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- PDB-3wtx: Crystal structure of the complex comprised of ETS1(Y329A), RUNX1,... -

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Basic information

Entry
Database: PDB / ID: 3wtx
TitleCrystal structure of the complex comprised of ETS1(Y329A), RUNX1, CBFBETA, and the tcralpha gene enhancer DNA
Components
  • Core-binding factor subunit beta
  • DNA (5'-D(*AP*GP*AP*GP*GP*AP*TP*GP*TP*GP*GP*CP*TP*TP*C)-3')
  • DNA (5'-D(*GP*AP*AP*GP*CP*CP*AP*CP*AP*TP*CP*CP*TP*CP*T)-3')
  • Protein C-ets-1
  • Runt-related transcription factor 1
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / DNA-BINDING / METHYLATION / NUCLEUS / PHOSPHOPROTEIN / TRANSCRIPTION REGULATION / ISOPEPTIDE BOND / PROTO-ONCOGENE / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


RUNX3 regulates p14-ARF / Transcriptional regulation by RUNX2 / RUNX2 regulates bone development / regulation of hair follicle cell proliferation / Organic cation transport / positive regulation of progesterone secretion / 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 ...RUNX3 regulates p14-ARF / Transcriptional regulation by RUNX2 / RUNX2 regulates bone development / regulation of hair follicle cell proliferation / Organic cation transport / positive regulation of progesterone secretion / 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 / positive regulation of granulocyte differentiation / 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 / positive regulation of cell maturation / negative regulation of CD4-positive, alpha-beta T cell differentiation / lymphocyte differentiation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RUNX1 regulates transcription of genes involved in differentiation of HSCs / PML body organization / neuron fate commitment / Estrogen-dependent gene expression / myeloid progenitor cell differentiation / myeloid cell differentiation / definitive hemopoiesis / regulation of T cell anergy / positive regulation of leukocyte adhesion to vascular endothelial cell / embryonic hemopoiesis / hair follicle morphogenesis / regulation of cell differentiation / behavioral response to pain / hemopoiesis / negative regulation of cell cycle / basement membrane / regulation of signal transduction / neuron development / positive regulation of blood vessel endothelial cell migration / chondrocyte differentiation / regulation of angiogenesis / response to retinoic acid / cell maturation / cellular response to transforming growth factor beta stimulus / positive regulation of interleukin-2 production / positive regulation of endothelial cell migration / positive regulation of erythrocyte differentiation / ossification / liver development / transcription corepressor binding / nuclear receptor coactivator activity / skeletal system development / central nervous system development / cell motility / promoter-specific chromatin binding / neuron differentiation / Oncogene Induced Senescence / positive regulation of miRNA transcription / positive regulation of inflammatory response / protein polyubiquitination / osteoblast differentiation / positive regulation of type II interferon production / positive regulation of angiogenesis / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / regulation of apoptotic process / DNA-binding transcription factor binding / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / nucleic acid binding / transcription coactivator activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / immune response / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / response to antibiotic / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of gene expression / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm
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. / Protein C-ets-1, pointed domain / Transforming protein C-ets / Ets1, N-terminal flanking region of Ets domain / Ets1 N-terminal flanking region of Ets domain / Core-binding factor, beta subunit / Core-binding factor, beta subunit superfamily / Core binding factor beta subunit / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Ets-domain signature 1. / Ets-domain signature 2. / Ets domain / ETS family / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Immunoglobulin-like - #720 / p53/RUNT-type transcription factor, DNA-binding domain superfamily / p53-like transcription factor, DNA-binding / Sterile alpha motif/pointed domain superfamily / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Immunoglobulin-like / Beta Barrel / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Protein C-ets-1 / Runt-related transcription factor 1 / Core-binding factor subunit beta
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsShiina, M. / Hamada, K. / Ogata, K.
CitationJournal: J.Mol.Biol. / Year: 2015
Title: A novel allosteric mechanism on protein-DNA interactions underlying the phosphorylation-dependent regulation of Ets1 target gene expressions.
Authors: Shiina, M. / Hamada, K. / Inoue-Bungo, T. / Shimamura, M. / Uchiyama, A. / Baba, S. / Sato, K. / Yamamoto, M. / Ogata, K.
History
DepositionApr 21, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Aug 24, 2022Group: Database references / Category: citation / database_2 / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Runt-related transcription factor 1
B: Core-binding factor subunit beta
C: Protein C-ets-1
F: Runt-related transcription factor 1
G: Core-binding factor subunit beta
H: Protein C-ets-1
D: DNA (5'-D(*GP*AP*AP*GP*CP*CP*AP*CP*AP*TP*CP*CP*TP*CP*T)-3')
E: DNA (5'-D(*AP*GP*AP*GP*GP*AP*TP*GP*TP*GP*GP*CP*TP*TP*C)-3')
I: DNA (5'-D(*GP*AP*AP*GP*CP*CP*AP*CP*AP*TP*CP*CP*TP*CP*T)-3')
J: DNA (5'-D(*AP*GP*AP*GP*GP*AP*TP*GP*TP*GP*GP*CP*TP*TP*C)-3')


