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- PDB-5d8l: Human HSF2 DNA Binding Domain in complex with 3-site HSE DNA at 2... -

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Basic information

Entry
Database: PDB / ID: 5d8l
TitleHuman HSF2 DNA Binding Domain in complex with 3-site HSE DNA at 2.1 Angstroms Resolution
Components
  • DNA (5'-D(*GP*GP*TP*TP*CP*TP*AP*GP*AP*AP*TP*AP*TP*TP*CP*AP*C)-3')
  • DNA (5'-D(P*GP*TP*GP*AP*AP*TP*AP*TP*TP*CP*TP*AP*GP*AP*AP*CP*C)-3')
  • Heat shock factor protein 2
Keywordstranscription/DNA / transcription factor / DNA / HSF / transcription-DNA complex
Function / homology
Function and homology information


RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / sequence-specific double-stranded DNA binding / spermatogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin / regulation of transcription by RNA polymerase II ...RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / sequence-specific double-stranded DNA binding / spermatogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / 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 2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / Resolution: 2.069 Å
AuthorsJaeger, A.M. / Pemble, C.W. / Thiele, D.J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2016
Title: Structures of HSF2 reveal mechanisms for differential regulation of human heat-shock factors.
Authors: Jaeger, A.M. / Pemble, C.W. / Sistonen, L. / Thiele, D.J.
History
DepositionAug 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Database references
Revision 1.2Feb 10, 2016Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: DNA (5'-D(P*GP*TP*GP*AP*AP*TP*AP*TP*TP*CP*TP*AP*GP*AP*AP*CP*C)-3')
B: Heat shock factor protein 2
C: DNA (5'-D(*GP*GP*TP*TP*CP*TP*AP*GP*AP*AP*TP*AP*TP*TP*CP*AP*C)-3')
D: Heat shock factor protein 2
E: DNA (5'-D(*GP*GP*TP*TP*CP*TP*AP*GP*AP*AP*TP*AP*TP*TP*CP*AP*C)-3')
F: Heat shock factor protein 2
G: DNA (5'-D(P*GP*TP*GP*AP*AP*TP*AP*TP*TP*CP*TP*AP*GP*AP*AP*CP*C)-3')
H: Heat shock factor protein 2


Theoretical massNumber of molelcules
Total (without water)73,0238
Polymers73,0238
Non-polymers00
Water5,441302
1
A: DNA (5'-D(P*GP*TP*GP*AP*AP*TP*AP*TP*TP*CP*TP*AP*GP*AP*AP*CP*C)-3')
B: Heat shock factor protein 2
C: DNA (5'-D(*GP*GP*TP*TP*CP*TP*AP*GP*AP*AP*TP*AP*TP*TP*CP*AP*C)-3')
D: Heat shock factor protein 2


Theoretical massNumber of molelcules
Total (without water)36,5124
Polymers36,5124
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-36 kcal/mol
Surface area16170 Å2
MethodPISA
2
E: DNA (5'-D(*GP*GP*TP*TP*CP*TP*AP*GP*AP*AP*TP*AP*TP*TP*CP*AP*C)-3')
F: Heat shock factor protein 2
G: DNA (5'-D(P*GP*TP*GP*AP*AP*TP*AP*TP*TP*CP*TP*AP*GP*AP*AP*CP*C)-3')
H: Heat shock factor protein 2


Theoretical massNumber of molelcules
Total (without water)36,5124
Polymers36,5124
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-39 kcal/mol
Surface area16190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.174, 47.140, 109.587
Angle α, β, γ (deg.)82.82, 90.03, 64.75
Int Tables number1
Space group name H-MP1

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Components

#1: DNA chain DNA (5'-D(P*GP*TP*GP*AP*AP*TP*AP*TP*TP*CP*TP*AP*GP*AP*AP*CP*C)-3')


Mass: 5210.410 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein
Heat shock factor protein 2 / / HSF 2 / Heat shock transcription factor 2 / HSTF 2


Mass: 13049.851 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSF2, HSTF2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q03933
#3: DNA chain DNA (5'-D(*GP*GP*TP*TP*CP*TP*AP*GP*AP*AP*TP*AP*TP*TP*CP*AP*C)-3')


Mass: 5201.396 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 2.55 Å3/Da / Density % sol: 51.68 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 7 mg/ml protein:DNA complexes were mixed at a ratio of 1:1.2 protein:DNA in 25 mM HEPES pH 7.5 and 150 mM NaCl and crystallized against 170 mM ammonium acetate, 85 mM sodium acetate pH 4.6, ...Details: 7 mg/ml protein:DNA complexes were mixed at a ratio of 1:1.2 protein:DNA in 25 mM HEPES pH 7.5 and 150 mM NaCl and crystallized against 170 mM ammonium acetate, 85 mM sodium acetate pH 4.6, 25.5% PEG 4000, and 15% Glycerol. Crystals grew in 3-4 days

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.069→24.41 Å / Num. obs: 38940 / % possible obs: 88.54 % / Redundancy: 2.5 % / Net I/σ(I): 11.8
Reflection shellResolution: 2.069→2.12 Å / Redundancy: 2.3 % / % possible all: 85

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Processing

Software
NameVersionClassification
PHENIX1.9_1675refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.069→24.41 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 35.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.273 1989 5.11 %
Rwork0.2171 --
obs0.2199 38940 88.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.069→24.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3442 1388 0 302 5132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0155097
X-RAY DIFFRACTIONf_angle_d1.4867162
X-RAY DIFFRACTIONf_dihedral_angle_d23.6261984
X-RAY DIFFRACTIONf_chiral_restr0.069760
X-RAY DIFFRACTIONf_plane_restr0.008684
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0687-2.12040.365470.3982851X-RAY DIFFRACTION28
2.1204-2.17770.4351340.34742494X-RAY DIFFRACTION85
2.1777-2.24180.34361490.32652765X-RAY DIFFRACTION91
2.2418-2.31410.39841430.33832594X-RAY DIFFRACTION89
2.3141-2.39670.32331450.2792754X-RAY DIFFRACTION92
2.3967-2.49260.33461470.2552768X-RAY DIFFRACTION92
2.4926-2.60590.32161450.25942706X-RAY DIFFRACTION92
2.6059-2.74310.32941530.25352794X-RAY DIFFRACTION94
2.7431-2.91470.27061540.25462823X-RAY DIFFRACTION95
2.9147-3.13940.31681570.25232876X-RAY DIFFRACTION96
3.1394-3.45450.29361440.21422782X-RAY DIFFRACTION94
3.4545-3.95260.27831530.18092927X-RAY DIFFRACTION97
3.9526-4.97290.19631590.1512902X-RAY DIFFRACTION98
4.9729-24.41720.18011590.15032915X-RAY DIFFRACTION98

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