[English] 日本語
Yorodumi
- PDB-7dcj: Crystal structure of HSF1 DNA-binding domain in complex with 2-si... -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / embryonic placenta development / mRNA transport / 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 / Hsp90 protein binding / cellular response to estradiol stimulus / 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 / cytoplasm / cytosol
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more