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- PDB-7dcu: Crystal structure of HSF2 DNA-binding domain in complex with 3-si... -

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Basic information

Entry
Database: PDB / ID: 7dcu
TitleCrystal structure of HSF2 DNA-binding domain in complex with 3-site HSE DNA (21 bp)
Components
  • DNA (5'-D(*AP*CP*CP*GP*CP*GP*AP*AP*TP*AP*TP*TP*CP*TP*AP*GP*AP*AP*CP*GP*C)-3')
  • DNA (5'-D(*TP*GP*CP*GP*TP*TP*CP*TP*AP*GP*AP*AP*TP*AP*TP*TP*CP*GP*CP*GP*G)-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 / 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 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: 1.75 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 27, 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 / pdbx_initial_refinement_model

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


Theoretical massNumber of molelcules
Total (without water)53,3418
Polymers53,2725
Non-polymers693
Water7,891438
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7970 Å2
ΔGint-51 kcal/mol
Surface area20260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.640, 67.060, 139.650
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

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


Mass: 13462.236 Da / Num. of mol.: 3 / 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 K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q03933
#2: DNA chain DNA (5'-D(*TP*GP*CP*GP*TP*TP*CP*TP*AP*GP*AP*AP*TP*AP*TP*TP*CP*GP*CP*GP*G)-3')


Mass: 6469.181 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: DNA chain DNA (5'-D(*AP*CP*CP*GP*CP*GP*AP*AP*TP*AP*TP*TP*CP*TP*AP*GP*AP*AP*CP*GP*C)-3')


Mass: 6416.175 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: DNA satellites (virus)
#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 / Water


Mass: 18.015 Da / Num. of mol.: 438 / 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: 2.06 Å3/Da / Density % sol: 40.19 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES pH 7.5 and 25% (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: 0.9774 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.75→69.83 Å / Num. obs: 44148 / % possible obs: 98 % / Redundancy: 10.4 % / Rpim(I) all: 0.033 / Net I/σ(I): 13.5
Reflection shellResolution: 1.75→1.84 Å / Rpim(I) all: 0.401

