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- PDB-2ldu: Solution NMR Structure of Heat shock factor protein 1 DNA binding... -

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Basic information

Entry
Database: PDB / ID: 2ldu
TitleSolution NMR Structure of Heat shock factor protein 1 DNA binding domain from homo sapiens, Northeast Structural Genomics Consortium Target HR3023C
ComponentsHeat shock factor protein 1
KeywordsCHAPERONE / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) / DNA-binding / PSI-Biology / Protein Structure Initiative
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 stress granule assembly / response to peptide / positive regulation of apoptotic DNA fragmentation / negative regulation of inclusion body assembly ...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 stress granule assembly / response to peptide / positive regulation of apoptotic DNA fragmentation / negative regulation of inclusion body assembly / positive regulation of inclusion body assembly / cellular response to sodium arsenite / translation elongation factor binding / nuclear stress granule / positive regulation of macrophage differentiation / cellular response to potassium ion / cellular response to angiotensin / 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 / mitotic spindle pole / response to testosterone / general transcription initiation factor binding / HSF1-dependent transactivation / cellular response to unfolded protein / HSF1 activation / Regulation of HSF1-mediated heat shock response / Attenuation phase / mRNA transport / negative regulation of protein-containing complex assembly / heterochromatin / regulation of cellular response to heat / positive regulation of tyrosine phosphorylation of STAT protein / heat shock protein binding / cellular response to copper ion / cellular response to cadmium ion / positive regulation of mitotic cell cycle / response to nutrient / response to activity / cellular response to estradiol stimulus / promoter-specific chromatin binding / positive regulation of DNA-binding transcription factor activity / Hsp90 protein binding / euchromatin / cellular response to gamma radiation / PML body / chromatin DNA binding / kinetochore / DNA-binding transcription repressor activity, RNA polymerase II-specific / defense response / cellular response to hydrogen peroxide / Aggrephagy / mRNA processing / 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 / protein-containing complex assembly / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / protein heterodimerization activity / ribonucleoprotein complex / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / DNA repair / centrosome / positive regulation of gene expression / chromatin / regulation of transcription by RNA polymerase II / protein kinase binding / 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 / 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-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily ...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-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
Heat shock factor protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry, molecular dynamics, simulated annealing, torsion angle dynamics
Model detailslowest energy, model 1
AuthorsLiu, G. / Xiao, R. / Ciccosanti, C. / Janjua, H. / Acton, T.B. / Lee, H. / Wang, H.B. / Huang, Y.B. / Everett, J.K. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target HR3023C
Authors: Liu, G. / Xiao, R. / Ciccosanti, C. / Janjua, H. / Acton, T.B. / Wang, H. / Lee, H.B. / Huang, Y.T. / Everett, J.K. / Montelione, G.T.
History
DepositionJun 1, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2012Group: Structure summary
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heat shock factor protein 1


Theoretical massNumber of molelcules
Total (without water)14,4011
Polymers14,4011
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

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


Mass: 14401.355 Da / Num. of mol.: 1 / Fragment: DNA binding region, residues 10-123
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSF1, HSF1_HUMAN, HSTF1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q00613

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1313D HNCO
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D 1H-13C arom NOESY
1713D simutaneous 13C-aromatic, 13C-aliphatic, 15N edited 1H-1H NOESY
1812D 1H-13C HSQC aromatic
1932D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.51 mM [U-100% 13C; U-100% 15N] HR3023C, 95% H2O/5% D2O95% H2O/5% D2O
20.43 mM [U-100% 13C; U-100% 15N] HR3023C, 95% H2O/5% D2O95% H2O/5% D2O
30.8 mM [U-100% 13C; U-100% 15N] HR3023C, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.51 mMHR3023C-1[U-100% 13C; U-100% 15N]1
0.43 mMHR3023C-2[U-100% 13C; U-100% 15N]2
0.8 mMHR3023C-3[U-100% 13C; U-100% 15N]3
0.8 mMHR3023C-4[U-100% 13C; U-100% 15N]4
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA6003

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinemen,structure solution,geometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement,geometry optimization,structure solution
AutoStructure2.1Huang, Tejero, Powers and Montelionedata analysis,refinement
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionedata analysis,chemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASYBartels et al.data analysis,peak picking,chemical shift assignment
TopSpinBruker Biospincollection
VnmrJVariancollection
SparkyGoddarddata analysis
TALOS+Shen, Cornilescu, Delaglio and Baxgeometry optimization
CYANArefinement,geometry optimization,structure solutionrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: distance geometry, molecular dynamics, simulated annealing, torsion angle dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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