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Yorodumi- PDB-3c11: Yeast Hsp82 N-terminal domain-Geldanamycin complex: effects of mu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3c11 | ||||||
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Title | Yeast Hsp82 N-terminal domain-Geldanamycin complex: effects of mutants 98-99 KS-AA | ||||||
Components | ATP-dependent molecular chaperone HSP82 | ||||||
Keywords | CHAPERONE/Antibiotic / GRP94 / HSP82 / HSP90 / HTPG / chaperone / ligand / GELDANAMYCIN / ATP-binding / Nucleotide-binding / Stress response / CHAPERONE-Antibiotic complex | ||||||
Function / homology | Function and homology information The NLRP3 inflammasome / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Extra-nuclear estrogen signaling / VEGFR2 mediated vascular permeability / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / HSF1-dependent transactivation / HSF1 activation / response to oxygen levels / protein targeting to mitochondrion ...The NLRP3 inflammasome / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Extra-nuclear estrogen signaling / VEGFR2 mediated vascular permeability / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / HSF1-dependent transactivation / HSF1 activation / response to oxygen levels / protein targeting to mitochondrion / box C/D snoRNP assembly / regulation of telomere maintenance / response to osmotic stress / 'de novo' protein folding / protein maturation / proteasome assembly / Neutrophil degranulation / positive regulation of telomere maintenance via telomerase / ATP-dependent protein folding chaperone / disordered domain specific binding / unfolded protein binding / protein folding / cellular response to heat / protein refolding / protein stabilization / perinuclear region of cytoplasm / ATP hydrolysis activity / protein-containing complex / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å | ||||||
Authors | Immormino, R.M. / Gewirth, D.T. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of GRP94 with the Specific Mutation KS168-169AA with Bound Geldanamycin Authors: Immormino, R.M. / Metzger IV, L.E. / Reardon, P.N. / Gewirth, D.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3c11.cif.gz | 113.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3c11.ent.gz | 86.1 KB | Display | PDB format |
PDBx/mmJSON format | 3c11.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3c11_validation.pdf.gz | 897.9 KB | Display | wwPDB validaton report |
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Full document | 3c11_full_validation.pdf.gz | 899.7 KB | Display | |
Data in XML | 3c11_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | 3c11_validation.cif.gz | 21.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c1/3c11 ftp://data.pdbj.org/pub/pdb/validation_reports/c1/3c11 | HTTPS FTP |
-Related structure data
Related structure data | 3c0eC 1zhwS 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 26970.666 Da / Num. of mol.: 1 / Fragment: N-terminal Domain (Residues 1-220) / Mutation: K98A, S99A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: HSP82, HSP90 / Plasmid: PET15b-yHsp82(1-220) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02829 | ||
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#2: Chemical | ChemComp-GDM / | ||
#3: Chemical | #4: 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: 2.83 Å3/Da / Density % sol: 56.47 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 100mM Na Succinate, 45-75 mM CaCl2, 10-15% PEG 550MME, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 31, 2007 |
Radiation | Monochromator: sagital crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 41538 / Num. obs: 41529 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Redundancy: 13.8 % / Biso Wilson estimate: 22.47 Å2 / Rsym value: 9 / Net I/σ(I): 15.73 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 12.85 % / Mean I/σ(I) obs: 3.17 / Num. unique all: 4270 / Rsym value: 95.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: pdb entry 1ZHW Resolution: 1.6→47.4 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 29.02 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→47.4 Å
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Refine LS restraints |
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