+Open data
-Basic information
Entry | Database: PDB / ID: 4h5r | ||||||
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Title | HSC70 NBD with Na, Cl and glycerol | ||||||
Components | Heat shock cognate 71 kDa protein | ||||||
Keywords | TRANSCRIPTION / HSC70 NBD domain | ||||||
Function / homology | Function and homology information lumenal side of lysosomal membrane / regulation of protein import / negative regulation of supramolecular fiber organization / protein carrier chaperone / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / Lipophagy / chaperone-mediated autophagy translocation complex disassembly / slow axonal transport / clathrin-uncoating ATPase activity / GABA synthesis, release, reuptake and degradation ...lumenal side of lysosomal membrane / regulation of protein import / negative regulation of supramolecular fiber organization / protein carrier chaperone / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / Lipophagy / chaperone-mediated autophagy translocation complex disassembly / slow axonal transport / clathrin-uncoating ATPase activity / GABA synthesis, release, reuptake and degradation / protein targeting to lysosome involved in chaperone-mediated autophagy / late endosomal microautophagy / C3HC4-type RING finger domain binding / clathrin coat disassembly / negative regulation of NLRP3 inflammasome complex assembly / CHL1 interactions / ATP-dependent protein disaggregase activity / regulation of protein complex stability / membrane organization / Prp19 complex / presynaptic cytosol / protein folding chaperone complex / postsynaptic cytosol / Lysosome Vesicle Biogenesis / chaperone-mediated autophagy / cellular response to steroid hormone stimulus / Golgi Associated Vesicle Biogenesis / non-chaperonin molecular chaperone ATPase / chaperone cofactor-dependent protein refolding / regulation of protein-containing complex assembly / HSF1-dependent transactivation / response to unfolded protein / autophagosome / Regulation of HSF1-mediated heat shock response / Attenuation phase / Protein methylation / ATP metabolic process / protein folding chaperone / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / heat shock protein binding / cellular response to starvation / mRNA Splicing - Major Pathway / lysosomal lumen / G protein-coupled receptor binding / AUF1 (hnRNP D0) binds and destabilizes mRNA / ATP-dependent protein folding chaperone / spliceosomal complex / Late endosomal microautophagy / regulation of protein stability / PKR-mediated signaling / terminal bouton / mRNA splicing, via spliceosome / Chaperone Mediated Autophagy / melanosome / unfolded protein binding / protein-macromolecule adaptor activity / protein folding / Clathrin-mediated endocytosis / MHC class II protein complex binding / protein-folding chaperone binding / protein refolding / blood microparticle / secretory granule lumen / Interleukin-4 and Interleukin-13 signaling / ficolin-1-rich granule lumen / lysosome / cadherin binding / ribonucleoprotein complex / lysosomal membrane / focal adhesion / negative regulation of DNA-templated transcription / dendrite / ubiquitin protein ligase binding / Neutrophil degranulation / nucleolus / enzyme binding / ATP hydrolysis activity / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.64 Å | ||||||
Authors | Stec, B. | ||||||
Citation | Journal: Biochimie / Year: 2015 Title: New crystal structures of HSC-70 ATP binding domain confirm the role of individual binding pockets and suggest a new method of inhibition. Authors: Zhang, Z. / Cellitti, J. / Teriete, P. / Pellecchia, M. / Stec, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4h5r.cif.gz | 176.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4h5r.ent.gz | 137.9 KB | Display | PDB format |
PDBx/mmJSON format | 4h5r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h5/4h5r ftp://data.pdbj.org/pub/pdb/validation_reports/h5/4h5r | HTTPS FTP |
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-Related structure data
Related structure data | 4h5nC 4h5tC 4h5vC 4h5wC 2bupS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 42165.648 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HSC70, HSP73, HSPA10, HSPA8 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P11142 |
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-Non-polymers , 6 types, 775 molecules
#2: Chemical | #3: Chemical | ChemComp-PO4 / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-GOL / #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE SEQUENCE MATCHES WITH ISOFORM 2 OF UNIPROT ENTRY P11142 WITH IDENTIFIER |
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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: 2.84 Å3/Da / Density % sol: 56.72 % |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M KCl in Tris, 30%PEG 400, pH 8.5, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jul 12, 2007 |
Radiation | Monochromator: Osmic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→48 Å / Num. all: 97171 / Num. obs: 97171 / % possible obs: 88 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 25 |
Reflection shell | Resolution: 1.64→1.71 Å / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.8 / % possible all: 70 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2bup Resolution: 1.64→48 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / SU B: 1.951 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: 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: 24.361 Å2
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Refinement step | Cycle: LAST / Resolution: 1.64→48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.64→1.681 Å / Total num. of bins used: 20
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