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Yorodumi- PDB-5mzu: Crystal structure of the myosin chaperone UNC-45 from C. elegans ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mzu | ||||||
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Title | Crystal structure of the myosin chaperone UNC-45 from C. elegans (alternative conformation) | ||||||
Components | UNC-45 | ||||||
Keywords | CHAPERONE / myosin folding / protein filament / UCS domain / ARM repeats | ||||||
Function / homology | Function and homology information egg-laying behavior / locomotion / embryo development ending in birth or egg hatching / muscle organ development / sarcomere organization / cleavage furrow / chaperone-mediated protein folding / protein folding chaperone / Hsp90 protein binding / cell cortex ...egg-laying behavior / locomotion / embryo development ending in birth or egg hatching / muscle organ development / sarcomere organization / cleavage furrow / chaperone-mediated protein folding / protein folding chaperone / Hsp90 protein binding / cell cortex / ubiquitin protein ligase binding / perinuclear region of cytoplasm / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Caenorhabditis elegans (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.8 Å | ||||||
Model details | Alternative conformation, with rearranged UCS domain | ||||||
Authors | Hellerschmied, D. / Gazda, L. / Clausen, T. | ||||||
Funding support | Austria, 1items
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Citation | Journal: Nat Commun / Year: 2018 Title: UFD-2 is an adaptor-assisted E3 ligase targeting unfolded proteins. Authors: Hellerschmied, D. / Roessler, M. / Lehner, A. / Gazda, L. / Stejskal, K. / Imre, R. / Mechtler, K. / Dammermann, A. / Clausen, T. #1: Journal: Cell / Year: 2013 Title: The myosin chaperone UNC-45 is organized in tandem modules to support myofilament formation in C. elegans. Authors: Gazda, L. / Pokrzywa, W. / Hellerschmied, D. / Loewe, T. / Forne, I. / Mueller-Planitz, F. / Hoppe, T. / Clausen, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mzu.cif.gz | 320.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mzu.ent.gz | 270.4 KB | Display | PDB format |
PDBx/mmJSON format | 5mzu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mzu_validation.pdf.gz | 433.4 KB | Display | wwPDB validaton report |
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Full document | 5mzu_full_validation.pdf.gz | 448.2 KB | Display | |
Data in XML | 5mzu_validation.xml.gz | 29.8 KB | Display | |
Data in CIF | 5mzu_validation.cif.gz | 40.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mz/5mzu ftp://data.pdbj.org/pub/pdb/validation_reports/mz/5mzu | HTTPS FTP |
-Related structure data
Related structure data | |
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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: 108552.898 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: unc-45, CELE_F30H5.1, F30H5.1 / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G5EG62 |
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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: 4.43 Å3/Da / Density % sol: 72.24 % / Mosaicity: 0.213 ° |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1M Hepes pH 7.0, 10% PEG8000, 12% ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 2, 2010 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.8→50 Å / Num. obs: 16050 / % possible obs: 93.5 % / Redundancy: 4.4 % / Biso Wilson estimate: 160.67 Å2 / Rmerge(I) obs: 0.085 / Χ2: 0.987 / Net I/σ(I): 7.4 / Num. measured all: 70085 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.8→29.4 Å / SU ML: 0.67 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.51 / 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 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 334.86 Å2 / Biso mean: 183.7562 Å2 / Biso min: 108.09 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.8→29.4 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5
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Refinement TLS params. | Method: refined / Origin x: 12.7028 Å / Origin y: -34.2048 Å / Origin z: 27.4897 Å
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Refinement TLS group | Selection details: all |