[English] 日本語
Yorodumi
- PDB-1e50: AML1/CBFbeta complex -

+
Open data


ID or keywords:

Loading...

-
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 / Organic cation transport / RUNX1 regulates transcription of genes involved in interleukin signaling / myeloid leukocyte differentiation / RUNX2 regulates bone development / core-binding factor complex ...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 / Organic cation transport / RUNX1 regulates transcription of genes involved in interleukin signaling / myeloid leukocyte differentiation / 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 / regulation of cardiac muscle cell proliferation / cardiac muscle tissue regeneration / negative regulation of granulocyte differentiation / negative regulation of CD4-positive, alpha-beta T cell 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 / RUNX2 regulates genes involved in differentiation of myeloid cells / Transcriptional regulation by RUNX2 / 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 / hematopoietic stem cell proliferation / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / regulation of cell differentiation / RUNX2 regulates osteoblast differentiation / RUNX3 regulates p14-ARF / hemopoiesis / positive regulation of collagen biosynthetic process / 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 / neuron differentiation / Pre-NOTCH Transcription and Translation / transcription coactivator binding / Transcriptional regulation of granulopoiesis / osteoblast differentiation / protein polyubiquitination / positive regulation of angiogenesis / Regulation of RUNX2 expression and activity / SARS-CoV-1 activates/modulates innate immune responses / 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 / transcription coactivator activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / intracellular membrane-bounded organelle / calcium ion binding / chromatin / regulation of transcription by RNA polymerase II / 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 / membrane / nucleus
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 / Immunoglobulin-like / Beta Barrel / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more