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- PDB-5hdk: Crystal structure of heat shock factor 2-DBD -

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Basic information

Entry
Database: PDB / ID: 5hdk
TitleCrystal structure of heat shock factor 2-DBD
ComponentsHeat shock factor protein 2
KeywordsTRANSCRIPTION / HSF1-DBD
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 / DNA-binding transcription activator activity, RNA polymerase II-specific / spermatogenesis / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / positive regulation of transcription by RNA polymerase II / nucleoplasm ...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 / DNA-binding transcription activator activity, RNA polymerase II-specific / spermatogenesis / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / 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 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 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 1.1Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heat shock factor protein 2
B: Heat shock factor protein 2
C: Heat shock factor protein 2
D: Heat shock factor protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,16922
Polymers53,6214
Non-polymers54818
Water9,782543
1
A: Heat shock factor protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5135
Polymers13,4051
Non-polymers1084
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area6220 Å2
MethodPISA
2
B: Heat shock factor protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5496
Polymers13,4051
Non-polymers1445
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area6280 Å2
MethodPISA
3
C: Heat shock factor protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4673
Polymers13,4051
Non-polymers622
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area6240 Å2
MethodPISA
4
D: Heat shock factor protein 2
hetero molecules


  • defined by author&software
  • 13.6 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)13,6398
Polymers13,4051
Non-polymers2347
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area7490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.660, 67.260, 93.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Heat shock factor protein 2 / HSF 2 / Heat shock transcription factor 2 / HSTF 2


Mass: 13405.185 Da / Num. of mol.: 4 / Fragment: UNP residues 7-112
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
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 543 / 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: 1.92 Å3/Da / Density % sol: 35.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 0.1 M Tris, pH 8.4 and 1.25 M potassium sodium tartrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97845 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97845 Å / Relative weight: 1
ReflectionResolution: 1.32→38.32 Å / Num. obs: 95303 / % possible obs: 99.8 % / Redundancy: 12 % / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 3.6
Reflection shellResolution: 1.32→1.39 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.657 / Mean I/σ(I) obs: 3 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XSCALEdata reduction
XDSdata scaling
XDSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HDG

5hdg


Resolution: 1.32→38.319 Å / SU ML: 0.1 / Cross valid method: NONE / σ(F): 0 / Phase error: 16.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1744 1966 2.06 %
Rwork0.1526 --
obs0.1531 95303 97.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.32→38.319 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3404 0 18 543 3965
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0163603
X-RAY DIFFRACTIONf_angle_d1.5394860
X-RAY DIFFRACTIONf_dihedral_angle_d15.6361334
X-RAY DIFFRACTIONf_chiral_restr0.082501
X-RAY DIFFRACTIONf_plane_restr0.009618
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.32-1.3530.17041260.16576250X-RAY DIFFRACTION93
1.353-1.38960.22611370.15866336X-RAY DIFFRACTION94
1.3896-1.43050.1911370.156475X-RAY DIFFRACTION96
1.4305-1.47670.19241420.14316540X-RAY DIFFRACTION97
1.4767-1.52940.20391380.13846581X-RAY DIFFRACTION97
1.5294-1.59070.18811350.13576598X-RAY DIFFRACTION98
1.5907-1.66310.19161380.12676707X-RAY DIFFRACTION99
1.6631-1.75080.16231450.12966699X-RAY DIFFRACTION99
1.7508-1.86040.18111470.1356761X-RAY DIFFRACTION99
1.8604-2.00410.17721340.14416721X-RAY DIFFRACTION98
2.0041-2.20570.17161510.146815X-RAY DIFFRACTION100
2.2057-2.52490.15991380.15486819X-RAY DIFFRACTION99
2.5249-3.18080.17371480.16986877X-RAY DIFFRACTION99
3.1808-38.33470.16921500.16217158X-RAY DIFFRACTION100

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