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- PDB-1io4: CRYSTAL STRUCTURE OF RUNX-1/AML1/CBFALPHA RUNT DOMAIN-CBFBETA COR... -

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Basic information

Entry
Database: PDB / ID: 1io4
TitleCRYSTAL STRUCTURE OF RUNX-1/AML1/CBFALPHA RUNT DOMAIN-CBFBETA CORE DOMAIN HETERODIMER AND C/EBPBETA BZIP HOMODIMER BOUND TO A DNA FRAGMENT FROM THE CSF-1R PROMOTER
Components
  • (CSF-1R PROMOTER) x 2
  • CAAT/ENHANCER BINDING PROTEIN BETA
  • CORE-BINDING FACTOR, BETA SUBUNIT
  • RUNT-RELATED TRANSCRIPTION FACTOR 1
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / TRANSCRIPTION FACTOR / BZIP / RUNX / RUNT / C/EBP / CBF / CORE BINDING FACTOR / AML1 / AML / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


RUNX3 regulates p14-ARF / Transcriptional regulation by RUNX2 / RUNX2 regulates bone development / C/EBP complex / granuloma formation / regulation of odontoblast differentiation / CHOP-C/EBP complex / regulation of hair follicle cell proliferation / positive regulation of sodium-dependent phosphate transport / Organic cation transport ...RUNX3 regulates p14-ARF / Transcriptional regulation by RUNX2 / RUNX2 regulates bone development / C/EBP complex / granuloma formation / regulation of odontoblast differentiation / CHOP-C/EBP complex / regulation of hair follicle cell proliferation / positive regulation of sodium-dependent phosphate transport / 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 / positive regulation of biomineral tissue development / myeloid cell development / integrated stress response signaling / T-helper 1 cell activation / 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 / positive regulation of cell maturation / Response of EIF2AK1 (HRI) to heme deficiency / negative regulation of CD4-positive, alpha-beta T cell differentiation / hepatocyte proliferation / lymphocyte differentiation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RUNX1 regulates transcription of genes involved in differentiation of HSCs / ATF4 activates genes in response to endoplasmic reticulum stress / neuron fate commitment / regulation of osteoclast differentiation / Estrogen-dependent gene expression / mammary gland epithelial cell differentiation / myeloid cell differentiation / condensed chromosome, centromeric region / myeloid progenitor cell differentiation / regulation of dendritic cell differentiation / definitive hemopoiesis / regulation of T cell anergy / regulation of interleukin-6 production / embryonic hemopoiesis / mammary gland epithelial cell proliferation / histone acetyltransferase binding / hair follicle morphogenesis / positive regulation of interleukin-4 production / behavioral response to pain / regulation of cell differentiation / ubiquitin-like protein ligase binding / Response of EIF2AK4 (GCN2) to amino acid deficiency / hemopoiesis / Transcriptional Regulation by VENTX / basement membrane / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / regulation of signal transduction / neuron development / embryonic placenta development / positive regulation of fat cell differentiation / RNA polymerase II core promoter sequence-specific DNA binding / chondrocyte differentiation / positive regulation of osteoblast differentiation / Nuclear events stimulated by ALK signaling in cancer / brown fat cell differentiation / negative regulation of T cell proliferation / response to retinoic acid / ovarian follicle development / cell maturation / cellular response to transforming growth factor beta stimulus / positive regulation of interleukin-2 production / response to endoplasmic reticulum stress / ossification / liver development / skeletal system development / central nervous system development / acute-phase response / liver regeneration / promoter-specific chromatin binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / cellular response to amino acid stimulus / neuron differentiation / chromatin DNA binding / kinase binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / nuclear matrix / histone deacetylase binding / Transcriptional regulation of white adipocyte differentiation / positive regulation of inflammatory response / osteoblast differentiation / Transcriptional regulation of granulopoiesis / protein polyubiquitination / RNA polymerase II transcription regulator complex / positive regulation of angiogenesis / sequence-specific double-stranded DNA binding / positive regulation of type II interferon production / positive regulation of cold-induced thermogenesis / Senescence-Associated Secretory Phenotype (SASP)
Similarity search - Function
Polyomavirus Enhancer Binding Protein 2; Chain: A; / Core binding factor, beta subunit / : / CCAAT/enhancer-binding protein, chordates / Runx, central domain superfamily / Acute myeloid leukemia 1 protein (AML1)/Runt / Runt domain / Runx, C-terminal domain / Runt-related transcription factor RUNX / Runt domain ...Polyomavirus Enhancer Binding Protein 2; Chain: A; / Core binding factor, beta subunit / : / CCAAT/enhancer-binding protein, chordates / 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 / Basic region leucine zipper / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain superfamily / Basic-leucine zipper domain / p53/RUNT-type transcription factor, DNA-binding domain superfamily / p53-like transcription factor, DNA-binding / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
: / DNA / DNA (> 10) / CCAAT/enhancer-binding protein beta / Runt-related transcription factor 1 / Core-binding factor subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsTahirov, T.H. / Ogata, K.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 2001
Title: Structural analyses of DNA recognition by the AML1/Runx-1 Runt domain and its allosteric control by CBFbeta.
Authors: Tahirov, T.H. / Inoue-Bungo, T. / Morii, H. / Fujikawa, A. / Sasaki, M. / Kimura, K. / Shiina, M. / Sato, K. / Kumasaka, T. / Yamamoto, M. / Ishii, S. / Ogata, K.
#1: Journal: To Be Published
Title: Crystallization and Preliminary X-Ray Analyses of Quaternary, Ternary and Binary Protein-DNA Complexes with Involvement of AML1/Runx-1/Cbfalpha Runt Domain, Cbfbeta and the C/EBPbeta bZIP Region
Authors: Tahirov, T.H. / Inoue, T. / Sasaki, M. / Shiina, M. / Kimura, K. / Sato, K. / Kumasaka, T. / Yamamoto, M. / Kamiya, N. / Ogata, K.
History
DepositionJan 10, 2001Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Mar 12, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: CSF-1R PROMOTER
F: CSF-1R PROMOTER
A: CAAT/ENHANCER BINDING PROTEIN BETA
B: CAAT/ENHANCER BINDING PROTEIN BETA
C: RUNT-RELATED TRANSCRIPTION FACTOR 1
D: CORE-BINDING FACTOR, BETA SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6589
Polymers65,0676
Non-polymers5913
Water1448
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.108, 163.600, 109.326
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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DNA chain , 2 types, 2 molecules EF

