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- PDB-7dcj: Crystal structure of HSF1 DNA-binding domain in complex with 2-si... -

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Basic information

Entry
Database: PDB / ID: 7dcj
TitleCrystal structure of HSF1 DNA-binding domain in complex with 2-site HSE DNA in the head-to-head orientation
Components
  • DNA (5'-D(*GP*CP*CP*GP*AP*AP*TP*AP*TP*TP*CP*GP*G)-3')
  • Heat shock factor protein 1
KeywordsDNA BINDING PROTEIN/DNA / DNA BINDING PROTEIN-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 / positive regulation of stress granule assembly / response to peptide / cellular response to sodium arsenite ...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 / positive regulation of stress granule assembly / response to peptide / cellular response to sodium arsenite / translation elongation factor binding / negative regulation of inclusion body assembly / positive regulation of inclusion body assembly / nuclear stress granule / positive regulation of macrophage differentiation / 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 / STAT family protein binding / response to psychosocial stress / cellular response to cadmium ion / mitotic spindle pole / response to testosterone / general transcription initiation factor binding / cellular response to angiotensin / Regulation of HSF1-mediated heat shock response / HSF1-dependent transactivation / mRNA transport / cellular response to unfolded protein / Mitochondrial unfolded protein response (UPRmt) / HSF1 activation / negative regulation of protein-containing complex assembly / Attenuation phase / heterochromatin / regulation of cellular response to heat / cellular response to copper ion / heat shock protein binding / response to nutrient / positive regulation of mitotic cell cycle / positive regulation of DNA-binding transcription factor activity / positive regulation of apoptotic signaling pathway / response to activity / promoter-specific chromatin binding / cellular response to estradiol stimulus / Hsp90 protein binding / defense response / euchromatin / cellular response to gamma radiation / PML body / kinetochore / chromatin DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / cellular response to hydrogen peroxide / mRNA processing / Aggrephagy / sequence-specific double-stranded DNA binding / MAPK cascade / cellular response to xenobiotic stimulus / positive regulation of cold-induced thermogenesis / cellular response to heat / cellular response to lipopolysaccharide / DNA-binding transcription activator activity, RNA polymerase II-specific / protein-containing complex assembly / 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 / protein heterodimerization activity / DNA-binding transcription factor activity / ribonucleoprotein complex / negative regulation of gene expression / 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 DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
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 / Resolution: 2.004 Å
AuthorsFeng, N. / Liu, W.
CitationJournal: Iscience / Year: 2021
Title: Structures of heat shock factor trimers bound to DNA.
Authors: Feng, N. / Feng, H. / Wang, S. / Punekar, A.S. / Ladenstein, R. / Wang, D.C. / Zhang, Q. / Ding, J. / Liu, W.
History
DepositionOct 26, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 15, 2021Group: Database references / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / database_2
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
C: DNA (5'-D(*GP*CP*CP*GP*AP*AP*TP*AP*TP*TP*CP*GP*G)-3')
D: DNA (5'-D(*GP*CP*CP*GP*AP*AP*TP*AP*TP*TP*CP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0366
Polymers34,9904
Non-polymers462
Water5,531307
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-30 kcal/mol
Surface area14330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.221, 62.765, 97.345
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 15 through 93 or resid 96 through 118))
21(chain B and (resid 15 through 82 or resid 85 or resid 96 through 118))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALGLUGLU(chain A and (resid 15 through 93 or resid 96 through 118))AA15 - 938 - 86
12ASPASPLYSLYS(chain A and (resid 15 through 93 or resid 96 through 118))AA96 - 11889 - 111
21VALVALVALVAL(chain B and (resid 15 through 82 or resid 85 or resid 96 through 118))BB15 - 828 - 75
22GLUGLUGLUGLU(chain B and (resid 15 through 82 or resid 85 or resid 96 through 118))BB8578
23ASPASPLYSLYS(chain B and (resid 15 through 82 or resid 85 or resid 96 through 118))BB96 - 11889 - 111

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Components

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


Mass: 13214.025 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSF1, HSTF1 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q00613
#2: DNA chain DNA (5'-D(*GP*CP*CP*GP*AP*AP*TP*AP*TP*TP*CP*GP*G)-3')


Mass: 4280.792 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.93 Å3/Da / Density % sol: 36.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris-HCl, pH 7.8 and 28% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→35.032 Å / Num. obs: 17803 / % possible obs: 99.8 % / Redundancy: 6 % / Rpim(I) all: 0.054 / Net I/σ(I): 15.5
Reflection shellResolution: 2→2.03 Å / Rpim(I) all: 0.232

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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: 5HDG

