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- PDB-2jhb: CORE BINDING FACTOR BETA -

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Basic information

Entry
Database: PDB / ID: 2jhb
TitleCORE BINDING FACTOR BETA
ComponentsPROTEIN (CORE BINDING FACTOR BETA)
KeywordsGENE REGULATION / CORE BINDING FACTOR / TRANSCRIPTION FACTOR
Function / homology
Function and homology information


Transcriptional regulation by RUNX2 / RUNX2 regulates bone development / RUNX3 regulates p14-ARF / 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 interacts with co-factors whose precise effect on RUNX1 targets is not known / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / core-binding factor complex ...Transcriptional regulation by RUNX2 / RUNX2 regulates bone development / RUNX3 regulates p14-ARF / 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 interacts with co-factors whose precise effect on RUNX1 targets is not known / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / core-binding factor complex / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / positive regulation of CD8-positive, alpha-beta T cell differentiation / Regulation of RUNX3 expression and activity / 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 / torsion angle dynamics
AuthorsHuang, X. / Peng, J. / Speck, N.A. / Bushweller, J.H.
Citation
Journal: Nat.Struct.Biol. / Year: 1999
Title: Solution structure of core binding factor beta and map of the CBF alpha binding site.
Authors: Huang, X. / Peng, J.W. / Speck, N.A. / Bushweller, J.H.
#1: Journal: J.Biol.Chem. / Year: 1998
Title: Overexpression, purification, and biophysical characterization of the heterodimerization domain of the core-binding factor beta subunit.
Authors: Huang, X. / Crute, B.E. / Sun, C. / Tang, Y.Y. / Kelley 3rd, J.J. / Lewis, A.F. / Hartman, K.L. / Laue, T.M. / Speck, N.A. / Bushweller, J.H.
#2: Journal: J.Biomol.Nmr / Year: 1998
Title: Complete heteronuclear NMR resonance assignments and secondary structure of core binding factor beta (1-141).
Authors: Huang, X. / Speck, N.A. / Bushweller, J.H.
History
DepositionMar 17, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jul 5, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Nov 6, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / citation ...atom_site / citation / citation_author / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 2.1Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (CORE BINDING FACTOR BETA)


Theoretical massNumber of molelcules
Total (without water)16,7581
Polymers16,7581
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 / 100LEAST RESTRAINT VIOLATION
Representative

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Components

#1: Protein PROTEIN (CORE BINDING FACTOR BETA) / CBFB


Mass: 16757.779 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: AR58 / Gene: CBFB141 / Plasmid: PGRXCBFB141 / Gene (production host): GRXCBFB141 / Production host: Escherichia coli (E. coli) / Strain (production host): AR58 / References: UniProt: Q08024

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HSQC
121HN(CA)CB
131HN(CO)CACB
141HN(CA)HA
151HNCA
161HN(CO)CA
171HNCO
181CT-HSQC
191C(CO)NNH
1101H(CCO)NNH
1111(H)CCH-TOCSY
1121(HB)CB(CGCD)HD
1131(HB)CB(CGCDCE)HE
1141HNHA
1151HNHB
1161HACAHB
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 15N/ 13C AND 15N-LABELED RECOMBINANT CBFB(141)

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Sample preparation

Sample conditionspH: 6.5 / Pressure: 1 atm / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
OPALLUGINBUHL,GUNTERT,BILLETER,WUTHRICHrefinement
DYANAstructure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 100 / Conformers submitted total number: 20

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