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- PDB-2hzd: NMR structure of the DNA-binding TEA domain and insights into TEF... -

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Basic information

Entry
Database: PDB / ID: 2hzd
TitleNMR structure of the DNA-binding TEA domain and insights into TEF-1 function
ComponentsTranscriptional enhancer factor TEF-1
KeywordsGENE REGULATION / DNA-BINDING / HELIX-TURN-HELIX
Function / homology
Function and homology information


TEAD-YAP complex / RUNX3 regulates YAP1-mediated transcription / YAP1- and WWTR1 (TAZ)-stimulated gene expression / hippo signaling / EGR2 and SOX10-mediated initiation of Schwann cell myelination / embryonic organ development / positive regulation of miRNA transcription / sequence-specific double-stranded DNA binding / positive regulation of cell growth / protein-containing complex assembly ...TEAD-YAP complex / RUNX3 regulates YAP1-mediated transcription / YAP1- and WWTR1 (TAZ)-stimulated gene expression / hippo signaling / EGR2 and SOX10-mediated initiation of Schwann cell myelination / embryonic organ development / positive regulation of miRNA transcription / sequence-specific double-stranded DNA binding / positive regulation of cell growth / protein-containing complex assembly / transcription regulator complex / 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 DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus
Similarity search - Function
TEA/ATTS domain / TEA/ATTS domain / Transcriptional enhancer factor, metazoa / TEA/ATTS domain superfamily / TEA/ATTS domain / TEA domain signature. / TEA domain profile. / TEA domain / YAP binding domain / YAP binding domain ...TEA/ATTS domain / TEA/ATTS domain / Transcriptional enhancer factor, metazoa / TEA/ATTS domain superfamily / TEA/ATTS domain / TEA domain signature. / TEA domain profile. / TEA domain / YAP binding domain / YAP binding domain / Arc Repressor Mutant, subunit A / Helix non-globular / Special
Similarity search - Domain/homology
Transcriptional enhancer factor TEF-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsAnbanandam, A. / Veeraraghavan, S.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Insights into transcription enhancer factor 1 (TEF-1) activity from the solution structure of the TEA domain.
Authors: Anbanandam, A. / Albarado, D.C. / Nguyen, C.T. / Halder, G. / Gao, X. / Veeraraghavan, S.
History
DepositionAug 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional enhancer factor TEF-1


Theoretical massNumber of molelcules
Total (without water)9,5491
Polymers9,5491
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Transcriptional enhancer factor TEF-1 / TEA domain family member 1 / TEAD-1 / Protein GT-IIC / Transcription factor 13 / NTEF-1


Mass: 9548.997 Da / Num. of mol.: 1 / Fragment: N-TERMINAL TEA DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TEAD1, TCF13, TEF1 / Plasmid: PET21D / Production host: Escherichia coli (E. coli) / References: UniProt: P28347

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
NMR detailsText: 3D TRIPLE RESONANCE EXPERIMENTS

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Sample preparation

DetailsContents: 1.3 mM TEA U-15N, 13C, 100 mM phosphate buffer, 95% H2O, 5% D2O
Solvent system: 100 mM phosphate buffer, 95% H2O, 5% D2O
Sample conditionsIonic strength: 100 mM NaCl / pH: 5.85 / Pressure: 1 atm / Temperature: 285 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR softwareName: CNS / Version: 1.1 / Developer: BRUNGER / Classification: refinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 25

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