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Yorodumi- PDB-6zyh: Crystal structure of GRP78 (70kDa heat shock protein 5 / BiP) ATP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zyh | ||||||
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Title | Crystal structure of GRP78 (70kDa heat shock protein 5 / BiP) ATPase domain in complex with ADP and calcium | ||||||
Components | Endoplasmic reticulum chaperone BiP | ||||||
Keywords | CHAPERONE / BiP / HSP70 / GRP78 / ATPase domain / NBD / ADP | ||||||
Function / homology | Function and homology information negative regulation of IRE1-mediated unfolded protein response / post-translational protein targeting to membrane, translocation / non-chaperonin molecular chaperone ATPase / negative regulation of protein-containing complex assembly / ATP-dependent protein folding chaperone / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / melanosome / endoplasmic reticulum lumen / endoplasmic reticulum membrane / negative regulation of apoptotic process ...negative regulation of IRE1-mediated unfolded protein response / post-translational protein targeting to membrane, translocation / non-chaperonin molecular chaperone ATPase / negative regulation of protein-containing complex assembly / ATP-dependent protein folding chaperone / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / melanosome / endoplasmic reticulum lumen / endoplasmic reticulum membrane / negative regulation of apoptotic process / perinuclear region of cytoplasm / cell surface / ATP hydrolysis activity / mitochondrion / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Cricetulus griseus (Chinese hamster) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å | ||||||
Authors | Yan, Y. / Preissler, S. / Ron, D. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Elife / Year: 2020 Title: Calcium depletion challenges endoplasmic reticulum proteostasis by destabilising BiP-substrate complexes. Authors: Preissler, S. / Rato, C. / Yan, Y. / Perera, L.A. / Czako, A. / Ron, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zyh.cif.gz | 165.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zyh.ent.gz | 127 KB | Display | PDB format |
PDBx/mmJSON format | 6zyh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zy/6zyh ftp://data.pdbj.org/pub/pdb/validation_reports/zy/6zyh | HTTPS FTP |
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-Related structure data
Related structure data | 6zyiC 6zyjC 7a4uC 7a4vC 3iucS 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: 41868.445 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Gene: HSPA5, GRP78, I79_019946 / Production host: Escherichia coli (E. coli) References: UniProt: G3I8R9, non-chaperonin molecular chaperone ATPase #2: Chemical | #3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.37 Å3/Da / Density % sol: 48.06 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 26% PEG6000, 0.2M CaCl2, 0.1MNaOAc Ph5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97628 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 24, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97628 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→29.14 Å / Num. obs: 62200 / % possible obs: 97.4 % / Redundancy: 8.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 1.88→1.92 Å / Rmerge(I) obs: 0.989 / Num. unique obs: 3792 / CC1/2: 0.669 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3IUC Resolution: 1.88→29.13 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.557 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 73.74 Å2 / Biso mean: 32.466 Å2 / Biso min: 21.28 Å2
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Refinement step | Cycle: final / Resolution: 1.88→29.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.88→1.929 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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