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Yorodumi- PDB-6fhk: Structure of a modified protein containing a genetically encoded ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fhk | |||||||||
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Title | Structure of a modified protein containing a genetically encoded phosphoserine | |||||||||
Components | Heat shock 70 kDa protein 1A | |||||||||
Keywords | CHAPERONE / phosphoserine / ADP | |||||||||
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 microtubule nucleation / ATP-dependent protein disaggregase activity ...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 / protein folding chaperone / 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 RNA splicing / positive regulation of erythrocyte differentiation / positive regulation of interleukin-8 production / AUF1 (hnRNP D0) binds and destabilizes mRNA / G protein-coupled receptor binding / ATP-dependent protein folding chaperone / negative regulation of transforming growth factor beta receptor signaling pathway / PKR-mediated signaling / negative regulation of cell growth / histone deacetylase binding / transcription corepressor activity / disordered domain specific 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 oxidative stress / cellular response to heat / protein refolding / vesicle / ficolin-1-rich granule lumen / blood microparticle / receptor ligand activity / protein stabilization / nuclear speck / ribonucleoprotein complex / cadherin binding / negative regulation of cell population proliferation / signaling receptor binding / focal adhesion / centrosome / ubiquitin protein ligase binding / Neutrophil degranulation / positive regulation of gene expression / negative regulation of apoptotic process / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / enzyme binding / endoplasmic reticulum / ATP hydrolysis activity / protein-containing complex / mitochondrion / RNA binding / extracellular space / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.657 Å | |||||||||
Authors | Mukherjee, M. / Bayliss, R. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Sci Signal / Year: 2018 Title: Mitotic phosphorylation regulates Hsp72 spindle localization by uncoupling ATP binding from substrate release. Authors: Mukherjee, M. / Sabir, S. / O'Regan, L. / Sampson, J. / Richards, M.W. / Huguenin-Dezot, N. / Ault, J.R. / Chin, J.W. / Zhuravleva, A. / Fry, A.M. / Bayliss, R. #1: Journal: Sci Signal / Year: 2018 Title: Mitotic phosphorylation regulates Hsp72 spindle localization by uncoupling ATP binding from substrate release. Authors: Mukherjee, M. / Sabir, S. / O'Regan, L. / Sampson, J. / Richards, M.W. / Huguenin-Dezot, N. / Ault, J.R. / Chin, J.W. / Zhuravleva, A. / Fry, A.M. / Bayliss, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fhk.cif.gz | 327.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fhk.ent.gz | 264 KB | Display | PDB format |
PDBx/mmJSON format | 6fhk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fh/6fhk ftp://data.pdbj.org/pub/pdb/validation_reports/fh/6fhk | HTTPS FTP |
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-Related structure data
Related structure data | 3ay9S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 42093.566 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HSPA1A, HSP72, HSPA1, HSX70 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DMV8 |
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-Non-polymers , 5 types, 587 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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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: 2.16 Å3/Da / Density % sol: 43 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1 M Succinic acid pH 7.0, 15% w/v Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 20, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.657→55.09 Å / Num. obs: 83152 / % possible obs: 98.3 % / Redundancy: 6.4 % / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 1.657→1.662 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3AY9 Resolution: 1.657→55.09 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.18
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.657→55.09 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 14.6467 Å / Origin y: 6.5478 Å / Origin z: 79.3449 Å
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Refinement TLS group | Selection details: all |