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Yorodumi- PDB-7f4z: X-ray crystal structure of Y149A mutated Hsp72-NBD in complex with ADP -
+Open data
-Basic information
Entry | Database: PDB / ID: 7f4z | ||||||
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Title | X-ray crystal structure of Y149A mutated Hsp72-NBD in complex with ADP | ||||||
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: 1.8 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7f4z.cif.gz | 99.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7f4z.ent.gz | 71.4 KB | Display | PDB format |
PDBx/mmJSON format | 7f4z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7f4z_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 7f4z_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 7f4z_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | 7f4z_validation.cif.gz | 28.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f4/7f4z ftp://data.pdbj.org/pub/pdb/validation_reports/f4/7f4z | HTTPS FTP |
-Related structure data
Related structure data | 7f4xC 7f50C 5aqzS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 42673.188 Da / Num. of mol.: 1 / Mutation: Y149A 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 |
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-Non-polymers , 6 types, 356 molecules
#2: Chemical | ChemComp-ADP / |
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#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-CL / |
#5: Chemical | ChemComp-K / |
#6: Chemical | ChemComp-PO4 / |
#7: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 31% PEG550 MME, 200 mM MgCl2, 300 mM KCl and 100 mM Bis-Tris pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 10, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→47.69 Å / Num. obs: 39659 / % possible obs: 99.1 % / Redundancy: 5.4 % / CC1/2: 0.998 / Rpim(I) all: 0.032 / Rrim(I) all: 0.076 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 2.6 / Num. unique obs: 3886 / CC1/2: 0.878 / Rpim(I) all: 0.287 / Rrim(I) all: 0.701 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5AQZ Resolution: 1.8→29.411 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 21.71 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→29.411 Å
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Refine LS restraints |
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LS refinement shell |
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