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- PDB-2pp4: Solution Structure of ETO-TAFH refined in explicit solvent -

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Basic information

Entry
Database: PDB / ID: 2pp4
TitleSolution Structure of ETO-TAFH refined in explicit solvent
ComponentsProtein ETO
KeywordsTRANSCRIPTION / transcriptional cofactor / Leukemia / 4-helix bundle
Function / homology
Function and homology information


negative regulation of fat cell differentiation / nuclear matrix / transcription corepressor activity / DNA-binding transcription factor binding / negative regulation of DNA-templated transcription / DNA-templated transcription / DNA binding / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
TAFH/NHR1 domain / Protein CBFA2T1 / CBFA2T family / NHR2-like / NHR2 domain like / TAFH/NHR1 domain superfamily / NHR1 homology to TAF / TAFH/NHR1 domain profile. / TAF homology / TAFH/NHR1 ...TAFH/NHR1 domain / Protein CBFA2T1 / CBFA2T family / NHR2-like / NHR2 domain like / TAFH/NHR1 domain superfamily / NHR1 homology to TAF / TAFH/NHR1 domain profile. / TAF homology / TAFH/NHR1 / MYND finger / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsWei, Y. / Liu, S. / Lausen, J. / Woodrell, C. / Cho, S. / Biris, N. / Kobayashi, N. / Yokoyama, S. / Werner, M.H.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2007
Title: A TAF4-homology domain from the corepressor ETO is a docking platform for positive and negative regulators of transcription
Authors: Wei, Y. / Liu, S. / Lausen, J. / Woodrell, C. / Cho, S. / Biris, N. / Kobayashi, N. / Wei, Y. / Yokoyama, S. / Werner, M.H.
History
DepositionApr 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: 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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein ETO


Theoretical massNumber of molelcules
Total (without water)12,1381
Polymers12,1381
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein ETO / Protein CBFA2T1 / Protein MTG8 / Eight twenty one protein / Cyclin-D-related protein / Zinc finger ...Protein CBFA2T1 / Protein MTG8 / Eight twenty one protein / Cyclin-D-related protein / Zinc finger MYND domain- containing protein 2


Mass: 12137.994 Da / Num. of mol.: 1 / Fragment: TAFH domain, residues 119-225 / Mutation: F136Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RUNX1T1, AML1T1, CBFA2T1, CDR, ETO, MTG8, ZMYND2 / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q06455

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY

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Sample preparation

DetailsContents: 1.1 mM protein, 200 mM phosphate buffer, 95% H2O, 5% D2O
Solvent system: 95% H2O/5% D2O
Sample conditionspH: 6.8 / Pressure: ambient / Temperature: 293 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 AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE9002

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Processing

NMR softwareName: XPLOR-NIH / Version: 2.14 / Developer: Schwieters, C.D. / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: the structures are based on 1644 NOE-derived distance constraints, 236 dihedral angle restraints,m106 distance restraints from hydrogen bonds, and 96 residual dipolar coupling restraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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