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Yorodumi- PDB-4ce3: Hsp90 N-terminal domain bound to macrolactam analogues of radicicol. -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ce3 | ||||||
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Title | Hsp90 N-terminal domain bound to macrolactam analogues of radicicol. | ||||||
Components | ATP-DEPENDENT MOLECULAR CHAPERONE HSP82 | ||||||
Keywords | CHAPERONE | ||||||
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 / 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 / MOLECULAR REPLACEMENT / Resolution: 2.31 Å | ||||||
Authors | Roe, S.M. / Parry-Morris, S. / Prodromou, C. | ||||||
Citation | Journal: Org.Biomol.Chem. / Year: 2014 Title: Synthesis of Macrolactam Analogues of Radicicol and Their Binding to Heat Shock Protein Hsp90. Authors: Dutton, B.L. / Kitson, R.R.A. / Parry-Morris, S. / Roe, S.M. / Prodromou, C. / Moody, C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ce3.cif.gz | 59.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ce3.ent.gz | 42.4 KB | Display | PDB format |
PDBx/mmJSON format | 4ce3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ce3_validation.pdf.gz | 793.7 KB | Display | wwPDB validaton report |
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Full document | 4ce3_full_validation.pdf.gz | 793.7 KB | Display | |
Data in XML | 4ce3_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 4ce3_validation.cif.gz | 16.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ce/4ce3 ftp://data.pdbj.org/pub/pdb/validation_reports/ce/4ce3 | HTTPS FTP |
-Related structure data
Related structure data | 4ce1C 4ce2C 1ah6S 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
#1: Protein | Mass: 24208.582 Da / Num. of mol.: 1 / Fragment: N-TERMINUS, RESIDUES 1-214 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P02829 |
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#2: Chemical | ChemComp-L4V / |
#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: 3.17 Å3/Da / Density % sol: 61 % / Description: NONE |
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Crystal grow | pH: 7 / Details: pH 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97961 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 28, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97961 Å / Relative weight: 1 |
Reflection | Resolution: 2.31→52.45 Å / Num. obs: 13834 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 47.73 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 2.31→2.37 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.5 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AH6 Resolution: 2.31→52.45 Å / Cor.coef. Fo:Fc: 0.9382 / Cor.coef. Fo:Fc free: 0.9104 / SU R Cruickshank DPI: 0.245 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.275 / SU Rfree Blow DPI: 0.21 / SU Rfree Cruickshank DPI: 0.202
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Displacement parameters | Biso mean: 43.82 Å2
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Refine analyze | Luzzati coordinate error obs: 0.26 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.31→52.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.31→2.5 Å / Total num. of bins used: 7
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