+Open data
-Basic information
Entry | Database: PDB / ID: 6h9u | |||||||||
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Title | Crystal structure of the BiP NBD and MANF SAP complex | |||||||||
Components |
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Keywords | CHAPERONE / MANF / BiP / NDI / HSP70 / ARMET | |||||||||
Function / homology | Function and homology information vasoconstriction of artery involved in ischemic response to lowering of systemic arterial blood pressure / regulation of response to endoplasmic reticulum stress / sulfatide binding / negative regulation of IRE1-mediated unfolded protein response / endoplasmic reticulum chaperone complex / sarcoplasmic reticulum lumen / Platelet degranulation / dopaminergic neuron differentiation / post-translational protein targeting to membrane, translocation / non-chaperonin molecular chaperone ATPase ...vasoconstriction of artery involved in ischemic response to lowering of systemic arterial blood pressure / regulation of response to endoplasmic reticulum stress / sulfatide binding / negative regulation of IRE1-mediated unfolded protein response / endoplasmic reticulum chaperone complex / sarcoplasmic reticulum lumen / Platelet degranulation / dopaminergic neuron differentiation / post-translational protein targeting to membrane, translocation / non-chaperonin molecular chaperone ATPase / response to unfolded protein / negative regulation of protein-containing complex assembly / endoplasmic reticulum unfolded protein response / ATP-dependent protein folding chaperone / growth factor activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / neuron projection development / melanosome / endoplasmic reticulum lumen / endoplasmic reticulum membrane / negative regulation of apoptotic process / perinuclear region of cytoplasm / cell surface / endoplasmic reticulum / ATP hydrolysis activity / mitochondrion / extracellular space / ATP binding / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Cricetulus griseus (Chinese hamster) Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 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 | 6h9u.cif.gz | 104.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6h9u.ent.gz | 76.7 KB | Display | PDB format |
PDBx/mmJSON format | 6h9u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6h9u_validation.pdf.gz | 445.4 KB | Display | wwPDB validaton report |
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Full document | 6h9u_full_validation.pdf.gz | 446.2 KB | Display | |
Data in XML | 6h9u_validation.xml.gz | 20.1 KB | Display | |
Data in CIF | 6h9u_validation.cif.gz | 29.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h9/6h9u ftp://data.pdbj.org/pub/pdb/validation_reports/h9/6h9u | HTTPS FTP |
-Related structure data
Related structure data | 6ha7C 6habC 3ldnS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 42557.039 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Gene: HSPA5, GRP78, I79_019946 / Production host: Escherichia coli M15 (bacteria) References: UniProt: G3I8R9, non-chaperonin molecular chaperone ATPase |
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#2: Protein/peptide | Mass: 5212.243 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Manf, Armet / Production host: Escherichia coli (E. coli) / References: UniProt: Q9CXI5 |
#3: Chemical | ChemComp-MLT / |
#4: Chemical | ChemComp-NA / |
#5: 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: 2.27 Å3/Da / Density % sol: 45.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.92 M sodium malonate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 30, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→42.47 Å / Num. obs: 59404 / % possible obs: 99.3 % / Redundancy: 3.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.05 / Rrim(I) all: 0.074 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.57→1.61 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.86 / Num. unique obs: 4405 / CC1/2: 0.52 / Rpim(I) all: 0.781 / Rrim(I) all: 1.165 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LDN Resolution: 1.57→42.47 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.049 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.082 / 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: 25.081 Å2
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Refinement step | Cycle: 1 / Resolution: 1.57→42.47 Å
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