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Yorodumi- PDB-6cz1: Crystal structure of ATPase domain of Human GRP78 bound to Ver155008 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6cz1 | ||||||
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Title | Crystal structure of ATPase domain of Human GRP78 bound to Ver155008 | ||||||
Components | Endoplasmic reticulum chaperone BiP | ||||||
Keywords | CHAPERONE / GRP78 / ATPase domain / Ver155008 | ||||||
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 / cerebellar Purkinje cell layer development / ATF6 (ATF6-alpha) activates chaperone genes ...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 / cerebellar Purkinje cell layer development / ATF6 (ATF6-alpha) activates chaperone genes / regulation of IRE1-mediated unfolded protein response / negative regulation of IRE1-mediated unfolded protein response / 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 / protein folding chaperone / heat shock protein binding / substantia nigra development / response to endoplasmic reticulum stress / negative regulation of transforming growth factor beta receptor signaling pathway / positive regulation of protein ubiquitination / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ATP-dependent protein folding chaperone / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å | ||||||
Authors | Antoshchenko, T. / Chen, Y. / Hughes, S. / Park, H. | ||||||
Citation | Journal: To be Published Title: Crystallographic selection of adenosine analogs that fit the mold of the active site of human GRP78 and beyond Authors: Antoshchenko, T. / Chen, Y. / Park, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6cz1.cif.gz | 312.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cz1.ent.gz | 250.8 KB | Display | PDB format |
PDBx/mmJSON format | 6cz1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6cz1_validation.pdf.gz | 833.2 KB | Display | wwPDB validaton report |
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Full document | 6cz1_full_validation.pdf.gz | 837.2 KB | Display | |
Data in XML | 6cz1_validation.xml.gz | 32 KB | Display | |
Data in CIF | 6cz1_validation.cif.gz | 47.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cz/6cz1 ftp://data.pdbj.org/pub/pdb/validation_reports/cz/6cz1 | HTTPS FTP |
-Related structure data
Related structure data | 5evzS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 42155.715 Da / Num. of mol.: 2 / Fragment: 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 (E. coli) References: UniProt: P11021, non-chaperonin molecular chaperone ATPase #2: Chemical | #3: Chemical | #4: 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: 2.09 Å3/Da / Density % sol: 41.26 % |
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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: Jul 31, 2016 |
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: 1.68→85.263 Å / Num. obs: 79224 / % possible obs: 99.5 % / Redundancy: 5 % / Rpim(I) all: 0.032 / Rrim(I) all: 0.073 / Rsym value: 0.065 / Net I/av σ(I): 9.9 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 1.68→1.72 Å / Num. unique obs: 5822 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5EVZ Resolution: 1.68→24.6 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.936 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.11 / SU Rfree Blow DPI: 0.104 / SU Rfree Cruickshank DPI: 0.104
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Displacement parameters | Biso max: 113.66 Å2 / Biso mean: 27.27 Å2 / Biso min: 8.8 Å2
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Refine analyze | Luzzati coordinate error obs: 0.21 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.68→24.6 Å
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LS refinement shell | Resolution: 1.68→1.72 Å / Rfactor Rfree error: 0 / 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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