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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: 1.75→69.825 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2046 2232 5.06 %
Rwork0.1721 41916 -
obs0.1738 44148 97.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.46 Å2 / Biso mean: 31.9455 Å2 / Biso min: 12.88 Å2
Refinement stepCycle: final / Resolution: 1.75→69.825 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2499 855 3 438 3795
Biso mean--28.49 38.11 -
Num. residues----337
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073527
X-RAY DIFFRACTIONf_angle_d0.9694937
X-RAY DIFFRACTIONf_chiral_restr0.053523
X-RAY DIFFRACTIONf_plane_restr0.005487
X-RAY DIFFRACTIONf_dihedral_angle_d15.2631922
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.75-1.78810.27041020.2393218282
1.7881-1.82970.26471350.2323234790
1.8297-1.87540.26721260.2236253596
1.8754-1.92620.27581340.2219262399
1.9262-1.98280.22871220.19792645100
1.9828-2.04680.22241360.18592670100
2.0468-2.120.20961270.17892650100
2.12-2.20490.21651590.17652638100
2.2049-2.30520.21921510.1752627100
2.3052-2.42680.18971300.1762674100
2.4268-2.57880.21551590.17482673100
2.5788-2.7780.20291500.18292654100
2.778-3.05750.23481490.19052683100
3.0575-3.49990.18571390.15882694100
3.4999-4.40950.18191410.13872759100
4.4095-69.820.18161720.16192862100
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)
10.00290.00710.00230.01260.00910.0077-0.1603-0.3150.27630.2150.01590.0019-0.22560.0633-0.00080.7088-0.12850.09950.4579-0.05890.4252-4.2086-18.860429.7167
20.01030.0021-0.00810.01080.00930.0122-0.0034-0.18420.1778-0.01450.11980.0572-0.00420.145100.19720.0193-0.00030.1941-0.03310.1893-6.5846-26.130931.8531
30.04150.01510.02380.05090.0290.0766-0.0996-0.26030.05620.3075-0.0415-0.09670.03940.0213-0.00080.28740.0998-0.0190.4143-0.02460.2455-6.5426-32.992939.65
40.0555-0.0172-0.02950.00350.00660.02470.026-0.1374-0.08620.1024-0.05830.10920.0381-0.2210.00090.20140.02750.00530.3090.02510.1941-17.1836-32.59935.2733
50.017-0.00050.02760.008-0.00350.0386-0.0368-0.08010.0477-0.04220.03720.03520.0146-0.051800.17750.0306-0.00110.18130.01510.1666-15.225-31.690524.4278
60.03590.03030.03960.06640.0120.04240.0354-0.1353-0.0949-0.0018-0.015-0.0840.18170.0183-0.00050.22140.00070.01050.23450.02050.2042-7.9661-40.429328.0498
70.0372-0.01780.02940.14690.00330.02750.0369-0.2578-0.0561-0.04620.1745-0.14030.09330.44880.03570.17790.0142-0.00540.3289-0.03830.1887-0.3632-35.135630.6007
80.0985-0.2462-0.01430.64240.02380.00420.12020.22070.113-0.354-0.03830.0035-0.16110.18570.01470.2493-0.0810.03270.3476-0.02520.22680.2-28.116521.5724
90.17550.0477-0.13420.1119-0.10620.1345-0.0577-0.2427-0.03160.1415-0.00690.09450.1233-0.3043-00.2078-0.00260.02010.292-0.00030.2023-36.6629-45.208424.4965
100.0445-0.0274-0.00160.02540.01390.01950.0518-0.1334-0.1735-0.05330.03140.04520.1093-0.08270.00020.1662-0.00730.0210.170.02220.2095-25.9052-48.369223.8886
110.32390.04220.20340.05220.07770.20170.0963-0.05530.06280.08840.13720.029-0.219-0.06090.1380.24770.03280.08050.1602-0.0180.2154-31.5287-36.415415.6888
120.00870.00320.0030.00110.00080.00060.0196-0.03630.08510.00210.0086-0.0503-0.03920.02460.00020.69120.21840.10170.7694-0.05360.6078-29.7631-26.933528.8193
130.05410.07620.03120.11550.07830.13660.00840.1972-0.06250.0892-0.0637-0.03360.1611-0.3096-0.0040.1674-0.01990.00970.2928-0.06320.2285-35.3485-47.318912.1623
140.0060.0038-0.00050.0152-0.01020.00870.06010.0004-0.043-0.19980.161-0.01730.0482-0.3511-0.00010.2640.0175-0.02840.2964-0.00260.1934-34.8643-21.345611.6794
150.0992-0.0342-0.06890.1410.10390.1052-0.1986-0.31350.05670.0215-0.08870.3756-0.1689-0.3528-0.05730.32390.1356-0.02640.5381-0.08430.2899-40.7308-11.058513.1068
160.1915-0.0156-0.05060.1514-0.04730.0368-0.112-0.0172-0.07130.1628-0.05460.1097-0.1455-0.0937-0.03030.31240.0533-0.00970.2769-0.06360.2492-30.0909-13.553222.2213
170.01260.0040.01330.02670.02850.0338-0.13070.04180.1328-0.10640.0449-0.1128-0.25010.1269-0.00010.32470.0566-0.02550.2156-0.00820.2384-27.592-10.98468.6047
180.01060.00460.00740.0074-0.00660.0144-0.05560.092-0.006-0.0915-0.1620.2318-0.0406-0.1611-0.00010.29450.0292-0.01230.3495-0.06050.2337-37.3238-16.90081.8536
190.00850.00430.00060.0270.01220.01510.05080.1496-0.2155-0.00430.09150.08750.19920.163700.25970.0321-0.03510.2721-0.00590.2177-30.3947-23.54872.1806
200.31680.032-0.14110.0098-0.03430.39180.0730.0096-0.1316-0.2708-0.1576-0.07490.06740.0427-0.03840.20660.0404-0.00520.1331-0.01330.206-17.3164-41.809114.6593
211.92551.5485-0.3191.361-0.47850.47190.14-0.32750.2741-0.0331-0.2121-0.2786-0.45450.1168-0.17040.3739-0.0505-0.00370.11180.05420.3725-11.592-7.308312.8125
220.0117-0.041-0.01280.39950.10580.0272-0.06660.00820.05980.0108-0.12910.0920.0404-0.1714-0.18780.786-0.0146-0.2043-0.1368-0.33670.8714-19.0009-4.26869.8045
230.3444-0.0202-0.0520.0280.01090.09610.05650.038-0.0622-0.1456-0.1675-0.0386-0.00660.0403-0.01340.1960.02390.02750.16390.02820.2187-14.3335-36.945314.8592
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 8 )A1 - 8
2X-RAY DIFFRACTION2chain 'A' and (resid 9 through 19 )A9 - 19
3X-RAY DIFFRACTION3chain 'A' and (resid 20 through 35 )A20 - 35
4X-RAY DIFFRACTION4chain 'A' and (resid 36 through 52 )A36 - 52
5X-RAY DIFFRACTION5chain 'A' and (resid 53 through 67 )A53 - 67
6X-RAY DIFFRACTION6chain 'A' and (resid 68 through 88 )A68 - 88
7X-RAY DIFFRACTION7chain 'A' and (resid 89 through 100 )A89 - 100
8X-RAY DIFFRACTION8chain 'A' and (resid 101 through 112 )A101 - 112
9X-RAY DIFFRACTION9chain 'B' and (resid 7 through 47 )B7 - 47
10X-RAY DIFFRACTION10chain 'B' and (resid 48 through 67 )B48 - 67
11X-RAY DIFFRACTION11chain 'B' and (resid 68 through 77 )B68 - 77
12X-RAY DIFFRACTION12chain 'B' and (resid 78 through 86 )B78 - 86
13X-RAY DIFFRACTION13chain 'B' and (resid 87 through 112 )B87 - 112
14X-RAY DIFFRACTION14chain 'C' and (resid 7 through 19 )C7 - 19
15X-RAY DIFFRACTION15chain 'C' and (resid 20 through 40 )C20 - 40
16X-RAY DIFFRACTION16chain 'C' and (resid 41 through 57 )C41 - 57
17X-RAY DIFFRACTION17chain 'C' and (resid 58 through 91 )C58 - 91
18X-RAY DIFFRACTION18chain 'C' and (resid 92 through 100 )C92 - 100
19X-RAY DIFFRACTION19chain 'C' and (resid 101 through 111 )C101 - 111
20X-RAY DIFFRACTION20chain 'D' and (resid 0 through 14 )D0 - 14
21X-RAY DIFFRACTION21chain 'D' and (resid 15 through 20 )D15 - 20
22X-RAY DIFFRACTION22chain 'E' and (resid 0 through 4 )E0 - 4
23X-RAY DIFFRACTION23chain 'E' and (resid 5 through 20 )E5 - 20

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