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- PDB-1e50: AML1/CBFbeta complex -

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Basic information

Entry
Database: PDB / ID: 1.0E+50
TitleAML1/CBFbeta complex
Components
  • CORE-BINDING FACTOR ALPHA SUBUNIT
  • CORE-BINDING FACTOR CBF-BETA
KeywordsTRANSCRIPTION / TRANSCRIPTION FACTOR
Function / homology
Function and homology information


regulation of connective tissue replacement / peripheral nervous system neuron development / positive regulation of granulocyte differentiation / RUNX3 regulates RUNX1-mediated transcription / RUNX1 regulates transcription of genes involved in BCR signaling / SLC-mediated transport of organic cations / RUNX1 regulates transcription of genes involved in interleukin signaling / RUNX2 regulates bone development / core-binding factor complex / RUNX1 regulates expression of components of tight junctions ...regulation of connective tissue replacement / peripheral nervous system neuron development / positive regulation of granulocyte differentiation / RUNX3 regulates RUNX1-mediated transcription / RUNX1 regulates transcription of genes involved in BCR signaling / SLC-mediated transport of organic cations / RUNX1 regulates transcription of genes involved in interleukin signaling / RUNX2 regulates bone development / core-binding factor complex / RUNX1 regulates expression of components of tight junctions / positive regulation of CD8-positive, alpha-beta T cell differentiation / RUNX2 regulates chondrocyte maturation / myeloid leukocyte differentiation / regulation of cardiac muscle cell proliferation / cardiac muscle tissue regeneration / negative regulation of CD4-positive, alpha-beta T cell differentiation / negative regulation of granulocyte differentiation / lymphocyte differentiation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / positive regulation of extracellular matrix organization / RUNX2 regulates genes involved in cell migration / Transcriptional regulation by RUNX2 / RUNX2 regulates genes involved in differentiation of myeloid cells / regulation of plasminogen activation / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / myeloid cell differentiation / RUNX3 Regulates Immune Response and Cell Migration / definitive hemopoiesis / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / Regulation of RUNX1 Expression and Activity / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / hematopoietic stem cell proliferation / RUNX2 regulates osteoblast differentiation / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / regulation of cell differentiation / positive regulation of collagen biosynthetic process / hemopoiesis / RUNX3 regulates p14-ARF / chondrocyte differentiation / cell maturation / positive regulation of interleukin-2 production / ossification / transcription corepressor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Regulation of RUNX3 expression and activity / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Pre-NOTCH Transcription and Translation / transcription coactivator binding / Transcriptional regulation of granulopoiesis / neuron differentiation / protein polyubiquitination / positive regulation of angiogenesis / Regulation of RUNX2 expression and activity / SARS-CoV-1 activates/modulates innate immune responses / osteoblast differentiation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / Estrogen-dependent gene expression / sequence-specific DNA binding / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription coactivator activity / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein heterodimerization activity / intracellular membrane-bounded organelle / calcium ion binding / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / ATP binding / nucleus / membrane
Similarity search - Function
Polyomavirus Enhancer Binding Protein 2; Chain: A; / Core binding factor, beta subunit / Runx, central domain superfamily / Acute myeloid leukemia 1 protein (AML1)/Runt / Runt domain / Runx, C-terminal domain / Runt-related transcription factor RUNX / Runt domain / Runx inhibition domain / Runt domain profile. ...Polyomavirus Enhancer Binding Protein 2; Chain: A; / Core binding factor, beta subunit / Runx, central domain superfamily / Acute myeloid leukemia 1 protein (AML1)/Runt / Runt domain / Runx, C-terminal domain / Runt-related transcription factor RUNX / Runt domain / Runx inhibition domain / Runt domain profile. / Core-binding factor, beta subunit / Core-binding factor, beta subunit superfamily / Core binding factor beta subunit / Immunoglobulin-like - #720 / p53/RUNT-type transcription factor, DNA-binding domain superfamily / p53-like transcription factor, DNA-binding / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Runt-related transcription factor 1 / Core-binding factor subunit beta
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsWarren, A.J. / Bravo, J. / Williams, R.L. / Rabbits, T.H.
CitationJournal: Embo J. / Year: 2000
Title: Structural Basis for the Heterodimeric Interaction between the Acute Leukaemia-Associated Transcription Factors Aml1 and Cbfbeta
Authors: Warren, A.J. / Bravo, J. / Williams, R.L. / Rabbits, T.H.
History
DepositionJul 13, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CORE-BINDING FACTOR ALPHA SUBUNIT
B: CORE-BINDING FACTOR CBF-BETA
C: CORE-BINDING FACTOR ALPHA SUBUNIT
D: CORE-BINDING FACTOR CBF-BETA
E: CORE-BINDING FACTOR ALPHA SUBUNIT
F: CORE-BINDING FACTOR CBF-BETA
G: CORE-BINDING FACTOR ALPHA SUBUNIT
H: CORE-BINDING FACTOR CBF-BETA
Q: CORE-BINDING FACTOR ALPHA SUBUNIT
R: CORE-BINDING FACTOR ALPHA SUBUNIT


