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- PDB-5hdg: crystal structure of heat shock factor 1-DBD -

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Basic information

Entry
Database: PDB / ID: 5hdg
Titlecrystal structure of heat shock factor 1-DBD
ComponentsHeat shock factor protein 1
KeywordsTRANSCRIPTION / SF1-DBD
Function / homology
Function and homology information


cellular response to nitroglycerin / sequence-specific single stranded DNA binding / embryonic process involved in female pregnancy / cellular response to diamide / response to hypobaric hypoxia / cellular response to L-glutamine / positive regulation of stress granule assembly / negative regulation of double-strand break repair via nonhomologous end joining / positive regulation of apoptotic DNA fragmentation / response to peptide ...cellular response to nitroglycerin / sequence-specific single stranded DNA binding / embryonic process involved in female pregnancy / cellular response to diamide / response to hypobaric hypoxia / cellular response to L-glutamine / positive regulation of stress granule assembly / negative regulation of double-strand break repair via nonhomologous end joining / positive regulation of apoptotic DNA fragmentation / response to peptide / cellular response to sodium arsenite / translation elongation factor binding / negative regulation of inclusion body assembly / nuclear stress granule / female meiotic nuclear division / positive regulation of macrophage differentiation / positive regulation of inclusion body assembly / positive regulation of multicellular organism growth / pronucleus / cellular response to potassium ion / protein folding chaperone complex / negative regulation of cardiac muscle cell apoptotic process / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / STAT family protein binding / response to psychosocial stress / mitotic spindle pole / response to testosterone / cellular response to cadmium ion / cellular response to angiotensin / general transcription initiation factor binding / negative regulation of tumor necrosis factor production / Regulation of HSF1-mediated heat shock response / HSF1-dependent transactivation / cellular response to unfolded protein / mRNA transport / HSF1 activation / Mitochondrial unfolded protein response (UPRmt) / embryonic placenta development / Attenuation phase / negative regulation of protein-containing complex assembly / heterochromatin / regulation of cellular response to heat / heat shock protein binding / response to nutrient / positive regulation of mitotic cell cycle / cellular response to copper ion / positive regulation of apoptotic signaling pathway / epithelial cell proliferation / response to activity / cellular response to estradiol stimulus / promoter-specific chromatin binding / Hsp90 protein binding / chromatin DNA binding / euchromatin / cellular response to gamma radiation / defense response / PML body / kinetochore / Aggrephagy / DNA-binding transcription repressor activity, RNA polymerase II-specific / cellular response to hydrogen peroxide / cellular response to xenobiotic stimulus / mRNA processing / negative regulation of epithelial cell proliferation / sequence-specific double-stranded DNA binding / MAPK cascade / positive regulation of cold-induced thermogenesis / cellular response to heat / cellular response to lipopolysaccharide / protein-containing complex assembly / DNA-binding transcription activator activity, RNA polymerase II-specific / spermatogenesis / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / ribonucleoprotein complex / protein heterodimerization activity / DNA repair / centrosome / positive regulation of gene expression / regulation of transcription by RNA polymerase II / protein kinase binding / chromatin / 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
Vertebrate heat shock transcription factor, C-terminal domain / Vertebrate heat shock transcription factor / HSF-type DNA-binding domain signature. / Heat shock factor (HSF)-type, DNA-binding / HSF-type DNA-binding / heat shock factor / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily ...Vertebrate heat shock transcription factor, C-terminal domain / Vertebrate heat shock transcription factor / HSF-type DNA-binding domain signature. / Heat shock factor (HSF)-type, DNA-binding / HSF-type DNA-binding / heat shock factor / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Heat shock factor protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsFeng, H. / Liu, W. / Wang, D.C.
CitationJournal: To Be Published
Title: HSF1-DBD crystal structure
Authors: Feng, H. / Liu, W. / Wang, D.C.
History
DepositionJan 5, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heat shock factor protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1802
Polymers13,1571
Non-polymers231
Water2,684149
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Heat shock factor protein 1
hetero molecules

A: Heat shock factor protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3604
Polymers26,3142
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
Buried area1560 Å2
ΔGint-5 kcal/mol
Surface area10280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.610, 64.420, 68.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-445-

HOH

21A-448-

HOH

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Components

#1: Protein Heat shock factor protein 1 / HSF 1 / Heat shock transcription factor 1 / HSTF 1


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
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 0.2M sodium formate, pH 7.2, 22%(w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XSCALEdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HTS

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
RfactorNum. reflection% reflection
Rfree0.2184 1225 10.06 %
Rwork0.1907 --
obs0.1935 12177 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→32.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms780 0 1 149 930
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003812
X-RAY DIFFRACTIONf_angle_d0.7531096
X-RAY DIFFRACTIONf_dihedral_angle_d12.696295
X-RAY DIFFRACTIONf_chiral_restr0.033114
X-RAY DIFFRACTIONf_plane_restr0.004141
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.76810.28591340.23371218X-RAY DIFFRACTION100
1.7681-1.84850.2781340.23281185X-RAY DIFFRACTION100
1.8485-1.9460.29521360.23811196X-RAY DIFFRACTION100
1.946-2.06790.26681320.21881204X-RAY DIFFRACTION100
2.0679-2.22750.22361350.21091212X-RAY DIFFRACTION100
2.2275-2.45160.26951320.2031212X-RAY DIFFRACTION100
2.4516-2.80620.22231430.20091224X-RAY DIFFRACTION100
2.8062-3.53480.21381390.1721239X-RAY DIFFRACTION100
3.5348-32.21580.17031400.1691262X-RAY DIFFRACTION97

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