+Open data
-Basic information
Entry | Database: PDB / ID: 3q9p | ||||||
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Title | HspB1 fragment | ||||||
Components | Heat shock protein beta-1Heat shock response | ||||||
Keywords | CHAPERONE / Alpha-crystallin domain / Charcot-Marie-Tooth disease / neuronopathy / Ig-like fold / Stress response / intra-cellular chaperones / nucleus | ||||||
Function / homology | Function and homology information anterograde axonal protein transport / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / cornified envelope / positive regulation of endothelial cell chemotaxis / regulation of translational initiation / regulation of canonical NF-kappaB signal transduction / protein kinase C inhibitor activity / response to unfolded protein / positive regulation of blood vessel endothelial cell migration / cellular response to vascular endothelial growth factor stimulus ...anterograde axonal protein transport / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / cornified envelope / positive regulation of endothelial cell chemotaxis / regulation of translational initiation / regulation of canonical NF-kappaB signal transduction / protein kinase C inhibitor activity / response to unfolded protein / positive regulation of blood vessel endothelial cell migration / cellular response to vascular endothelial growth factor stimulus / chaperone-mediated protein folding / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein folding chaperone / axon cytoplasm / proteasome complex / protein kinase C binding / ubiquitin binding / positive regulation of interleukin-1 beta production / regulation of autophagy / AUF1 (hnRNP D0) binds and destabilizes mRNA / regulation of protein phosphorylation / negative regulation of protein kinase activity / MAPK6/MAPK4 signaling / response to virus / spindle / platelet aggregation / Z disc / VEGFA-VEGFR2 Pathway / positive regulation of angiogenesis / unfolded protein binding / positive regulation of tumor necrosis factor production / response to heat / protein refolding / RNA polymerase II-specific DNA-binding transcription factor binding / Extra-nuclear estrogen signaling / cytoskeleton / intracellular signal transduction / focal adhesion / negative regulation of apoptotic process / protein kinase binding / protein homodimerization activity / extracellular space / RNA binding / extracellular exosome / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Baranova, E.V. / Beelen, S. / Gusev, N.B. / Strelkov, S.V. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: Three-Dimensional Structure of alpha-Crystallin Domain Dimers of Human Small Heat Shock Proteins HSPB1 and HSPB6 Authors: Baranova, E.V. / Weeks, S.D. / Beelen, S. / Bukach, O.V. / Gusev, N.B. / Strelkov, S.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3q9p.cif.gz | 30.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3q9p.ent.gz | 19 KB | Display | PDB format |
PDBx/mmJSON format | 3q9p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q9/3q9p ftp://data.pdbj.org/pub/pdb/validation_reports/q9/3q9p | HTTPS FTP |
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-Related structure data
Related structure data | 3q9qC 2bolS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 9289.354 Da / Num. of mol.: 1 / Fragment: residues 90-171 / Mutation: E125A, E126A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HSPB1 / Plasmid: pPEP-TEV / Production host: Escherichia coli (E. coli) / References: UniProt: P04792 |
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#2: 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: 2.94 Å3/Da / Density % sol: 58.21 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 2.2M ammonium sulfate, 0.2M di-ammonium tartrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9878 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2007 / Details: Dynamically bendable mirror |
Radiation | Monochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9878 Å / Relative weight: 1 |
Reflection | Resolution: 2→46.4 Å / Num. obs: 10565 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.3 % / Rsym value: 0.048 / Net I/σ(I): 23.9 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 9.5 % / Mean I/σ(I) obs: 4.7 / Rsym value: 0.47 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2BOL Resolution: 2→46.363 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.07 / σ(F): 1.34 / Phase error: 26.54 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.195 Å2 / ksol: 0.349 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 91 Å2 / Biso mean: 41.4575 Å2 / Biso min: 21.32 Å2
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Refinement step | Cycle: LAST / Resolution: 2→46.363 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6 / % reflection obs: 100 %
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