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- PDB-5hdn: Crystal structure of heat shock factor1-DBD complex with ds-DNA a... -

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Basic information

Entry
Database: PDB / ID: 5hdn
TitleCrystal structure of heat shock factor1-DBD complex with ds-DNA and TtT
Components
  • DNA (5'-D(*GP*GP*TP*TP*CP*TP*AP*GP*AP*AP*CP*C)-3')
  • Heat shock factor protein 1
KeywordsTRANSCRIPTION / HSF1-DBD / TtT
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 / response to psychosocial stress / STAT family protein binding / 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 / cellular response to unfolded protein / HSF1-dependent transactivation / Mitochondrial unfolded protein response (UPRmt) / HSF1 activation / mRNA transport / 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 / epithelial cell proliferation / positive regulation of apoptotic signaling pathway / response to activity / promoter-specific chromatin binding / cellular response to estradiol stimulus / Hsp90 protein binding / cellular response to gamma radiation / euchromatin / defense response / PML body / chromatin DNA binding / kinetochore / DNA-binding transcription repressor activity, RNA polymerase II-specific / cellular response to xenobiotic stimulus / cellular response to hydrogen peroxide / mRNA processing / negative regulation of epithelial cell proliferation / Aggrephagy / 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
CITRIC ACID / DNA / DNA (> 10) / Heat shock factor protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 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 / 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
B: Heat shock factor protein 1
E: DNA (5'-D(*GP*GP*TP*TP*CP*TP*AP*GP*AP*AP*CP*C)-3')
F: DNA (5'-D(*GP*GP*TP*TP*CP*TP*AP*GP*AP*AP*CP*C)-3')
C: Heat shock factor protein 1
D: Heat shock factor protein 1
G: DNA (5'-D(*GP*GP*TP*TP*CP*TP*AP*GP*AP*AP*CP*C)-3')
H: DNA (5'-D(*GP*GP*TP*TP*CP*TP*AP*GP*AP*AP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,53912
Polymers67,2788
Non-polymers2614
Water12,755708
1
A: Heat shock factor protein 1
B: Heat shock factor protein 1
E: DNA (5'-D(*GP*GP*TP*TP*CP*TP*AP*GP*AP*AP*CP*C)-3')
F: DNA (5'-D(*GP*GP*TP*TP*CP*TP*AP*GP*AP*AP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8777
Polymers33,6394
Non-polymers2383
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Heat shock factor protein 1
D: Heat shock factor protein 1
G: DNA (5'-D(*GP*GP*TP*TP*CP*TP*AP*GP*AP*AP*CP*C)-3')
H: DNA (5'-D(*GP*GP*TP*TP*CP*TP*AP*GP*AP*AP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6625
Polymers33,6394
Non-polymers231
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.415, 127.367, 55.268
Angle α, β, γ (deg.)90.00, 100.55, 90.00
Int Tables number4
Space group name H-MP1211

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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.: 4 / 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: DNA chain
DNA (5'-D(*GP*GP*TP*TP*CP*TP*AP*GP*AP*AP*CP*C)-3')


Mass: 3662.404 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 708 / 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: 2.1 Å3/Da / Density % sol: 41.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.8
Details: 6%v/v Ethylene glycol, 0.1M citric acid PH3.8, 10%w/v PEG6000.

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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: Dec 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97845 Å / Relative weight: 1
ReflectionResolution: 1.68→41.334 Å / Num. obs: 118571 / % possible obs: 98.38 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 15.68
Reflection shellResolution: 1.68→1.72 Å / Redundancy: 2.64 % / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 3 / Rsym value: 0.477 / % possible all: 88.6

