+Open data
-Basic information
Entry | Database: PDB / ID: 4h5t | ||||||
---|---|---|---|---|---|---|---|
Title | HSC70 NBD with ADP and Mg | ||||||
Components | Heat shock cognate 71 kDa protein | ||||||
Keywords | TRANSCRIPTION / HSC70 NBD | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4h5t.cif.gz | 94.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4h5t.ent.gz | 70.2 KB | Display | PDB format |
PDBx/mmJSON format | 4h5t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4h5t_validation.pdf.gz | 773.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4h5t_full_validation.pdf.gz | 782.1 KB | Display | |
Data in XML | 4h5t_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | 4h5t_validation.cif.gz | 27.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h5/4h5t ftp://data.pdbj.org/pub/pdb/validation_reports/h5/4h5t | HTTPS FTP |
-Related structure data
Related structure data | 4h5nC 4h5rC 4h5vC 4h5wC 2bupS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 42165.648 Da / Num. of mol.: 1 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 | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | ChemComp-ADP / | ||||||
#3: Chemical | #4: Chemical | ChemComp-PO4 / | #5: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE MATCHES WITH ISOFORM 2 OF UNIPROT ENTRY P11142 WITH IDENTIFIER | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.46 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9.5 Details: 0.1 M TRIS buffer, 1.5M NaCl, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: May 18, 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: 1.9→48 Å / Num. all: 31245 / Num. obs: 31245 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 1.9→1.94 Å / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.2 / % possible all: 87 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2bup Resolution: 1.9→48 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.921 / SU B: 7.511 / SU ML: 0.206 / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 44.002 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→48 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.944 Å / Total num. of bins used: 20
|