[English] 日本語
Yorodumi- PDB-3fp4: Crystal structure of Tom71 complexed with Ssa1 C-terminal fragment -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fp4 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Tom71 complexed with Ssa1 C-terminal fragment | ||||||
Components |
| ||||||
Keywords | TRANSPORT PROTEIN / Tom71 / Hsp70 / Mitochondria / translocation / Chaperone / Phosphoprotein / TPR repeat | ||||||
Function / homology | Function and homology information HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / HSF1-dependent transactivation / Protein methylation / protein aggregate center / Regulation of HSF1-mediated heat shock response / Clathrin-mediated endocytosis / Neutrophil degranulation / mitochondrion targeting sequence binding / protein import into mitochondrial matrix / protein insertion into mitochondrial inner membrane ...HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / HSF1-dependent transactivation / Protein methylation / protein aggregate center / Regulation of HSF1-mediated heat shock response / Clathrin-mediated endocytosis / Neutrophil degranulation / mitochondrion targeting sequence binding / protein import into mitochondrial matrix / protein insertion into mitochondrial inner membrane / misfolded protein binding / protein targeting to mitochondrion / chaperone cofactor-dependent protein refolding / protein transmembrane transporter activity / response to unfolded protein / cellular response to unfolded protein / vesicle-mediated transport / protein folding chaperone / heat shock protein binding / unfolded protein binding / protein refolding / mitochondrial outer membrane / cytoplasmic translation / ATP hydrolysis activity / mitochondrion / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å | ||||||
Authors | Li, J. / Qian, X. / Hu, J. / Sha, B. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Molecular chaperone Hsp70/Hsp90 prepares the mitochondrial outer membrane translocon receptor Tom71 for preprotein loading. Authors: Li, J. / Qian, X. / Hu, J. / Sha, B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3fp4.cif.gz | 121.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3fp4.ent.gz | 92.2 KB | Display | PDB format |
PDBx/mmJSON format | 3fp4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fp/3fp4 ftp://data.pdbj.org/pub/pdb/validation_reports/fp/3fp4 | HTTPS FTP |
---|
-Related structure data
Related structure data | 3fp2C 3fp3SC 3fp1 C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein / Protein/peptide , 2 types, 2 molecules AQ
#1: Protein | Mass: 60571.273 Da / Num. of mol.: 1 / Fragment: UNP residues 107-639 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: YHR117W / Production host: Escherichia coli (E. coli) / References: UniProt: P38825 |
---|---|
#2: Protein/peptide | Mass: 1202.183 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in yeast. / References: UniProt: Q10265*PLUS |
-Non-polymers , 4 types, 281 molecules
#3: Chemical | ChemComp-CL / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.38 Å3/Da / Density % sol: 63.64 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG6K, 5% Ethylene Glyco, 0.15M NaCl, Tris 10mM, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 200 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 8, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→8 Å / Num. obs: 39166 / % possible obs: 0.89 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Highest resolution: 2.14 Å / % possible all: 0.89 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3FP3 Resolution: 2.14→8 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.901 / SU B: 10.296 / SU ML: 0.132 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.213 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.851 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.14→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.141→2.192 Å / Total num. of bins used: 20
|