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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: 1.68→41.334 Å / SU ML: 0.18 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 22.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2019 6012 5.07 %
Rwork0.1741 --
obs0.1755 118571 98.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.68→41.334 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3332 972 16 710 5030
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064530
X-RAY DIFFRACTIONf_angle_d0.9436319
X-RAY DIFFRACTIONf_dihedral_angle_d20.0751725
X-RAY DIFFRACTIONf_chiral_restr0.042666
X-RAY DIFFRACTIONf_plane_restr0.005651
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.69910.31581790.26353345X-RAY DIFFRACTION87
1.6991-1.71910.26671870.25453503X-RAY DIFFRACTION90
1.7191-1.740.28711660.25263455X-RAY DIFFRACTION93
1.74-1.76210.26382050.24053647X-RAY DIFFRACTION96
1.7621-1.78530.24872310.23523829X-RAY DIFFRACTION99
1.7853-1.80970.27132130.23433744X-RAY DIFFRACTION100
1.8097-1.83560.25461750.21983835X-RAY DIFFRACTION100
1.8356-1.8630.22161380.21563906X-RAY DIFFRACTION100
1.863-1.89210.24792220.22063768X-RAY DIFFRACTION100
1.8921-1.92310.27311770.21993769X-RAY DIFFRACTION99
1.9231-1.95630.24062040.20083841X-RAY DIFFRACTION100
1.9563-1.99180.20342070.1963834X-RAY DIFFRACTION100
1.9918-2.03010.25322030.18793758X-RAY DIFFRACTION100
2.0301-2.07160.23252120.19633822X-RAY DIFFRACTION99
2.0716-2.11660.24182220.18633768X-RAY DIFFRACTION100
2.1166-2.16590.20431950.18583812X-RAY DIFFRACTION100
2.1659-2.220.25242120.1893822X-RAY DIFFRACTION100
2.22-2.280.23812030.193743X-RAY DIFFRACTION99
2.28-2.34710.21651880.18113805X-RAY DIFFRACTION100
2.3471-2.42290.25662310.17863760X-RAY DIFFRACTION100
2.4229-2.50950.2092070.17243821X-RAY DIFFRACTION100
2.5095-2.60990.1982130.17393818X-RAY DIFFRACTION100
2.6099-2.72870.19072120.18943775X-RAY DIFFRACTION100
2.7287-2.87250.19751700.17473798X-RAY DIFFRACTION100
2.8725-3.05240.22362130.18433862X-RAY DIFFRACTION100
3.0524-3.2880.18752060.15763749X-RAY DIFFRACTION99
3.288-3.61870.15932010.14553795X-RAY DIFFRACTION99
3.6187-4.14190.17222410.14443730X-RAY DIFFRACTION100
4.1419-5.21680.16312060.13153778X-RAY DIFFRACTION99
5.2168-41.34640.16681730.17033667X-RAY DIFFRACTION95
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)
12.053-0.0781-0.16891.0973-0.05832.04320.07190.1849-0.1113-0.1889-0.0125-0.0851-0.01520.11530.00780.150.0016-0.00350.16580.00350.12312.52837.60579.8898
20.4427-0.55390.09071.32470.23030.4238-0.09630.21670.2447-0.41970.0902-1.0686-0.27610.3592-0.0060.2575-0.06420.04680.2723-0.04320.264523.240312.8513.1433
30.8363-0.17230.39660.26160.19810.66040.2294-0.12270.36330.176-0.17940.0018-0.49880.10860.15060.2955-0.0323-0.0170.1945-0.00330.15115.180315.526220.791
40.2962-0.2405-0.10771.0054-0.51080.4691-0.0278-0.1234-0.4570.444-0.08890.4714-0.13510.1974-0.00220.18920.0112-0.01970.18550.02030.18867.37165.952321.6719
50.24130.23660.14630.42250.2810.15450.0811-0.4704-0.4956-0.026-0.3614-0.60270.19860.5012-0.01170.27060.06290.02230.36180.09180.471621.3184-6.107220.1127
60.54030.4223-0.0620.4279-0.29720.60710.08360.0009-0.4405-0.0566-0.01620.00040.1686-0.00760.00660.14250.0168-0.01460.15770.01130.14897.18913.585613.8397
70.8057-0.0289-0.38370.36540.19441.21070.1471-0.13070.4210.0160.26480.0911-0.5988-0.34650.12390.20180.0287-0.02110.2108-0.0060.1913-0.142712.708214.7529
81.7657-0.44441.82411.7692-0.8752.42860.0829-0.1005-0.11270.0513-0.02090.39250.019-0.43820.00120.1528-0.02410.04860.19370.00610.2506-4.621-11.737624.1509
90.2257-0.080.01460.2856-0.00710.0654-0.1635-0.5978-0.19450.21470.01980.8764-0.2145-0.55230.00020.2709-0.02230.06320.40240.05160.3923-2.8652-17.591635.6839
100.2049-0.25480.16670.3621-0.09840.36470.0485-0.0436-0.1913-0.07310.0181-0.18110.38110.16790.00130.2217-0.005-0.00330.16220.00310.27585.2821-20.220328.3528
