[English] 日本語
Yorodumi- PDB-4pa0: Omecamtiv Mercarbil binding site on the Human Beta-Cardiac Myosin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pa0 | ||||||
---|---|---|---|---|---|---|---|
Title | Omecamtiv Mercarbil binding site on the Human Beta-Cardiac Myosin Motor Domain | ||||||
Components | Myosin-7,Green fluorescent protein | ||||||
Keywords | Motor/Fluorescent Protein / Cardiac / Myosin / Motor / omecamtiv mercarbil / Motor-Fluorescent Protein complex | ||||||
Function / homology | Function and homology information regulation of slow-twitch skeletal muscle fiber contraction / regulation of the force of skeletal muscle contraction / muscle myosin complex / muscle filament sliding / transition between fast and slow fiber / regulation of the force of heart contraction / myosin filament / adult heart development / cardiac muscle hypertrophy in response to stress / myosin II complex ...regulation of slow-twitch skeletal muscle fiber contraction / regulation of the force of skeletal muscle contraction / muscle myosin complex / muscle filament sliding / transition between fast and slow fiber / regulation of the force of heart contraction / myosin filament / adult heart development / cardiac muscle hypertrophy in response to stress / myosin II complex / myosin complex / ventricular cardiac muscle tissue morphogenesis / sarcomere organization / microfilament motor activity / myofibril / skeletal muscle contraction / striated muscle contraction / muscle contraction / cardiac muscle contraction / stress fiber / ATP metabolic process / regulation of heart rate / sarcomere / Z disc / actin filament binding / serine-type endopeptidase inhibitor activity / calmodulin binding / extracellular space / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Winkelmann, D.A. / Miller, M.T. / Stock, A.M. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Nat Commun / Year: 2015 Title: Structural basis for drug-induced allosteric changes to human beta-cardiac myosin motor activity. Authors: Winkelmann, D.A. / Forgacs, E. / Miller, M.T. / Stock, A.M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4pa0.cif.gz | 389.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4pa0.ent.gz | 308.7 KB | Display | PDB format |
PDBx/mmJSON format | 4pa0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pa0_validation.pdf.gz | 1011.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4pa0_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 4pa0_validation.xml.gz | 70.5 KB | Display | |
Data in CIF | 4pa0_validation.cif.gz | 96.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pa/4pa0 ftp://data.pdbj.org/pub/pdb/validation_reports/pa/4pa0 | HTTPS FTP |
-Related structure data
Related structure data | 4p7hS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Details | monomer in solution based on gel filtration |
-Components
#1: Protein | Mass: 116609.812 Da / Num. of mol.: 2 Fragment: UNP P12883 residues 1-787, UNP P42212 residues 5-234 Mutation: Q80R, V163A, I167T, S175G, D190N Source method: isolated from a genetically manipulated source Details: cloned cDNA Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Aequorea victoria (jellyfish) Tissue: muscle / Cell: cardiomyocyte / Gene: MYH7, MYHCB, GFP / Organ: Heart Details (production host): replication defective adenovirus infection Cell (production host): myoblast / Cell line (production host): C2C12 cells / Organ (production host): skeletal muscle / Production host: Mus (mice) / Tissue (production host): muscle / References: UniProt: P12883, UniProt: P42212 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | YKDHD are a minimal Flag epitope tag engineered into the sequence to facilitate purification by the author | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.4 % / Description: small orthorhombic crystals, green in color |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 Details: Tacsimate, pH 6.0, PEG 3350, glycerol, MgCL2, TCEP and ligand, omecamptiv mercarbil PH range: 5.8-6.4 / Temp details: room temperature |
-Data collection
Diffraction | Mean temperature: 100 K Ambient temp details: crystals cryopreserved in mother liquor |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 24, 2014 |
Radiation | Monochromator: Rosenbaum-Rock double crystal sagittal focusing monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→46.042 Å / Num. obs: 106961 / % possible obs: 93.8 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.128 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2.25→2.29 Å / Redundancy: 3.3 % / Rmerge(I) obs: 1.499 / Mean I/σ(I) obs: 0.8 / % possible all: 84 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4P7H Resolution: 2.25→45.961 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.84 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→45.961 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|