+Open data
-Basic information
Entry | Database: PDB / ID: 6hab | |||||||||
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Title | Crystal structure of BiP V461F (apo) | |||||||||
Components | Endoplasmic reticulum chaperone BiP | |||||||||
Keywords | CHAPERONE / BiP / GRP78 / HSP70 | |||||||||
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: 2.08 Å | |||||||||
Authors | Yan, Y. / Ron, D. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Nat Commun / Year: 2019 Title: MANF antagonizes nucleotide exchange by the endoplasmic reticulum chaperone BiP. Authors: Yan, Y. / Rato, C. / Rohland, L. / Preissler, S. / Ron, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hab.cif.gz | 108.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hab.ent.gz | 80.5 KB | Display | PDB format |
PDBx/mmJSON format | 6hab.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ha/6hab ftp://data.pdbj.org/pub/pdb/validation_reports/ha/6hab | HTTPS FTP |
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-Related structure data
Related structure data | 6h9uC 6ha7C 3ldnS 5e85S 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: 57485.980 Da / Num. of mol.: 1 / Mutation: V461F 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 | ||
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#2: Chemical | #3: 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: 2.1 Å3/Da / Density % sol: 41.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 8% PEG1000, 0.1M Tris-HCl pH8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 23, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92819 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→50.2 Å / Num. obs: 28693 / % possible obs: 99.2 % / Redundancy: 3.4 % / CC1/2: 1 / Rmerge(I) obs: 0.029 / Rrim(I) all: 0.039 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 2.08→2.13 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.775 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2082 / CC1/2: 0.602 / Rrim(I) all: 1.063 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LDN, 5E85 Resolution: 2.08→50.2 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.941 / SU B: 8.026 / SU ML: 0.202 / Cross valid method: THROUGHOUT / ESU R: 0.278 / ESU R Free: 0.213 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.145 Å2
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Refinement step | Cycle: 1 / Resolution: 2.08→50.2 Å
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Refine LS restraints |
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