Theoretical massNumber of molelcules
Total (without water)152,71810
Polymers152,71810
Non-polymers00
Water2,828157
1
A: CORE-BINDING FACTOR ALPHA SUBUNIT
B: CORE-BINDING FACTOR CBF-BETA


Theoretical massNumber of molelcules
Total (without water)30,7252
Polymers30,7252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: CORE-BINDING FACTOR ALPHA SUBUNIT
D: CORE-BINDING FACTOR CBF-BETA


Theoretical massNumber of molelcules
Total (without water)30,7252
Polymers30,7252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
E: CORE-BINDING FACTOR ALPHA SUBUNIT
F: CORE-BINDING FACTOR CBF-BETA


Theoretical massNumber of molelcules
Total (without water)30,7252
Polymers30,7252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
G: CORE-BINDING FACTOR ALPHA SUBUNIT
H: CORE-BINDING FACTOR CBF-BETA


Theoretical massNumber of molelcules
Total (without water)30,7252
Polymers30,7252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
Q: CORE-BINDING FACTOR ALPHA SUBUNIT


Theoretical massNumber of molelcules
Total (without water)14,9091
Polymers14,9091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
6
R: CORE-BINDING FACTOR ALPHA SUBUNIT


Theoretical massNumber of molelcules
Total (without water)14,9091
Polymers14,9091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)103.260, 79.380, 130.100
Angle α, β, γ (deg.)90.00, 101.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
CORE-BINDING FACTOR ALPHA SUBUNIT / CBFA2/PEPBP2AB/RUNX1 / AML1


Mass: 14909.090 Da / Num. of mol.: 6 / Fragment: RUNT DOMAIN RESIDUES 50-183
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Gene: AML1 / Plasmid: PRSET / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q01196
#2: Protein
CORE-BINDING FACTOR CBF-BETA


Mass: 15815.746 Da / Num. of mol.: 4 / Fragment: HETERODIMERISATION DOMAIN RESIDUES 2-135
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Gene: CBFB / Plasmid: PRSET / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q13951
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60 %
Crystal growpH: 6.5 / Details: pH 6.50
Crystal grow
*PLUS
Temperature: 21 ℃ / Method: vapor diffusion, hanging drop / Details: used macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMimidazole1reservoir
26 %PEG80001reservoir
35 %sucrose1reservoir
45 mMdithiothreitol1reservoir
512 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9366
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 15, 1999 / Details: MIRRORS
RadiationMonochromator: DIAMOND (111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9366 Å / Relative weight: 1
ReflectionResolution: 2.6→25 Å / Num. obs: 63354 / % possible obs: 99.3 % / Redundancy: 3.7 % / Biso Wilson estimate: 66 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 5.6
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.3 / Rsym value: 0.48 / % possible all: 99.3
Reflection
*PLUS
Num. measured all: 259515
Reflection shell
*PLUS
% possible obs: 99.2 % / Rmerge(I) obs: 0.28

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→23.82 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1357943.02 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1905 3 %SHELLS
Rwork0.268 ---
obs0.268 63323 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41 Å2 / ksol: 0.364249 e/Å3
Displacement parametersBiso mean: 56 Å2
Baniso -1Baniso -2Baniso -3
1--8.59 Å20 Å20.96 Å2
2--4.23 Å20 Å2
3---4.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.6→23.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9539 0 0 157 9696
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.041.5
X-RAY DIFFRACTIONc_mcangle_it3.362
X-RAY DIFFRACTIONc_scbond_it3.122
X-RAY DIFFRACTIONc_scangle_it4.62.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.451 320 3.1 %
Rwork0.375 10162 -
obs--99.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77

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