+Open data
-Basic information
Entry | Database: PDB / ID: 5hdg | ||||||
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Title | crystal structure of heat shock factor 1-DBD | ||||||
Components | Heat shock factor protein 1 | ||||||
Keywords | TRANSCRIPTION / SF1-DBD | ||||||
Function / homology | Function and homology information cellular response to nitroglycerin / response to hypobaric hypoxia / sequence-specific single stranded DNA binding / cellular response to L-glutamine / cellular response to diamide / negative regulation of double-strand break repair via nonhomologous end joining / cellular response to sodium arsenite / positive regulation of apoptotic DNA fragmentation / translation elongation factor binding / negative regulation of inclusion body assembly ...cellular response to nitroglycerin / response to hypobaric hypoxia / sequence-specific single stranded DNA binding / cellular response to L-glutamine / cellular response to diamide / negative regulation of double-strand break repair via nonhomologous end joining / cellular response to sodium arsenite / positive regulation of apoptotic DNA fragmentation / translation elongation factor binding / negative regulation of inclusion body assembly / positive regulation of inclusion body assembly / nuclear stress granule / cellular response to potassium ion / positive regulation of macrophage differentiation / protein folding chaperone complex / cellular response to angiotensin / negative regulation of cardiac muscle cell apoptotic process / response to psychosocial stress / STAT family protein binding / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / response to testosterone / mitotic spindle pole / general transcription initiation factor binding / HSF1-dependent transactivation / Regulation of HSF1-mediated heat shock response / HSF1 activation / mRNA transport / Attenuation phase / cellular response to unfolded protein / negative regulation of protein-containing complex assembly / heterochromatin / regulation of cellular response to heat / positive regulation of tyrosine phosphorylation of STAT protein / cellular response to copper ion / cellular response to cadmium ion / heat shock protein binding / positive regulation of mitotic cell cycle / response to nutrient / response to activity / cellular response to estradiol stimulus / promoter-specific chromatin binding / Hsp90 protein binding / euchromatin / cellular response to gamma radiation / defense response / PML body / chromatin DNA binding / kinetochore / cellular response to hydrogen peroxide / mRNA processing / DNA-binding transcription repressor activity, RNA polymerase II-specific / Aggrephagy / : / positive regulation of DNA-binding transcription factor activity / MAPK cascade / cellular response to xenobiotic stimulus / sequence-specific double-stranded DNA binding / cellular response to heat / positive regulation of cold-induced thermogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / protein-containing complex assembly / cellular response to lipopolysaccharide / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / ribonucleoprotein complex / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein heterodimerization activity / negative regulation of gene expression / DNA repair / centrosome / chromatin / positive regulation of gene expression / regulation of transcription by RNA polymerase II / protein kinase binding / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Feng, H. / Liu, W. / Wang, D.C. | ||||||
Citation | Journal: To Be Published Title: HSF1-DBD crystal structure Authors: Feng, H. / Liu, W. / Wang, D.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hdg.cif.gz | 38.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hdg.ent.gz | 24 KB | Display | PDB format |
PDBx/mmJSON format | 5hdg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hd/5hdg ftp://data.pdbj.org/pub/pdb/validation_reports/hd/5hdg | HTTPS FTP |
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-Related structure data
Related structure data | 5hdkC 5hdnC 3htsS 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 13156.973 Da / Num. of mol.: 1 / Fragment: UNP residues 15-120 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HSF1, HSTF1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q00613 |
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#2: Chemical | ChemComp-NA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 0.2M sodium formate, pH 7.2, 22%(w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 6, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→32.21 Å / Num. obs: 12343 / % possible obs: 99.5 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.12 / Rsym value: 0.12 / Net I/σ(I): 4.1 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 3 / Rsym value: 0.527 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3HTS Resolution: 1.7→32.21 Å / SU ML: 0.18 / Cross valid method: NONE / σ(F): 1.39 / Phase error: 22.83 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→32.21 Å
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Refine LS restraints |
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LS refinement shell |
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