Theoretical massNumber of molelcules
Total (without water)135,80410
Polymers135,80410
Non-polymers00
Water37821
1
A: Runt-related transcription factor 1
B: Core-binding factor subunit beta
C: Protein C-ets-1
D: DNA (5'-D(*GP*AP*AP*GP*CP*CP*AP*CP*AP*TP*CP*CP*TP*CP*T)-3')
E: DNA (5'-D(*AP*GP*AP*GP*GP*AP*TP*GP*TP*GP*GP*CP*TP*TP*C)-3')


Theoretical massNumber of molelcules
Total (without water)67,9025
Polymers67,9025
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6980 Å2
ΔGint-41 kcal/mol
Surface area21190 Å2
MethodPISA
2
F: Runt-related transcription factor 1
G: Core-binding factor subunit beta
H: Protein C-ets-1
I: DNA (5'-D(*GP*AP*AP*GP*CP*CP*AP*CP*AP*TP*CP*CP*TP*CP*T)-3')
J: DNA (5'-D(*AP*GP*AP*GP*GP*AP*TP*GP*TP*GP*GP*CP*TP*TP*C)-3')


Theoretical massNumber of molelcules
Total (without water)67,9025
Polymers67,9025
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6810 Å2
ΔGint-34 kcal/mol
Surface area20920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.727, 101.988, 194.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 3 types, 6 molecules AFBGCH

#1: Protein Runt-related transcription factor 1 / Acute myeloid leukemia 1 protein / Core-binding factor subunit alpha-2 / CBF-alpha-2 / Oncogene AML- ...Acute myeloid leukemia 1 protein / Core-binding factor subunit alpha-2 / CBF-alpha-2 / Oncogene AML-1 / Polyomavirus enhancer-binding protein 2 alpha B subunit / PEA2-alpha B / PEBP2-alpha B / SL3-3 enhancer factor 1 alpha B subunit / SL3/AKV core-binding factor alpha B subunit


Mass: 22913.791 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 60-263 / Mutation: L94K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Aml1, Cbfa2, Pebp2ab, Runx1 / Plasmid: PET23A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q03347
#2: Protein Core-binding factor subunit beta / CBF-beta / Polyomavirus enhancer-binding protein 2 beta subunit / PEA2-beta / PEBP2-beta / SL3-3 ...CBF-beta / Polyomavirus enhancer-binding protein 2 beta subunit / PEA2-beta / PEBP2-beta / SL3-3 enhancer factor 1 subunit beta / SL3/AKV core-binding factor beta subunit


Mass: 16684.729 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-142
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cbfb, Pebp2b, Pebpb2 / Plasmid: PET23A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q08024
#3: Protein Protein C-ets-1 / p54


Mass: 19124.635 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 276-441 / Mutation: Y329A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ETS1, EWSR2 / Plasmid: PET23A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P14921

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DNA chain , 2 types, 4 molecules DIEJ

#4: DNA chain DNA (5'-D(*GP*AP*AP*GP*CP*CP*AP*CP*AP*TP*CP*CP*TP*CP*T)-3')


Mass: 4513.950 Da / Num. of mol.: 2 / Source method: obtained synthetically
#5: DNA chain DNA (5'-D(*AP*GP*AP*GP*GP*AP*TP*GP*TP*GP*GP*CP*TP*TP*C)-3')


Mass: 4665.032 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Non-polymers , 1 types, 21 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.88 Å3/Da / Density % sol: 57.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 10% PEG 4000, 0.25M AMMONIUM ACETATE, 0.05M SODIUM ACETATE PH5.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 24, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 38872 / % possible obs: 98.4 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 11.8
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 8 % / Rmerge(I) obs: 0.405 / % possible all: 88.6

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Processing

Software
NameVersionClassification
PHASERphasing
CNS1.2refinement
HKL-2000data reduction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3WTS

3wts


Resolution: 2.8→45.18 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1386084 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.271 3891 10 %RANDOM
Rwork0.237 ---
obs0.237 38789 98.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.96 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 86.25 Å2
Baniso -1Baniso -2Baniso -3
1-11.15 Å20 Å20 Å2
2--21.53 Å20 Å2
3----32.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.73 Å0.62 Å
Refinement stepCycle: LAST / Resolution: 2.8→45.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5701 1218 0 21 6940
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_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.01
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.341.5
X-RAY DIFFRACTIONc_mcangle_it2.372
X-RAY DIFFRACTIONc_scbond_it1.912
X-RAY DIFFRACTIONc_scangle_it3.072.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.46 618 10.5 %
Rwork0.406 5265 -
obs--91.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP

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