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- PDB-1ilf: NMR STRUCTURE OF APO CBFB -

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Basic information

Entry
Database: PDB / ID: 1ilf
TitleNMR STRUCTURE OF APO CBFB
ComponentsCORE-BINDING FACTOR
KeywordsTRANSCRIPTION / partially open beta barrel
Function / homology
Function and homology information


RUNX3 regulates p14-ARF / Transcriptional regulation by RUNX2 / RUNX2 regulates bone development / RUNX1 regulates estrogen receptor mediated transcription / RUNX1 regulates transcription of genes involved in BCR signaling / RUNX1 regulates transcription of genes involved in interleukin signaling / Regulation of RUNX1 Expression and Activity / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / core-binding factor complex ...RUNX3 regulates p14-ARF / Transcriptional regulation by RUNX2 / RUNX2 regulates bone development / RUNX1 regulates estrogen receptor mediated transcription / RUNX1 regulates transcription of genes involved in BCR signaling / RUNX1 regulates transcription of genes involved in interleukin signaling / Regulation of RUNX1 Expression and Activity / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / core-binding factor complex / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / Regulation of RUNX3 expression and activity / positive regulation of CD8-positive, alpha-beta T cell differentiation / negative regulation of CD4-positive, alpha-beta T cell differentiation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RUNX1 regulates transcription of genes involved in differentiation of HSCs / lymphocyte differentiation / Estrogen-dependent gene expression / myeloid cell differentiation / definitive hemopoiesis / cell maturation / ossification / protein polyubiquitination / osteoblast differentiation / transcription coactivator activity / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Polyomavirus Enhancer Binding Protein 2; Chain: A; / Core binding factor, beta subunit / Core-binding factor, beta subunit / Core-binding factor, beta subunit superfamily / Core binding factor beta subunit / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Core-binding factor subunit beta
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
AuthorsWolf-Watz, M. / Grundstrom, T. / Hard, T.
CitationJournal: Biochemistry / Year: 2001
Title: Structure and backbone dynamics of Apo-CBFbeta in solution.
Authors: Wolf-Watz, M. / Grundstrom, T. / Hard, T.
History
DepositionMay 8, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
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: CORE-BINDING FACTOR


Theoretical massNumber of molelcules
Total (without water)16,6141
Polymers16,6141
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)25 / 58structures with the lowest energy
RepresentativeModel #4lowest energy

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Components

#1: Protein CORE-BINDING FACTOR


Mass: 16613.648 Da / Num. of mol.: 1 / Fragment: BETA-SUBUNIT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q08024

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1223D 15N-separated NOESY
1332D NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

Details
Solution-IDContentsSolvent system
11.6mM CBFb U-15N, 13C25mM phosphate buffer, 3mM DTT, 100 % D2O
21.6mM CBFb U-15N25mM phosphate buffer, 3mM DTT, 10 % D2O
30.8mM CBFb25mM phosphate buffer,3mM DTT, 100 % D2O
Sample conditionsIonic strength: 150mM sodium chloride / pH: 6.6 / Pressure: 1 atm / Temperature: 297 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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 INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002
Bruker AVANCEBrukerAVANCE6003

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.5processing
NMRPipe1.8Delaglioprocessing
VNMR5.3processing
Ansig for Windows1Helgstranddata analysis
CNS1Brungerrefinement
MOLMOL2K.1Koradirefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
Details: The structures are based on 2139 NOE-derived restraints, 215 dihedral angle restraints and 86 distance restraints from 43 hydrogen bonds
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 58 / Conformers submitted total number: 25

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