac myofibril assembly / detection of muscle stretch / muscle alpha-actinin binding / cytoskeletal anchor activity ...3M complex / sarcomerogenesis / structural molecule activity conferring elasticity / telethonin binding / skeletal muscle myosin thick filament assembly / protein localization to Golgi apparatus / cardiac myofibril assembly / detection of muscle stretch / muscle alpha-actinin binding / cytoskeletal anchor activity / cardiac muscle tissue morphogenesis / regulation of catalytic activity / Striated Muscle Contraction / mitotic chromosome condensation / cardiac muscle hypertrophy / M band / actinin binding / I band / cardiac muscle cell development / regulation of protein kinase activity / positive regulation of dendrite morphogenesis / structural constituent of muscle / sarcomere organization / regulation of mitotic nuclear division / Golgi organization / skeletal muscle thin filament assembly / striated muscle thin filament / intercalated disc / striated muscle contraction / protein kinase A signaling / cytoskeleton organization / cardiac muscle contraction / muscle contraction / condensed nuclear chromosome / positive regulation of protein secretion / microtubule cytoskeleton organization / Z disc / response to calcium ion / : / actin filament binding / Platelet degranulation / Neddylation / protein tyrosine kinase activity / protease binding / calmodulin binding / non-specific serine/threonine protein kinase / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / calcium ion binding / positive regulation of gene expression / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / enzyme binding / extracellular exosome / extracellular region / ATP binding / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Pernigo, S. / Fukuzawa, A. / Gautel, M. / Steiner, R.A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Structural Insight Into M-Band Assembly and Mechanics from the Titin-Obscurin-Like-1 Complex. Authors: Pernigo, S. / Fukuzawa, A. / Bertz, M. / Holt, M. / Rief, M. / Steiner, R.A. / Gautel, M. | ||||||
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 | 2wwm.cif.gz | 93.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wwm.ent.gz | 73.8 KB | Display | PDB format |
PDBx/mmJSON format | 2wwm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ww/2wwm ftp://data.pdbj.org/pub/pdb/validation_reports/ww/2wwm | HTTPS FTP |
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-Related structure data
Related structure data | 2wp3SC 2wwkC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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: 11125.619 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-106 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA 2 / References: UniProt: O75147 #2: Protein | Mass: 10981.231 Da / Num. of mol.: 2 / Fragment: M10, RESIDUES 34252-34350 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA 2 References: UniProt: Q8WZ42, non-specific serine/threonine protein kinase #3: Water | ChemComp-HOH / | Sequence details | INITIAL GSS ARE FROM THE EXPRESSION | |
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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: 2.49 Å3/Da / Density % sol: 50.27 % / Description: NONE |
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Crystal grow | pH: 5 / Details: 0.1 M MIB BUFFER PH 5.0, 25% PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Aug 12, 2009 / Details: MIRRORS |
Radiation | Monochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→36.13 Å / Num. obs: 17094 / % possible obs: 92.6 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 47.3 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 4.3 / % possible all: 93.1 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WP3 Resolution: 2.3→35.88 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.92 / SU B: 17.898 / SU ML: 0.192 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.418 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.149 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→35.88 Å
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Refine LS restraints |
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