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Yorodumi- PDB-1a4h: STRUCTURE OF THE N-TERMINAL DOMAIN OF THE YEAST HSP90 CHAPERONE I... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1a4h | ||||||
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Title | STRUCTURE OF THE N-TERMINAL DOMAIN OF THE YEAST HSP90 CHAPERONE IN COMPLEX WITH GELDANAMYCIN | ||||||
Components | HEAT SHOCK PROTEIN 90 | ||||||
Keywords | CHAPERONE / ATP-BINDING / HEAT SHOCK | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Prodromou, C. / Roe, S.M. / Pearl, L.H. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 1997 Title: Identification and structural characterization of the ATP/ADP-binding site in the Hsp90 molecular chaperone Authors: Prodromou, C. / Roe, S.M. / O'Brien, R. / Ladbury, J.E. / Piper, P.W. / Pearl, L.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a4h.cif.gz | 61 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a4h.ent.gz | 43.2 KB | Display | PDB format |
PDBx/mmJSON format | 1a4h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a4h_validation.pdf.gz | 895.1 KB | Display | wwPDB validaton report |
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Full document | 1a4h_full_validation.pdf.gz | 903.2 KB | Display | |
Data in XML | 1a4h_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 1a4h_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a4/1a4h ftp://data.pdbj.org/pub/pdb/validation_reports/a4/1a4h | HTTPS FTP |
-Related structure data
Related structure data | 1am1C 1amwC 1ah6S 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
#1: Protein | Mass: 26134.799 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN / Source method: isolated from a natural source / Details: GELDANAMYCIN IN ATP BINDING SITE / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P02829 |
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#2: Chemical | ChemComp-GDM / |
#3: Water | ChemComp-HOH / |
Compound details | THIS IS THE TETRAGONAL CRYSTAL FORM OF HSP90. THE SIX RESIDUE HISTIDINE TAG USED FOR PURIFICATION ...THIS IS THE TETRAGONAL |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.25 Å3/Da / Density % sol: 62 % |
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Crystal grow | Method: under oil / pH: 5 Details: THE PROTEIN/GELDANAMYCIN COMPLEX WAS CRYSTALLISED UNDER OIL IN TERASAKI PLATES. THE DROPS CONTAINED 27MG/ML PROTEIN, 9.75% PEGME 550, 65MM AMMONIUM SULFATE, 25% GLYCEROL AND 32.5MM SODIUM ...Details: THE PROTEIN/GELDANAMYCIN COMPLEX WAS CRYSTALLISED UNDER OIL IN TERASAKI PLATES. THE DROPS CONTAINED 27MG/ML PROTEIN, 9.75% PEGME 550, 65MM AMMONIUM SULFATE, 25% GLYCEROL AND 32.5MM SODIUM SUCCINATE AT PH 5.0, under oil |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Detector: IMAGE PLATE / Date: May 1, 1996 / Details: YALE/MSC MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. obs: 10938 / % possible obs: 97.4 % / Observed criterion σ(I): 1 / Redundancy: 4.8 % / Biso Wilson estimate: 37.6 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.5→2.55 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 6.6 / % possible all: 85.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AH6 Resolution: 2.5→30 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / σ(F): 1 Details: BULK SOLVENT MODEL USED. THIS IS THE TETRAGONAL CRYSTAL FORM OF HSP90. THE SIX RESIDUE HISTIDINE TAG USED FOR PURIFICATION WAS NOT REMOVED PRIOR TO CRYSTALLISATION. IT IS NOT SEEN IN THE ELECTRON DENSITY MAPS.
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Displacement parameters | Biso mean: 29.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.29 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.38 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Total num. of bins used: 6 /
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Xplor file |
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