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- PDB-5d5u: Crystal structure of human Hsf1 with HSE DNA -

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Basic information

Entry
Database: PDB / ID: 5d5u
TitleCrystal structure of human Hsf1 with HSE DNA
Components
  • Heat shock Element DNA
  • Heat shock factor protein 1
KeywordsTRANSCRIPTION/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 apoptotic DNA fragmentation / translation elongation factor binding / negative regulation of inclusion body assembly / positive 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 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 / 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 / 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 / cellular response to gamma radiation / chromatin DNA binding / kinetochore / PML body / mRNA processing / defense response / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of DNA-binding transcription factor activity / 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 / 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 / protein heterodimerization activity / DNA-binding transcription factor 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
Vertebrate heat shock transcription factor, C-terminal domain / Vertebrate heat shock transcription factor / Heat shock factor (HSF)-type, DNA-binding / Heat shock transcription factor family / HSF-type DNA-binding / HSF-type DNA-binding domain signature. / 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 ...Vertebrate heat shock transcription factor, C-terminal domain / Vertebrate heat shock transcription factor / Heat shock factor (HSF)-type, DNA-binding / Heat shock transcription factor family / HSF-type DNA-binding / HSF-type DNA-binding domain signature. / 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
DNA / DNA (> 10) / Heat shock factor protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.91 Å
AuthorsNeudegger, T. / Verghese, J. / Hayer-Hartl, M. / Hartl, F.U. / Bracher, A.
CitationJournal: 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
DepositionAug 11, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Database references
Revision 1.2Jan 20, 2016Group: Structure summary
Revision 1.3Feb 10, 2016Group: Database references
Revision 1.4Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heat shock Element DNA
B: Heat shock factor protein 1


Theoretical massNumber of molelcules
Total (without water)18,2132
Polymers18,2132
Non-polymers00
Water362
1
A: Heat shock Element DNA
B: Heat shock factor protein 1

A: Heat shock Element DNA
B: Heat shock factor protein 1


Theoretical massNumber of molelcules
Total (without water)36,4264
Polymers36,4264
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Buried area4080 Å2
ΔGint-37 kcal/mol
Surface area13790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.436, 39.820, 94.384
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
SymmetryPoint symmetry: (Schoenflies symbol: D2 (2x2 fold dihedral))

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Components

#1: DNA chain Heat shock Element DNA


Mass: 3662.404 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Protein Heat shock factor protein 1 / / HSF 1 / Heat shock transcription factor 1 / HSTF 1


Mass: 14550.622 Da / Num. of mol.: 1 / Fragment: UNP residues 13-120
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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 21 % PEG-3350, 0.2 M (NH4)2_SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.91→47.19 Å / Num. obs: 3303 / % possible obs: 96.9 % / Redundancy: 4.9 % / Biso Wilson estimate: 41.9 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.069 / Net I/σ(I): 9 / Num. measured all: 16032 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.91-3.094.80.8212.121564490.750.40382.7
8.73-47.194.20.04721.66701580.9980.02498.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
MOLREPphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D5W

5d5w


Resolution: 2.91→30 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.885 / WRfactor Rfree: 0.2569 / WRfactor Rwork: 0.209 / FOM work R set: 0.8258 / SU B: 42.569 / SU ML: 0.342 / SU R Cruickshank DPI: 0.4506 / SU Rfree: 0.463 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.463 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2673 145 4.4 %RANDOM
Rwork0.2228 ---
obs0.2247 3137 96.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 135.72 Å2 / Biso mean: 61.167 Å2 / Biso min: 27.9 Å2
Baniso -1Baniso -2Baniso -3
1-6.75 Å2-0 Å2-0 Å2
2---2.67 Å20 Å2
3----4.08 Å2
Refinement stepCycle: final / Resolution: 2.91→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms810 243 0 2 1055
Biso mean---35.84 -
Num. residues----112
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0171104
X-RAY DIFFRACTIONr_bond_other_d0.0010.02906
X-RAY DIFFRACTIONr_angle_refined_deg0.8831.7191544
X-RAY DIFFRACTIONr_angle_other_deg0.85332085
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.648598
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.1624.18643
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.65115135
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.363154
X-RAY DIFFRACTIONr_chiral_restr0.0510.2156
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211088
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02272
LS refinement shellResolution: 2.912→2.987 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.458 7 -
Rwork0.372 142 -
all-149 -
obs--63.95 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.1786-2.90910.06610.2538-2.23834.4053-0.0524-0.3744-0.070.2206-0.0129-1.43330.0752-0.04890.06530.0474-0.0265-0.01540.04160.00810.322513.08190.3060.6721
24.6599-1.69950.19249.0172-2.814611.57040.1771-0.339-0.13740.74180.00670.62060.1089-0.383-0.18380.1351-0.0060.10480.1784-0.03610.29692.24595.750513.6867
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B13 - 119
2X-RAY DIFFRACTION2B-10 - 9999

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