110.1895-0.09210.13540.1486-0.09010.2441-0.02670.0735-0.1336-0.5249-0.0637-0.5789-0.25180.20220.00050.19110.01320.03310.23060.00860.26297.455-10.544920.8935
120.7504-0.32720.37320.7071-0.28630.4934-0.1356-0.43420.28190.5097-0.06820.1595-0.13490.104-0.00410.28020.0035-0.00650.2446-0.00730.22185.8556-1.169329.5813
130.82550.73450.30130.9429-0.34481.0601-0.13760.3233-0.3438-0.41350.2440.16470.23790.11220.01650.25460.0249-0.00030.2129-0.05820.3008-0.5517-13.151913.7569
141.31971.21830.44451.5658-0.36091.28580.08020.2109-0.13690.0708-0.00370.18530.0665-0.43760.00160.19850.00260.00460.22360.03170.278610.6865-16.357542.9851
151.6957-0.68430.18820.84380.72281.0599-0.2072-0.1921-0.21340.36560.12350.42170.1442-0.2581-0.00110.33440.02560.10780.23330.01850.286110.4629-12.406852.7963
160.3937-0.1226-0.03450.57590.0050.47230.0308-0.4702-0.47270.6156-0.005-0.00860.41290.22220.00420.33450.0750.01580.29070.05580.323819.2828-20.822451.3167
170.73830.81050.17941.22680.52380.166-0.114-0.3683-0.11330.39770.06870.23450.08920.16330.00080.32260.04860.0160.3097-0.02970.203219.7352-2.79554.3915
180.85140.8965-0.19561.06820.29151.2681-0.02450.1793-0.1434-0.40080.1197-0.1511-0.12740.17410.02230.2291-0.0070.02320.282-0.02910.277817.7533-13.822236.5182
191.18840.75790.37151.6748-0.38791.7987-0.18910.2893-0.1317-0.6360.327-0.7615-0.26010.46950.01730.4425-0.09420.12020.3719-0.08450.345328.75988.458536.9728
202.03350.0169-0.03290.7867-0.38550.7605-0.2419-0.38840.85630.13030.6175-1.2328-0.51540.72020.48870.3012-0.13540.02340.4829-0.23580.682734.414613.83346.3326
211.51721.59510.49772.30290.70332.1724-0.09280.15530.0033-0.42690.13420.0784-0.25010.03280.00040.2732-0.0032-0.0310.2502-0.02770.178421.09566.397342.9256
220.85080.08710.1351-0.06220.0511-0.0419-0.09980.07640.03290.0130.01330.10570.0305-0.0240.00010.2274-0.0011-0.01320.2445-0.02750.31072.485428.32823.3083
230.3108-0.3222-0.41390.32740.3774-0.2999-0.4519-0.3189-0.3640.0470.1970.00720.05220.0687-0.07170.1820.01180.04480.19540.00770.28152.179229.922823.4886
241.1058-0.3966-0.34770.9843-0.08630.0725-0.5187-0.3501-0.3315-0.03920.11870.0774-0.0801-0.009300.3977-0.0147-0.01430.42020.00080.4020.639-34.755.711
251.35630.571-0.46480.94230.44770.389-0.2946-0.20990.02280.15230.0182-0.0491-0.0308-0.0715-0.00610.4868-0.0336-0.12130.46570.01380.5278-0.119-36.09656.251
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 14 through 48 )
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 60 )
3X-RAY DIFFRACTION3chain 'A' and (resid 61 through 75 )
4X-RAY DIFFRACTION4chain 'A' and (resid 76 through 81 )
5X-RAY DIFFRACTION5chain 'A' and (resid 82 through 95 )
6X-RAY DIFFRACTION6chain 'A' and (resid 96 through 108 )
7X-RAY DIFFRACTION7chain 'A' and (resid 109 through 118 )
8X-RAY DIFFRACTION8chain 'B' and (resid 13 through 48 )
9X-RAY DIFFRACTION9chain 'B' and (resid 49 through 60 )
10X-RAY DIFFRACTION10chain 'B' and (resid 61 through 75 )
11X-RAY DIFFRACTION11chain 'B' and (resid 76 through 81 )
12X-RAY DIFFRACTION12chain 'B' and (resid 82 through 100 )
13X-RAY DIFFRACTION13chain 'B' and (resid 101 through 118 )
14X-RAY DIFFRACTION14chain 'C' and (resid 12 through 37 )
15X-RAY DIFFRACTION15chain 'C' and (resid 38 through 60 )
16X-RAY DIFFRACTION16chain 'C' and (resid 61 through 76 )
17X-RAY DIFFRACTION17chain 'C' and (resid 77 through 100 )
18X-RAY DIFFRACTION18chain 'C' and (resid 101 through 118 )
19X-RAY DIFFRACTION19chain 'D' and (resid 14 through 48 )
20X-RAY DIFFRACTION20chain 'D' and (resid 49 through 75 )
21X-RAY DIFFRACTION21chain 'D' and (resid 76 through 118 )
22X-RAY DIFFRACTION22chain 'E' and (resid 1 through 12 )
23X-RAY DIFFRACTION23chain 'F' and (resid 1 through 12 )
24X-RAY DIFFRACTION24chain 'G' and (resid 1 through 12 )
25X-RAY DIFFRACTION25chain 'H' and (resid 1 through 12 )

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