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Yorodumi- PDB-3esk: Structure of HOP TPR2A domain in complex with the non-cognate Hsc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3esk | ||||||
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Title | Structure of HOP TPR2A domain in complex with the non-cognate Hsc70 peptide ligand | ||||||
Components |
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Keywords | CHAPERONE / TPR2A / Hsp90 / Hsc70 / tetratricopeptide repeat / Nucleus / TPR repeat / Stress response | ||||||
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 / dynein axonemal particle / 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 / cellular response to interleukin-7 / protein folding chaperone complex / positive regulation of mRNA splicing, via spliceosome / postsynaptic specialization membrane / RND1 GTPase cycle / 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 / Hsp90 protein binding / 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 Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Kajander, T. / Regan, L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Electrostatic interactions of Hsp-organizing protein tetratricopeptide domains with Hsp70 and Hsp90: computational analysis and protein engineering. Authors: Kajander, T. / Sachs, J.N. / Goldman, A. / Regan, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3esk.cif.gz | 43.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3esk.ent.gz | 29.6 KB | Display | PDB format |
PDBx/mmJSON format | 3esk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3esk_validation.pdf.gz | 437.9 KB | Display | wwPDB validaton report |
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Full document | 3esk_full_validation.pdf.gz | 437.9 KB | Display | |
Data in XML | 3esk_validation.xml.gz | 8.4 KB | Display | |
Data in CIF | 3esk_validation.cif.gz | 11.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/es/3esk ftp://data.pdbj.org/pub/pdb/validation_reports/es/3esk | HTTPS FTP |
-Related structure data
Related structure data | 1elrS 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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Unit cell |
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-Components
#1: Protein | Mass: 15254.223 Da / Num. of mol.: 1 / Fragment: TPR2A domain, UNP residues 223-350 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: STIP1 / Plasmid: pPROXHTA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P31948 |
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#2: Protein/peptide | Mass: 1161.175 Da / Num. of mol.: 1 / Fragment: Hsc70 C-terminal peptide, UNP residues 635-646 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P11142 |
#3: Chemical | ChemComp-NI / |
#4: 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: 2.04 Å3/Da / Density % sol: 39.77 % |
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Crystal grow | Temperature: 298 K / pH: 8.5 Details: TRIS pH 8.5, PEG MME 2000, NiCl2, Xylitol, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 28, 2005 / Details: MIRROS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. obs: 8178 / % possible obs: 94.7 % / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Rsym value: 0.074 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2.05→2.1 Å / Mean I/σ(I) obs: 3.9 / Rsym value: 0.239 / % possible all: 81.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ELR Resolution: 2.05→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.899 / SU B: 5.14 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.257 / ESU R Free: 0.21 / 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: 16.65 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.1 Å / Total num. of bins used: 20
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