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Yorodumi- PDB-6b1n: Disrupted hydrogen bond network impairs ATPase activity in an Hsc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6b1n | ||||||
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Title | Disrupted hydrogen bond network impairs ATPase activity in an Hsc70 cysteine mutant | ||||||
Components | Heat shock protein family A (Hsp70) member 8 | ||||||
Keywords | CHAPERONE / Hsp70 family member / ATPase | ||||||
Function / homology | Function and homology information lumenal side of lysosomal membrane / regulation of protein import / protein transmembrane import into intracellular organelle / negative regulation of supramolecular fiber organization / positive regulation of protein refolding / prostaglandin binding / chaperone-mediated autophagy translocation complex disassembly / slow axonal transport / clathrin-uncoating ATPase activity / positive regulation of lysosomal membrane permeability ...lumenal side of lysosomal membrane / regulation of protein import / protein transmembrane import into intracellular organelle / negative regulation of supramolecular fiber organization / positive regulation of protein refolding / prostaglandin binding / chaperone-mediated autophagy translocation complex disassembly / slow axonal transport / clathrin-uncoating ATPase activity / positive regulation of lysosomal membrane permeability / lysosomal matrix / A1 adenosine receptor binding / late endosomal microautophagy / protein carrier chaperone / response to nickel cation / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / Respiratory syncytial virus genome transcription / Lipophagy / GABA synthesis, release, reuptake and degradation / protein targeting to lysosome involved in chaperone-mediated autophagy / response to odorant / positive regulation by host of viral genome replication / synaptic vesicle uncoating / C3HC4-type RING finger domain binding / clathrin coat disassembly / negative regulation of NLRP3 inflammasome complex assembly / ATP-dependent protein disaggregase activity / CHL1 interactions / regulation of protein complex stability / photoreceptor ribbon synapse / maintenance of postsynaptic specialization structure / membrane organization / glycinergic synapse / Prp19 complex / presynaptic cytosol / protein folding chaperone complex / positive regulation of mRNA splicing, via spliceosome / postsynaptic specialization membrane / intermediate filament / regulation of postsynapse organization / negative regulation of cardiac muscle cell apoptotic process / Lysosome Vesicle Biogenesis / chaperone-mediated autophagy / postsynaptic cytosol / cellular response to steroid hormone stimulus / Golgi Associated Vesicle Biogenesis / phosphatidylserine binding / non-chaperonin molecular chaperone ATPase / positive regulation of proteolysis / chaperone cofactor-dependent protein refolding / HSF1-dependent transactivation / response to unfolded protein / estrous cycle / autophagosome / cellular response to cadmium ion / Regulation of HSF1-mediated heat shock response / regulation of protein-containing complex assembly / Attenuation phase / Protein methylation / ATP metabolic process / positive regulation of phagocytosis / skeletal muscle tissue development / forebrain development / protein folding chaperone / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / photoreceptor inner segment / cellular response to starvation / lysosomal lumen / mRNA Splicing - Major Pathway / cerebellum development / peptide binding / response to activity / kidney development / dendritic shaft / AUF1 (hnRNP D0) binds and destabilizes mRNA / response to progesterone / G protein-coupled receptor binding / ATP-dependent protein folding chaperone / spliceosomal complex / Late endosomal microautophagy / regulation of protein stability / PKR-mediated signaling / terminal bouton / G1/S transition of mitotic cell cycle / ADP binding / mRNA splicing, via spliceosome / Chaperone Mediated Autophagy / cellular response to hydrogen peroxide / positive regulation of T cell mediated cytotoxicity / protein import into nucleus / unfolded protein binding / Clathrin-mediated endocytosis / melanosome / late endosome / protein folding / synaptic vesicle / response to estradiol / MHC class II protein complex binding / protein-macromolecule adaptor activity Similarity search - Function | ||||||
Biological species | Homo Sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | O'Donnell, J.P. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2018 Title: Disrupted Hydrogen-Bond Network and Impaired ATPase Activity in an Hsc70 Cysteine Mutant. Authors: O'Donnell, J.P. / Marsh, H.M. / Sondermann, H. / Sevier, C.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6b1n.cif.gz | 324.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6b1n.ent.gz | 261 KB | Display | PDB format |
PDBx/mmJSON format | 6b1n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6b1n_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 6b1n_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 6b1n_validation.xml.gz | 37 KB | Display | |
Data in CIF | 6b1n_validation.cif.gz | 56.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b1/6b1n ftp://data.pdbj.org/pub/pdb/validation_reports/b1/6b1n | HTTPS FTP |
-Related structure data
Related structure data | 6b1iSC 6b1mC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 44134.797 Da / Num. of mol.: 2 / Mutation: C17W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo Sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P11142 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: 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: 2.53 Å3/Da / Density % sol: 51.36 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: NaCl, Tris, PEG 3350, MgCl2, ADP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.977 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 4, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→47.3 Å / Num. obs: 87978 / % possible obs: 96.3 % / Redundancy: 4.3 % / CC1/2: 0.993 / Net I/σ(I): 7.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6B1I Resolution: 1.8→37.048 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.18
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→37.048 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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