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Yorodumi- PDB-5exw: Crystal structure of human GRP78 (70kDa heat shock protein 5 / BI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5exw | ||||||
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Title | Crystal structure of human GRP78 (70kDa heat shock protein 5 / BIP) ATPase domain in complex with 7-deaza-ATP | ||||||
Components | 78 kDa glucose-regulated protein | ||||||
Keywords | CHAPERONE / ATPase domain / nucleotide-binding / endoplasmic reticulum | ||||||
Function / homology | Function and homology information regulation of ATF6-mediated unfolded protein response / regulation of PERK-mediated unfolded protein response / regulation of protein folding in endoplasmic reticulum / cerebellum structural organization / ATF6 (ATF6-alpha) activates chaperones / ATF6B (ATF6-beta) activates chaperones / maintenance of protein localization in endoplasmic reticulum / IRE1alpha activates chaperones / ATF6 (ATF6-alpha) activates chaperone genes / regulation of IRE1-mediated unfolded protein response ...regulation of ATF6-mediated unfolded protein response / regulation of PERK-mediated unfolded protein response / regulation of protein folding in endoplasmic reticulum / cerebellum structural organization / ATF6 (ATF6-alpha) activates chaperones / ATF6B (ATF6-beta) activates chaperones / maintenance of protein localization in endoplasmic reticulum / IRE1alpha activates chaperones / ATF6 (ATF6-alpha) activates chaperone genes / regulation of IRE1-mediated unfolded protein response / negative regulation of IRE1-mediated unfolded protein response / cerebellar Purkinje cell layer development / endoplasmic reticulum chaperone complex / PERK regulates gene expression / protein folding in endoplasmic reticulum / misfolded protein binding / post-translational protein targeting to membrane, translocation / ER overload response / non-chaperonin molecular chaperone ATPase / endoplasmic reticulum-Golgi intermediate compartment / chaperone cofactor-dependent protein refolding / Regulation of HSF1-mediated heat shock response / cellular response to interleukin-4 / negative regulation of protein-containing complex assembly / cellular response to glucose starvation / ERAD pathway / endoplasmic reticulum unfolded protein response / heat shock protein binding / protein folding chaperone / response to endoplasmic reticulum stress / substantia nigra development / positive regulation of protein ubiquitination / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ATP-dependent protein folding chaperone / negative regulation of transforming growth factor beta receptor signaling pathway / unfolded protein binding / melanosome / Platelet degranulation / ribosome binding / protein-folding chaperone binding / midbody / protein refolding / positive regulation of cell migration / cadherin binding / protein domain specific binding / endoplasmic reticulum lumen / intracellular membrane-bounded organelle / focal adhesion / ubiquitin protein ligase binding / calcium ion binding / endoplasmic reticulum membrane / negative regulation of apoptotic process / enzyme binding / cell surface / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / protein-containing complex / mitochondrion / extracellular exosome / ATP binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Hughes, S.J. / Antoshchenko, T. / Song, J.H. / Pizarro, J. / Park, H.W. | ||||||
Citation | Journal: Plos One / Year: 2016 Title: Probing the ATP Site of GRP78 with Nucleotide Triphosphate Analogs. Authors: Hughes, S.J. / Antoshchenko, T. / Chen, Y. / Lu, H. / Pizarro, J.C. / Park, H.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5exw.cif.gz | 321.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5exw.ent.gz | 259.7 KB | Display | PDB format |
PDBx/mmJSON format | 5exw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5exw_validation.pdf.gz | 1012.6 KB | Display | wwPDB validaton report |
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Full document | 5exw_full_validation.pdf.gz | 1014.8 KB | Display | |
Data in XML | 5exw_validation.xml.gz | 33.9 KB | Display | |
Data in CIF | 5exw_validation.cif.gz | 51.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ex/5exw ftp://data.pdbj.org/pub/pdb/validation_reports/ex/5exw | HTTPS FTP |
-Related structure data
Related structure data | 5evzC 5ex5C 5ey4C 5f0xC 5f1xC 5f2rC 3ldnS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 44356.090 Da / Num. of mol.: 2 / Fragment: ATPase domain (UNP residues 26-407) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HSPA5, GRP78 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P11021 #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.08 Å3/Da / Density % sol: 40.88 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 24-26% PEG3350, 0.1 M Tris-HCl, 0.2 M sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: May 6, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.851→88.593 Å / Num. all: 57406 / Num. obs: 57406 / % possible obs: 100 % / Redundancy: 4.9 % / Rpim(I) all: 0.027 / Rrim(I) all: 0.062 / Rsym value: 0.055 / Net I/av σ(I): 8.493 / Net I/σ(I): 19.1 / Num. measured all: 282674 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3LDN Resolution: 1.9→40 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.2181 / WRfactor Rwork: 0.1721 / FOM work R set: 0.8824 / SU B: 5.321 / SU ML: 0.089 / SU R Cruickshank DPI: 0.1561 / SU Rfree: 0.1408 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.156 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 81.28 Å2 / Biso mean: 27.278 Å2 / Biso min: 7.95 Å2
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Refinement step | Cycle: final / Resolution: 1.9→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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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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