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- PDB-2knh: The Solution structure of the eTAFH domain of AML1-ETO complexed ... -

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Basic information

Entry
Database: PDB / ID: 2knh
TitleThe Solution structure of the eTAFH domain of AML1-ETO complexed with HEB peptide
Components
  • Protein CBFA2T1
  • Transcription factor 12
KeywordsTRANSCRIPTION REGULATOR / AML1-ETO / eTAFH / HEB / DNA-binding / Metal-binding / Nucleus / Proto-oncogene / Transcription / Transcription regulation / Zinc-finger / Developmental protein / Phosphoprotein
Function / homology
Function and homology information


response to gonadotropin-releasing hormone / cAMP response element binding / HMG box domain binding / bHLH transcription factor binding / NGF-stimulated transcription / muscle organ development / negative regulation of fat cell differentiation / Myogenesis / E-box binding / SMAD binding ...response to gonadotropin-releasing hormone / cAMP response element binding / HMG box domain binding / bHLH transcription factor binding / NGF-stimulated transcription / muscle organ development / negative regulation of fat cell differentiation / Myogenesis / E-box binding / SMAD binding / cis-regulatory region sequence-specific DNA binding / positive regulation of neuron differentiation / nuclear matrix / RNA polymerase II transcription regulator complex / transcription corepressor activity / sequence-specific double-stranded DNA binding / gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / nervous system development / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / immune response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein heterodimerization activity / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / DNA-templated transcription / chromatin / positive regulation of gene expression / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
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. / Helix-loop-helix DNA-binding domain / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Protein CBFA2T1 / Transcription factor 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsPark, S. / Cierpicki, T. / Tonelli, M. / Bushweller, J.H.
CitationJournal: Blood / Year: 2009
Title: Structure of the AML1-ETO eTAFH domain-HEB peptide complex and its contribution to AML1-ETO activity.
Authors: Park, S. / Chen, W. / Cierpicki, T. / Tonelli, M. / Cai, X. / Speck, N.A. / Bushweller, J.H.
History
DepositionAug 25, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein CBFA2T1
B: Transcription factor 12


Theoretical massNumber of molelcules
Total (without water)13,6142
Polymers13,6142
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)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 11623.448 Da / Num. of mol.: 1 / Fragment: eTAFH domain (UNP residues 119-216)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RUNX1T1, AML1T1, CBFA2T1, CDR, ETO, MTG8, ZMYND2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q06455
#2: Protein/peptide Transcription factor 12 / / Transcription factor HTF-4 / E-box-binding protein / DNA-binding protein HTF4


Mass: 1990.214 Da / Num. of mol.: 1 / Fragment: HEB peptide (UNP residues 11-28)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q99081

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D (H)CCH-TOCSY
1613D HNHA
1713D HNCO
1813D 1H-15N NOESY
1913D 1H-13C NOESY

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Sample preparation

DetailsContents: 25 mM Bis-Tris, 1 mM EDTA, 350 mM sodium chloride, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
25 mMBis-Tris-11
1 mMEDTA-21
350 mMsodium chloride-31
Sample conditionsIonic strength: 350 / pH: 6 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA5002
Bruker AvanceBrukerAVANCE9003

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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