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- PDB-7dci: Crystal structure of HSF2 DNA-binding domain in complex with 2-si... -

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Basic information

Entry
Database: PDB / ID: 7dci
TitleCrystal structure of HSF2 DNA-binding domain in complex with 2-site HSE DNA in the head-to-head orientation
Components
  • DNA (5'-D(*GP*GP*GP*AP*AP*TP*AP*TP*TP*CP*CP*C)-3')
  • Heat shock factor protein 2
KeywordsDNA BINDING PROTEIN/DNA / DNA BINDING PROTEIN-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 / DNA-binding transcription activator activity, RNA polymerase II-specific / spermatogenesis / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / 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 / DNA-binding transcription activator activity, RNA polymerase II-specific / spermatogenesis / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / 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 DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Heat shock factor protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsWei, L. / Wei, L.
CitationJournal: To Be Published
Title: Crystal structure of HSF2 DNA-binding domain in complex with 2-site HSE DNA in the head-to-head orientation
Authors: Wei, L. / Wei, L.
History
DepositionOct 26, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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 2
B: DNA (5'-D(*GP*GP*GP*AP*AP*TP*AP*TP*TP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0753
Polymers16,0522
Non-polymers231
Water3,081171
1
A: Heat shock factor protein 2
B: DNA (5'-D(*GP*GP*GP*AP*AP*TP*AP*TP*TP*CP*CP*C)-3')
hetero molecules

A: Heat shock factor protein 2
B: DNA (5'-D(*GP*GP*GP*AP*AP*TP*AP*TP*TP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1496
Polymers32,1034
Non-polymers462
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area3850 Å2
ΔGint-25 kcal/mol
Surface area12650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.268, 38.472, 38.654
Angle α, β, γ (deg.)90.000, 100.740, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-121-

HOH

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Components

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


Mass: 12389.110 Da / Num. of mol.: 1 / Mutation: D86N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSF2, HSTF2 / Production host: DNA satellites (virus) / References: UniProt: Q03933
#2: DNA chain DNA (5'-D(*GP*GP*GP*AP*AP*TP*AP*TP*TP*CP*CP*C)-3')


Mass: 3662.404 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: DNA satellites (virus)
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.28 Å3/Da / Density % sol: 41.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M lithium citrate and 23% PEG 3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.7→37.98 Å / Num. obs: 13957 / % possible obs: 94 % / Redundancy: 7.44 % / Rpim(I) all: 0.034 / Net I/σ(I): 25.4
Reflection shellResolution: 1.7→1.76 Å / Num. unique obs: 13957 / Rpim(I) all: 0.15

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HDK

5hdk


Resolution: 1.7→37.977 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.43 / Phase error: 23.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2094 724 5.19 %
Rwork0.1791 13233 -
obs0.1806 13957 94.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.2 Å2 / Biso mean: 27.2933 Å2 / Biso min: 10.74 Å2
Refinement stepCycle: final / Resolution: 1.7→37.977 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms787 243 1 171 1202
Biso mean--18.32 37.87 -
Num. residues----105
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051080
X-RAY DIFFRACTIONf_angle_d0.741506
X-RAY DIFFRACTIONf_chiral_restr0.046159
X-RAY DIFFRACTIONf_plane_restr0.004152
X-RAY DIFFRACTIONf_dihedral_angle_d14.245593
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7004-1.83160.24871360.2408231183
1.8316-2.01590.24711600.203267096
2.0159-2.30760.21211430.1754270697
2.3076-2.90720.20931350.1871276398
2.9072-37.9770.19021500.1614278397
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)
10.03690.0381-0.03470.0393-0.06070.0822-0.0216-0.30950.26290.07020.03390.2553-0.0469-0.1840.00990.22760.04970.00540.2168-0.04920.2009-19.2502-11.609712.5063
21.02370.324-0.25250.14640.08140.9496-0.07960.04350.5360.5440.1862-0.1699-0.68810.00850.04680.28390.0522-0.13810.06780.01220.4259-18.8401-2.06645.2952
30.0893-0.1401-0.04480.13790.03930.0784-0.0890.12650.1475-0.3051-0.02830.0624-0.0888-0.01260.00680.2073-0.0058-0.08670.18590.04160.2596-20.3205-8.8814-1.1317
40.10450.00860.00790.37530.05760.08280.17120.07340.2397-0.0187-0.2557-0.2791-0.03640.008-0.010.2866-0.0232-0.11780.15840.06370.389-6.536-2.53693.9974
50.1724-0.14960.11870.1213-0.11090.1973-0.1674-0.08530.24950.20650.02-0.1125-0.09440.0404-0.11810.17160.0062-0.0790.1369-0.0080.2042-8.7291-12.14539.9752
60.0541-0.01310.04810.0418-0.0290.02820.01020.0720.2745-0.4346-0.1088-0.0749-0.10110.1652-0.00350.3162-0.0101-0.0220.2060.01850.1814-13.5177-14.8022-2.6243
70.28840.1994-0.02990.36290.13440.2803-0.0012-0.06920.00110.04630.07490.2420.0526-0.1228-0.00930.1374-0.00520.00620.18970.05560.186-22.6203-18.63226.9683
80.18120.07060.15050.4597-0.17260.41040.0902-0.0597-0.00370.00470.00420.03360.0820.019-00.17220.0065-0.00650.20650.01620.1384-4.2656-22.38318.5138
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 19 )A7 - 19
2X-RAY DIFFRACTION2chain 'A' and (resid 20 through 29 )A20 - 29
3X-RAY DIFFRACTION3chain 'A' and (resid 30 through 40 )A30 - 40
4X-RAY DIFFRACTION4chain 'A' and (resid 41 through 47 )A41 - 47
5X-RAY DIFFRACTION5chain 'A' and (resid 48 through 68 )A48 - 68
6X-RAY DIFFRACTION6chain 'A' and (resid 69 through 88 )A69 - 88
7X-RAY DIFFRACTION7chain 'A' and (resid 89 through 110 )A89 - 110
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 12 )B1 - 12

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