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Yorodumi- PDB-3fzm: Crystal Structures of Hsc70/Bag1 in Complex with Small Molecule I... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fzm | ||||||
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Title | Crystal Structures of Hsc70/Bag1 in Complex with Small Molecule Inhibitors | ||||||
Components |
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Keywords | CHAPERONE / HSP70 / HSC70 / BAG1 / heat shock / protein folding / adenosine / nucleotide / nucleotide exchange factor / small molecule inhibitor / ATP-binding / nucleotide-binding / stress response / apoptosis | ||||||
Function / homology | Function and homology information lumenal side of lysosomal membrane / regulation of protein import / negative regulation of supramolecular fiber organization / positive regulation of protein refolding / prostaglandin binding / positive regulation of lysosomal membrane permeability / lysosomal matrix / A1 adenosine receptor binding / protein carrier chaperone / response to nickel cation ...lumenal side of lysosomal membrane / regulation of protein import / negative regulation of supramolecular fiber organization / positive regulation of protein refolding / prostaglandin binding / positive regulation of lysosomal membrane permeability / lysosomal matrix / A1 adenosine receptor binding / protein carrier chaperone / response to nickel cation / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / Respiratory syncytial virus genome transcription / protein transmembrane import into intracellular organelle / 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 / adenyl-nucleotide exchange factor activity / late endosomal microautophagy / response to odorant / positive regulation by host of viral genome replication / synaptic vesicle uncoating / C3HC4-type RING finger domain binding / positive regulation of smooth muscle cell apoptotic process / negative regulation of NLRP3 inflammasome complex assembly / clathrin coat disassembly / CHL1 interactions / ATP-dependent protein disaggregase activity / regulation of protein complex stability / photoreceptor ribbon synapse / maintenance of postsynaptic specialization structure / membrane organization / Prp19 complex / glycinergic synapse / presynaptic cytosol / postsynaptic specialization membrane / protein folding chaperone complex / positive regulation of mRNA splicing, via spliceosome / postsynaptic cytosol / regulation of postsynapse organization / negative regulation of cardiac muscle cell apoptotic process / Lysosome Vesicle Biogenesis / intermediate filament / chaperone-mediated autophagy / cellular response to steroid hormone stimulus / Golgi Associated Vesicle Biogenesis / phosphatidylserine binding / non-chaperonin molecular chaperone ATPase / chaperone cofactor-dependent protein refolding / positive regulation of proteolysis / HSF1-dependent transactivation / response to unfolded protein / estrous cycle / Regulation of HSF1-mediated heat shock response / autophagosome / regulation of protein-containing complex assembly / Attenuation phase / Protein methylation / protein folding chaperone / ATP metabolic process / positive regulation of phagocytosis / skeletal muscle tissue development / forebrain development / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / cellular response to cadmium ion / cellular response to starvation / photoreceptor inner segment / lysosomal lumen / mRNA Splicing - Major Pathway / cerebellum development / dendritic shaft / response to activity / AUF1 (hnRNP D0) binds and destabilizes mRNA / kidney development / G protein-coupled receptor binding / response to progesterone / ATP-dependent protein folding chaperone / peptide binding / Late endosomal microautophagy / spliceosomal complex / PKR-mediated signaling / regulation of protein stability / terminal bouton / ADP binding / mRNA splicing, via spliceosome / Chaperone Mediated Autophagy / cellular response to hydrogen peroxide / G1/S transition of mitotic cell cycle / positive regulation of T cell mediated cytotoxicity / protein import into nucleus / unfolded protein binding / melanosome / protein folding / late endosome / synaptic vesicle / response to estradiol / MHC class II protein complex binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Dokurno, P. / Williamson, D.S. / Murray, J.B. / Surgenor, A.E. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2009 Title: Novel adenosine-derived inhibitors of 70 kDa heat shock protein, discovered through structure-based design Authors: Williamson, D.S. / Borgognoni, J. / Clay, A. / Daniels, Z. / Dokurno, P. / Drysdale, M.J. / Foloppe, N. / Francis, G.L. / Graham, C.J. / Howes, R. / Macias, A.T. / Murray, J.B. / Parsons, R. ...Authors: Williamson, D.S. / Borgognoni, J. / Clay, A. / Daniels, Z. / Dokurno, P. / Drysdale, M.J. / Foloppe, N. / Francis, G.L. / Graham, C.J. / Howes, R. / Macias, A.T. / Murray, J.B. / Parsons, R. / Shaw, T. / Surgenor, A.E. / Terry, L. / Wang, Y. / Wood, M. / Massey, A.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fzm.cif.gz | 116.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fzm.ent.gz | 88.2 KB | Display | PDB format |
PDBx/mmJSON format | 3fzm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3fzm_validation.pdf.gz | 810.1 KB | Display | wwPDB validaton report |
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Full document | 3fzm_full_validation.pdf.gz | 817.8 KB | Display | |
Data in XML | 3fzm_validation.xml.gz | 23.5 KB | Display | |
Data in CIF | 3fzm_validation.cif.gz | 33.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fz/3fzm ftp://data.pdbj.org/pub/pdb/validation_reports/fz/3fzm | HTTPS FTP |
-Related structure data
Related structure data | 3fzfC 3fzhC 3fzkC 3fzlC 1hx1S 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 42086.547 Da / Num. of mol.: 1 / Fragment: UNP residues 4-381 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HSPA8, HSC70, HSP73, HSPA10 / Plasmid: pET101 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P11142 |
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#2: Protein | Mass: 13157.168 Da / Num. of mol.: 1 / Fragment: UNP residues 222-334 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BAG1, HAP / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99933 |
#3: Chemical | ChemComp-3GO / |
#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: 2.31 Å3/Da / Density % sol: 46.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 15% PEG3350, 0.1M Tris buffer, 25mM sodium-potassium tartrate, pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 22, 2008 / Details: mirrors |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→28.1 Å / Num. all: 28267 / Num. obs: 28267 / % possible obs: 96.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.29 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 5.1 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 4.37 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 1.5 / % possible all: 94.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HX1 Resolution: 2.3→24.59 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.922 / SU B: 8.645 / SU ML: 0.212 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.532 / ESU R Free: 0.277 / 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: 43.271 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→24.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.359 Å / Total num. of bins used: 20
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