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Yorodumi- PDB-3ay9: Crystal structure of human Hsp70 NBD in the ADP-, Mg ion-, and K ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ay9 | ||||||
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Title | Crystal structure of human Hsp70 NBD in the ADP-, Mg ion-, and K ion-bound state | ||||||
Components | Heat shock 70 kDa protein 1A/1B | ||||||
Keywords | CHAPERONE / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI / ATPase / ADP binding | ||||||
Function / homology | Function and homology information : / positive regulation of endoribonuclease activity / denatured protein binding / cellular heat acclimation / death receptor agonist activity / negative regulation of inclusion body assembly / : / Viral RNP Complexes in the Host Cell Nucleus / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / C3HC4-type RING finger domain binding ...: / positive regulation of endoribonuclease activity / denatured protein binding / cellular heat acclimation / death receptor agonist activity / negative regulation of inclusion body assembly / : / Viral RNP Complexes in the Host Cell Nucleus / 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 / misfolded protein binding / regulation of mitotic spindle assembly / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of tumor necrosis factor-mediated signaling pathway / transcription regulator inhibitor activity / aggresome / lysosomal transport / cellular response to steroid hormone stimulus / mRNA catabolic process / regulation of protein ubiquitination / chaperone cofactor-dependent protein refolding / HSF1-dependent transactivation / response to unfolded protein / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / chaperone-mediated protein complex assembly / Regulation of HSF1-mediated heat shock response / Attenuation phase / cellular response to unfolded protein / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / ATP metabolic process / inclusion body / vesicle-mediated transport / negative regulation of protein ubiquitination / protein folding chaperone / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / centriole / positive regulation of RNA splicing / positive regulation of erythrocyte differentiation / negative regulation of transforming growth factor beta receptor signaling pathway / positive regulation of interleukin-8 production / AUF1 (hnRNP D0) binds and destabilizes mRNA / G protein-coupled receptor binding / ATP-dependent protein folding chaperone / PKR-mediated signaling / negative regulation of cell growth / histone deacetylase binding / transcription corepressor activity / disordered domain specific binding / unfolded protein binding / virus receptor activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of NF-kappaB transcription factor activity / cellular response to oxidative stress / cellular response to heat / protein refolding / vesicle / ficolin-1-rich granule lumen / blood microparticle / receptor ligand activity / protein stabilization / nuclear speck / cadherin binding / 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 / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / ATP hydrolysis activity / protein-containing complex / mitochondrion / RNA binding / extracellular space / 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: 1.75 Å | ||||||
Authors | Arakawa, A. / Handa, N. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Protein Sci. / Year: 2011 Title: Biochemical and structural studies on the high affinity of Hsp70 for ADP. Authors: Arakawa, A. / Handa, N. / Shirouzu, M. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ay9.cif.gz | 97.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ay9.ent.gz | 70.2 KB | Display | PDB format |
PDBx/mmJSON format | 3ay9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ay9_validation.pdf.gz | 783.5 KB | Display | wwPDB validaton report |
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Full document | 3ay9_full_validation.pdf.gz | 783.9 KB | Display | |
Data in XML | 3ay9_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | 3ay9_validation.cif.gz | 26.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/3ay9 ftp://data.pdbj.org/pub/pdb/validation_reports/ay/3ay9 | HTTPS FTP |
-Related structure data
Related structure data | 3atuSC 3atvC 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 43150.766 Da / Num. of mol.: 1 / Fragment: nucleotide-binding domain (UNP RESIDUES 1-388) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: Hsp70, HSPA1, HSPA1A, HSPA1B / Plasmid: pET32 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) / References: UniProt: P08107, UniProt: P0DMV8*PLUS |
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-Non-polymers , 7 types, 272 molecules
#2: Chemical | ChemComp-ADP / |
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#3: Chemical | ChemComp-PO4 / |
#4: Chemical | ChemComp-MG / |
#5: Chemical | ChemComp-K / |
#6: Chemical | ChemComp-CL / |
#7: Chemical | ChemComp-CA / |
#8: 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: 2.32 Å3/Da / Density % sol: 46.95 % Description: the entry contains Friedel pairs in F_Plus/Minus columns |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.7 Details: 0.05M calcium chloride, 0.1M bis-tris (pH6.5), 30% PEG MME 550, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1.54 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. obs: 36093 / % possible obs: 92.5 % / Redundancy: 6.21842 % / Rsym value: 0.129 / Net I/σ(I): 10.1349 |
Reflection shell | Resolution: 1.75→1.81 Å / Mean I/σ(I) obs: 3.60131 / Rsym value: 0.523 / % possible all: 87.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ATU Resolution: 1.75→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.29 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: the entry contains Friedel pairs in F_Plus/Minus columns. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 26.317 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.751→1.796 Å / Total num. of bins used: 20
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