+Open data
-Basic information
Entry | Database: PDB / ID: 4xa4 | ||||||
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Title | Crystal Structure of the coiled-coil surrounding Skip 3 of MYH7 | ||||||
Components | Xrcc4-MYH7(1551-1609) chimera protein | ||||||
Keywords | MOTOR PROTEIN / Myosin / coiled coil / skip residue / fusion / Gp7 / EB1 / MYH7 / Cardiac | ||||||
Function / homology | Function and homology information FHA domain binding / regulation of slow-twitch skeletal muscle fiber contraction / regulation of the force of skeletal muscle contraction / positive regulation of ligase activity / DNA ligase IV complex / DNA ligation involved in DNA repair / muscle myosin complex / muscle filament sliding / DNA-dependent protein kinase-DNA ligase 4 complex / transition between fast and slow fiber ...FHA domain binding / regulation of slow-twitch skeletal muscle fiber contraction / regulation of the force of skeletal muscle contraction / positive regulation of ligase activity / DNA ligase IV complex / DNA ligation involved in DNA repair / muscle myosin complex / muscle filament sliding / DNA-dependent protein kinase-DNA ligase 4 complex / transition between fast and slow fiber / immunoglobulin V(D)J recombination / nonhomologous end joining complex / regulation of the force of heart contraction / myosin filament / protein localization to site of double-strand break / 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 / cellular response to lithium ion / 2-LTR circle formation / skeletal muscle contraction / response to X-ray / SUMOylation of DNA damage response and repair proteins / striated muscle contraction / muscle contraction / cardiac muscle contraction / stress fiber / ATP metabolic process / regulation of heart rate / sarcomere / Nonhomologous End-Joining (NHEJ) / Z disc / actin filament binding / double-strand break repair via nonhomologous end joining / double-strand break repair / site of double-strand break / calmodulin binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.327 Å | ||||||
Authors | Taylor, K.C. / Buvoli, M. / Korkmaz, E.N. / Buvoli, A. / Zheng, Y. / Heinz, N.T. / Qiang, C. / Leinwand, L.A. / Rayment, I. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2015 Title: Skip residues modulate the structural properties of the myosin rod and guide thick filament assembly. Authors: Taylor, K.C. / Buvoli, M. / Korkmaz, E.N. / Buvoli, A. / Zheng, Y. / Heinze, N.T. / Cui, Q. / Leinwand, L.A. / Rayment, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xa4.cif.gz | 92.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xa4.ent.gz | 69.6 KB | Display | PDB format |
PDBx/mmJSON format | 4xa4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xa4_validation.pdf.gz | 434.3 KB | Display | wwPDB validaton report |
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Full document | 4xa4_full_validation.pdf.gz | 437.2 KB | Display | |
Data in XML | 4xa4_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | 4xa4_validation.cif.gz | 20.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xa/4xa4 ftp://data.pdbj.org/pub/pdb/validation_reports/xa/4xa4 | HTTPS FTP |
-Related structure data
Related structure data | 4xa1C 4xa3C 4xa6C 1ik9S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23810.619 Da / Num. of mol.: 2 Fragment: UNP Q13426 residues 2-147,UNP P12883 residues 1551-1609 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: XRCC4, MYH7, MYHCB / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13426, UniProt: P12883 #2: Water | ChemComp-HOH / | |
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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: 2.65 Å3/Da / Density % sol: 54 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 30% (w/v) polyethylene glycol 1500, 250 mM tetramethylammonium chloride, 100 mM 3-[4-(2-Hydroxyethyl)-1-piperazinyl]propanesulfonic acid (HEPPS) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 4, 2012 |
Radiation | Monochromator: Rosenbaum-Rock double-crystal monochromator: Water cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.327→50 Å / Num. obs: 22289 / % possible obs: 99 % / Redundancy: 7.5 % / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.06 / Net I/av σ(I): 32.9 / Net I/σ(I): 23.4 |
Reflection shell | Resolution: 2.327→2.37 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 8.5 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1IK9 Resolution: 2.327→34.542 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.07 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.327→34.542 Å
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Refine LS restraints |
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LS refinement shell |
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