+Open data
-Basic information
Entry | Database: PDB / ID: 5d5v | ||||||
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Title | Crystal structure of human Hsf1 with Satellite III repeat DNA | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / protein-DNA complex / double helix / helix-turn-helix / transcription-DNA complex | ||||||
Function / homology | Function and homology information cellular response to nitroglycerin / response to hypobaric hypoxia / sequence-specific single stranded DNA binding / cellular response to diamide / cellular response to L-glutamine / negative regulation of double-strand break repair via nonhomologous end joining / positive regulation of stress granule assembly / 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 diamide / cellular response to L-glutamine / negative regulation of double-strand break repair via nonhomologous end joining / positive regulation of stress granule assembly / 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 sodium arsenite / cellular response to potassium ion / positive regulation of macrophage differentiation / cellular response to angiotensin / protein folding chaperone complex / 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 / Attenuation phase / cellular response to unfolded protein / mRNA transport / 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 / heat shock protein binding / cellular response to cadmium ion / 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 / chromatin DNA binding / cellular response to gamma radiation / mRNA processing / PML body / kinetochore / defense response / positive regulation of DNA-binding transcription factor activity / DNA-binding transcription repressor activity, RNA polymerase II-specific / Aggrephagy / cellular response to hydrogen peroxide / : / MAPK cascade / sequence-specific double-stranded DNA binding / cellular response to xenobiotic stimulus / positive regulation of cold-induced thermogenesis / cellular response to heat / protein-containing complex assembly / DNA-binding transcription activator activity, RNA polymerase II-specific / cellular response to lipopolysaccharide / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / ribonucleoprotein complex / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / DNA repair / centrosome / positive regulation of gene expression / chromatin / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 Å | ||||||
Authors | Neudegger, T. / Verghese, J. / Hayer-Hartl, M. / Hartl, F.U. / Bracher, A. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2016 Title: Structure of human heat-shock transcription factor 1 in complex with DNA. Authors: Neudegger, T. / Verghese, J. / Hayer-Hartl, M. / Hartl, F.U. / Bracher, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5d5v.cif.gz | 74.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5d5v.ent.gz | 51 KB | Display | PDB format |
PDBx/mmJSON format | 5d5v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5d5v_validation.pdf.gz | 448.9 KB | Display | wwPDB validaton report |
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Full document | 5d5v_full_validation.pdf.gz | 449.6 KB | Display | |
Data in XML | 5d5v_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 5d5v_validation.cif.gz | 15.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d5/5d5v ftp://data.pdbj.org/pub/pdb/validation_reports/d5/5d5v | HTTPS FTP |
-Related structure data
Related structure data | 5d5uSC 5d5wC 5d5xC 5d5yC 5d5zC 5d60C S: Starting model for refinement C: citing same article (ref.) |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: THR / End label comp-ID: THR / Refine code: _ / Auth seq-ID: 14 - 120 / Label seq-ID: 25 - 131
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-Components
#1: Protein | Mass: 14550.622 Da / Num. of mol.: 2 / Fragment: DNA BINDING DOMAIN, UNP residues 1-120 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HSF1, HSTF1 / Plasmid: pProEx-HtB / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus-RIL / References: UniProt: Q00613 #2: DNA chain | | Mass: 3751.466 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #3: DNA chain | | Mass: 3573.342 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.69 Å3/Da / Density % sol: 73.79 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 31 % PEG-4000, 0.09 M Mg-acetate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 15, 2015 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.55→39.83 Å / Num. obs: 15087 / % possible obs: 99.6 % / Redundancy: 4.4 % / Biso Wilson estimate: 28.8 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.069 / Net I/σ(I): 9.3 / Num. measured all: 66855 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5D5U Resolution: 2.55→30 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.917 / WRfactor Rfree: 0.215 / WRfactor Rwork: 0.173 / FOM work R set: 0.847 / SU B: 7.85 / SU ML: 0.171 / SU R Cruickshank DPI: 0.3225 / SU Rfree: 0.2408 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.323 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 103.82 Å2 / Biso mean: 32.413 Å2 / Biso min: 10.6 Å2
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Refinement step | Cycle: final / Resolution: 2.55→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 5333 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.55→2.616 Å / Total num. of bins used: 20
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