[English] 日本語
Yorodumi- PDB-7f50: X-ray crystal structure of Y149A mutated Hsp72-NBD in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7f50 | ||||||
---|---|---|---|---|---|---|---|
Title | X-ray crystal structure of Y149A mutated Hsp72-NBD in complex with AMPPnP | ||||||
Components | Heat shock 70 kDa protein 1B | ||||||
Keywords | HYDROLASE / Complex / Chaperone / nuclueotide-binding domain | ||||||
Function / homology | Function and homology information cellular heat acclimation / negative regulation of inclusion body assembly / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / C3HC4-type RING finger domain binding / positive regulation of microtubule nucleation / ATP-dependent protein disaggregase activity / regulation of mitotic spindle assembly / positive regulation of tumor necrosis factor-mediated signaling pathway / aggresome / cellular response to steroid hormone stimulus ...cellular heat acclimation / negative regulation of inclusion body assembly / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / C3HC4-type RING finger domain binding / positive regulation of microtubule nucleation / ATP-dependent protein disaggregase activity / regulation of mitotic spindle assembly / positive regulation of tumor necrosis factor-mediated signaling pathway / aggresome / cellular response to steroid hormone stimulus / mRNA catabolic process / regulation of protein ubiquitination / chaperone cofactor-dependent protein refolding / HSF1-dependent transactivation / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / Regulation of HSF1-mediated heat shock response / Attenuation phase / ATP metabolic process / protein folding chaperone / inclusion body / negative regulation of protein ubiquitination / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / centriole / positive regulation of erythrocyte differentiation / positive regulation of interleukin-8 production / G protein-coupled receptor binding / ATP-dependent protein folding chaperone / PKR-mediated signaling / negative regulation of cell growth / histone deacetylase binding / unfolded protein binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / virus receptor activity / positive regulation of NF-kappaB transcription factor activity / cellular response to heat / cellular response to oxidative stress / protein refolding / vesicle / ficolin-1-rich granule lumen / blood microparticle / protein stabilization / nuclear speck / ribonucleoprotein complex / negative regulation of cell population proliferation / focal adhesion / signaling receptor binding / centrosome / ubiquitin protein ligase binding / Neutrophil degranulation / positive regulation of gene expression / negative regulation of apoptotic process / perinuclear region of cytoplasm / enzyme binding / endoplasmic reticulum / ATP hydrolysis activity / protein-containing complex / mitochondrion / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.703 Å | ||||||
Authors | Yokoyama, T. / Fujii, S. / Nabeshima, Y. / Mizuguchi, M. | ||||||
Citation | Journal: Iucrj / Year: 2022 Title: Neutron crystallographic analysis of the nucleotide-binding domain of Hsp72 in complex with ADP. Authors: Yokoyama, T. / Fujii, S. / Ostermann, A. / Schrader, T.E. / Nabeshima, Y. / Mizuguchi, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7f50.cif.gz | 98.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7f50.ent.gz | 71 KB | Display | PDB format |
PDBx/mmJSON format | 7f50.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7f50_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7f50_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 7f50_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | 7f50_validation.cif.gz | 27.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f5/7f50 ftp://data.pdbj.org/pub/pdb/validation_reports/f5/7f50 | HTTPS FTP |
-Related structure data
Related structure data | 7f4xC 7f4zC 5aqzS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 42673.188 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HSPA1B, HSP72 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DMV9 | ||||||||
---|---|---|---|---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-ANP / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.22 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 29% PEG550 MME, 200 mM MgCl2 and 100 mM Tris-HCl pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 28, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→37.75 Å / Num. obs: 44823 / % possible obs: 98.8 % / Redundancy: 4.5 % / CC1/2: 0.998 / Rpim(I) all: 0.034 / Rrim(I) all: 0.074 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4381 / CC1/2: 0.771 / Rpim(I) all: 0.337 / Rrim(I) all: 0.713 / % possible all: 97.6 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5AQZ Resolution: 1.703→36.846 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.65 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.703→36.846 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|