5hdg


Resolution: 2.004→35.032 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2215 910 5.11 %
Rwork0.1829 16893 -
obs0.1848 17803 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.92 Å2 / Biso mean: 28.3952 Å2 / Biso min: 12.94 Å2
Refinement stepCycle: final / Resolution: 2.004→35.032 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1685 530 2 307 2524
Biso mean--21.41 35.83 -
Num. residues----230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062328
X-RAY DIFFRACTIONf_angle_d0.8743253
X-RAY DIFFRACTIONf_chiral_restr0.045345
X-RAY DIFFRACTIONf_plane_restr0.005329
X-RAY DIFFRACTIONf_dihedral_angle_d16.4671269
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A852X-RAY DIFFRACTION7.498TORSIONAL
12B852X-RAY DIFFRACTION7.498TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.004-2.12940.25741470.2291268997
2.1294-2.29370.2261640.199274899
2.2937-2.52450.251530.1951280699
2.5245-2.88970.24371630.2051278199
2.8897-3.64010.22181590.173285499
3.6401-6.560.18541240.1641301599
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)
10.13790.0766-0.10080.07730.07340.1383-0.12330.27750.0994-0.14120.23780.15670.1071-0.3541-0.00020.1997-0.0099-0.02810.2080.0170.178511.773845.9215-40.7194
20.59120.44590.23670.425-0.11340.5239-0.01560.19180.1131-0.22890.00520.104-0.03930.1656-0.00030.1949-0.01560.00630.20380.02590.182122.530552.0949-42.9338
30.47940.5565-0.19940.4533-0.0730.0909-0.0675-0.3915-0.04670.0051-0.0410.01510.02070.0964-0.00520.2188-0.00180.04780.20120.00550.16617.147751.7246-29.5567
40.14650.0772-0.07720.01070.00710.080.159-0.2069-0.13360.3511-0.27820.05940.2281-0.3821-0.00270.1856-0.0074-0.01050.1699-0.00530.150618.659539.7197-32.8406
50.9741-0.4105-0.0571.2032-0.87380.70010.03320.1466-0.0047-0.08090.0582-0.267-0.10780.1689-0.00030.17560.0027-0.00430.1919-0.01840.258624.761143.5093-42.1598
60.52180.3022-0.0210.2322-0.11850.42430.01980.0168-0.0708-0.1956-0.22190.4030.4571-0.0780.00030.239-0.0095-0.00960.32050.00850.256111.236936.5488-44.7837
70.0606-0.014-0.0533-0.01590.013-0.01130.2075-0.2819-0.4320.4182-0.22450.0028-0.40170.0941-0.00020.3512-0.04520.03230.31470.00480.303117.710932.5451-10.8526
80.40540.21560.10850.3837-0.16670.21060.0437-0.160.23360.0184-0.03470.0164-0.30610.20540.00020.23350.00110.02070.1972-0.01540.1872.142646.2655-5.1265
90.4072-0.0558-0.20330.06360.15160.15080.28140.049-0.10420.29160.1630.7937-0.3375-0.4380.01140.27480.0270.08090.2175-0.01230.3029-7.033443.5668-2.7879
100.366-0.3199-0.32190.56010.6171.03720.08380.02210.4011-0.2276-0.0338-0.0501-0.8689-0.05480.00450.32860.04710.0270.24540.01530.28870.445150.0428-15.935
110.0549-0.0209-0.02710.0001-0.05380.1008-0.01470.30690.1668-0.12490.0191-0.07370.1206-0.12470.00030.2280.00710.03210.20770.00310.2011-1.59538.2614-16.6939
120.16-0.13280.25030.3051-0.12760.45050.13120.7108-0.44190.0568-0.26740.25370.0771-0.46080.00050.2211-0.0004-0.00510.2603-0.05650.2633-10.432934.9559-7.7853
130.1555-0.09790.0789-0.0325-0.00040.0513-0.3491-0.13190.52980.03530.2395-0.1558-0.1656-0.1529-0.00180.2957-0.01410.06520.34080.00360.3695-20.174342.8919-5.5663
140.3361-0.1378-0.01530.4192-0.1970.1708-0.3031-0.60290.21170.2080.323-0.2130.09620.01-0.00050.23940.05470.00190.24440.02190.28513.547134.3848-0.5914
150.0751-0.0722-0.05720.06690.08370.0544-0.11330.5071-0.2347-0.07570.44730.17370.74930.31650.0050.3882-0.02020.08440.3842-0.00770.31335.319928.9621-14.7763
160.1567-0.4244-0.09942.1604-0.03341.9876-0.19150.0229-0.09850.130.03470.05410.0954-0.0501-0.14560.1359-0.0594-0.02060.1810.0020.17939.858734.293-26.4977
170.65780.9785-0.61721.7389-0.34411.4687-0.1724-0.0474-0.0465-0.06040.00310.17180.15770.0075-0.28570.19790.02670.05160.1494-0.01630.184710.383933.5721-24.535
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 27 )A15 - 27
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 48 )A28 - 48
3X-RAY DIFFRACTION3chain 'A' and (resid 49 through 65 )A49 - 65
4X-RAY DIFFRACTION4chain 'A' and (resid 66 through 76 )A66 - 76
5X-RAY DIFFRACTION5chain 'A' and (resid 77 through 108 )A77 - 108
6X-RAY DIFFRACTION6chain 'A' and (resid 109 through 118 )A109 - 118
7X-RAY DIFFRACTION7chain 'B' and (resid 8 through 16 )B8 - 16
8X-RAY DIFFRACTION8chain 'B' and (resid 17 through 37 )B17 - 37
9X-RAY DIFFRACTION9chain 'B' and (resid 38 through 48 )B38 - 48
10X-RAY DIFFRACTION10chain 'B' and (resid 49 through 65 )B49 - 65
11X-RAY DIFFRACTION11chain 'B' and (resid 66 through 75 )B66 - 75
12X-RAY DIFFRACTION12chain 'B' and (resid 76 through 85 )B76 - 85
13X-RAY DIFFRACTION13chain 'B' and (resid 86 through 99 )B86 - 99
14X-RAY DIFFRACTION14chain 'B' and (resid 100 through 114 )B100 - 114
15X-RAY DIFFRACTION15chain 'B' and (resid 115 through 120 )B115 - 120
16X-RAY DIFFRACTION16chain 'C' and (resid 1 through 13 )C1 - 13
17X-RAY DIFFRACTION17chain 'D' and (resid 2 through 14 )D2 - 14

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