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Yorodumi- PDB-5wlq: Crystal Structure of Amino Acids 1677-1755 of Human Beta Cardiac ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wlq | ||||||
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Title | Crystal Structure of Amino Acids 1677-1755 of Human Beta Cardiac Myosin Fused to Gp7 and Eb1 | ||||||
Components | Capsid assembly scaffolding protein,Myosin-7,Microtubule-associated protein RP/EB family member 1 | ||||||
Keywords | MOTOR PROTEIN / Myosin / Gp7 / Coiled-Coil / Eb1 | ||||||
Function / homology | Function and homology information viral scaffold / protein localization to astral microtubule / regulation of slow-twitch skeletal muscle fiber contraction / cortical microtubule cytoskeleton / regulation of the force of skeletal muscle contraction / mitotic spindle astral microtubule end / protein localization to microtubule / muscle myosin complex / microtubule plus-end / muscle filament sliding ...viral scaffold / protein localization to astral microtubule / regulation of slow-twitch skeletal muscle fiber contraction / cortical microtubule cytoskeleton / regulation of the force of skeletal muscle contraction / mitotic spindle astral microtubule end / protein localization to microtubule / muscle myosin complex / microtubule plus-end / muscle filament sliding / cell projection membrane / regulation of the force of heart contraction / transition between fast and slow fiber / myosin filament / attachment of mitotic spindle microtubules to kinetochore / microtubule plus-end binding / myosin II complex / non-motile cilium assembly / adult heart development / microtubule bundle formation / cardiac muscle hypertrophy in response to stress / protein localization to centrosome / myosin complex / sarcomere organization / microtubule organizing center / virion assembly / negative regulation of microtubule polymerization / microfilament motor activity / ventricular cardiac muscle tissue morphogenesis / myofibril / mitotic spindle pole / microtubule polymerization / establishment of mitotic spindle orientation / skeletal muscle contraction / striated muscle contraction / spindle assembly / regulation of microtubule polymerization or depolymerization / spindle midzone / cytoplasmic microtubule / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / ATP metabolic process / stress fiber / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / positive regulation of microtubule polymerization / cardiac muscle contraction / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Resolution of Sister Chromatid Cohesion / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / regulation of heart rate / sarcomere / AURKA Activation by TPX2 / ciliary basal body / muscle contraction / RHO GTPases Activate Formins / protein localization / Z disc / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / Regulation of PLK1 Activity at G2/M Transition / actin filament binding / cell migration / microtubule / molecular adaptor activity / calmodulin binding / cadherin binding / cell division / focal adhesion / centrosome / protein kinase binding / Golgi apparatus / DNA binding / RNA binding / ATP binding / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus phage phi29 (virus) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.104 Å | ||||||
Authors | Andreas, M.P. / Ajay, G. / Gellings, J. / Rayment, I. | ||||||
Funding support | United States, 1items
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Citation | Journal: J. Struct. Biol. / Year: 2017 Title: Design considerations in coiled-coil fusion constructs for the structural determination of a problematic region of the human cardiac myosin rod. Authors: Andreas, M.P. / Ajay, G. / Gellings, J.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 | 5wlq.cif.gz | 60.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wlq.ent.gz | 42.2 KB | Display | PDB format |
PDBx/mmJSON format | 5wlq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wl/5wlq ftp://data.pdbj.org/pub/pdb/validation_reports/wl/5wlq | HTTPS FTP |
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-Related structure data
Related structure data | 5wj7C 5wjbC 5wlzC 5wmeC 1ik9S 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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Unit cell |
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-Components
#1: Protein | Mass: 20781.934 Da / Num. of mol.: 1 Fragment: UNP P13848 residues 2-48 UNP Q15691 residues 208-256, UNP P12883 residues 1677-1755 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus phage phi29 (virus), (gene. exp.) Homo sapiens (human) Gene: MYH7, MYHCB, MAPRE1 / Production host: Escherichia coli (E. coli) References: UniProt: P13848, UniProt: P12883, UniProt: Q15691 | ||
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#2: Chemical | ChemComp-SO4 / | ||
#3: Chemical | ChemComp-TMO / #4: 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: 6.3 Å3/Da / Density % sol: 80.4 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 1.6 M Ammonium Aulfate, 500 mM Trimethyl Ammonium N-Oxide, 100 mM Bis-tris Propane pH 9.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 7, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. obs: 9815 / % possible obs: 100 % / Redundancy: 19.6 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 24.2 |
Reflection shell | Resolution: 3.1→3.15 Å / Redundancy: 19.5 % / Rmerge(I) obs: 0.667 / Mean I/σ(I) obs: 4.46 / Num. unique obs: 478 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1IK9 Resolution: 3.104→41.161 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.75
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.104→41.161 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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