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- PDB-2h7b: Solution structure of the eTAFH domain from the human leukemia-as... -

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Basic information

Entry
Database: PDB / ID: 2h7b
TitleSolution structure of the eTAFH domain from the human leukemia-associated fusion protein AML1-ETO
ComponentsCore-binding factor, ML1-ETO
KeywordsTRANSCRIPTION / 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 / calcium ion binding / 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. / EF hand / Four Helix Bundle (Hemerythrin (Met), subunit A) / EF-hand domain pair / EF-hand, calcium binding motif / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Protein CBFA2T1 / Calmodulin, putative
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsPlevin, M.J. / Zhang, J. / Guo, C. / Roeder, R.G. / Ikura, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2006
Title: The acute myeloid leukemia fusion protein AML1-ETO targets E proteins via a paired amphipathic helix-like TBP-associated factor homology domain
Authors: Plevin, M.J. / Zhang, J. / Guo, C. / Roeder, R.G. / Ikura, M.
History
DepositionJun 1, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2006Provider: 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: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 29, 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: Core-binding factor, ML1-ETO


Theoretical massNumber of molelcules
Total (without water)11,8881
Polymers11,8881
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 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Core-binding factor, ML1-ETO / runt domain / alpha subunit 2 / translocated to 1 / cyclin D-related


Mass: 11887.721 Da / Num. of mol.: 1 / Fragment: residues 83-185, / Mutation: C169A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ETO / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta / References: UniProt: Q7Z4J5, UniProt: Q06455*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
1214D 13C/15N-separated NOESY
NMR detailsText: This entry is the solution conformation of eTAFH bound to 17 residue AD1 peptide from human HEB. Structure of the bound AD1 peptide was not determined due to chemical exchange broadening of ...Text: This entry is the solution conformation of eTAFH bound to 17 residue AD1 peptide from human HEB. Structure of the bound AD1 peptide was not determined due to chemical exchange broadening of resonances from this molecule

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Sample preparation

DetailsContents: 0.7 mM eTAFH U-15N, 13C, 20 mM sodium phosphate, pH 6.0, 50 mM NaCl, 1mM PMSF, 1mM AEBSF, 0.25 mM sodium azide, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 70 mM / pH: 6 / Pressure: AMBIENT / Temperature: 25 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
Varian UNITYPLUSVarianUNITYPLUS5001
Varian UNITYPLUSVarianUNITYPLUS6002
Varian UNITYPLUSVarianUNITYPLUS8003

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Processing

NMR software
NameDeveloperClassification
CYANAGUNTERT, P. ET AL.refinement
CYANAGUNTERT, P. ET AL.structure solution
RefinementMethod: 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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