#1: DNA chain CSF-1R PROMOTER


Mass: 8018.176 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain CSF-1R PROMOTER


Mass: 7956.156 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Protein , 3 types, 4 molecules ABCD

#3: Protein CAAT/ENHANCER BINDING PROTEIN BETA / C/EBP BETA


Mass: 9381.868 Da / Num. of mol.: 2 / Fragment: BZIP DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PAR2156 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P17676
#4: Protein RUNT-RELATED TRANSCRIPTION FACTOR 1 / CORE-BINDING FACTOR / ALPHA B SUBUNIT / PEPB2-ALPHA B


Mass: 13715.696 Da / Num. of mol.: 1 / Fragment: RUNT DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PAR2156 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q03347
#5: Protein CORE-BINDING FACTOR, BETA SUBUNIT / PEBP2-BETA / CBF-BETA


Mass: 16613.648 Da / Num. of mol.: 1 / Fragment: CORE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PAR2156 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q08024

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Non-polymers , 2 types, 11 molecules

#6: Chemical ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Au
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 4.12 Å3/Da / Density % sol: 69.9 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2 M potassium chloride, 0.01 M magnesium chloride, 0.01 M DTT, 4.5% V/V PEG 8000, 1% V/V glycerol, 1% V/V MPD, 0.05 M MES buffer pH 5.6, pH 5.60, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Components of the solutions
IDNameCrystal-IDSol-ID
1KCl11
2MgCl211
3glycerol11
4MPD11
5DTT11
6PEG 800011
7MES11
8KCl12
9MgCl212
10MPD12
Crystal grow
*PLUS
Details: Tahirov, T.H., (2001) Acta Crystallogr., D57, 850.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein-DNA solution1drop
20.1 M1reservoirKCl
30.01 M1reservoirMgCl2
410 %(v/v)PEG4001reservoir
50.05 MMES1reservoir
61
71
81
91
101

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 7, 2000 / Details: MIRRORS
RadiationMonochromator: DIAMOND / Protocol: THREE WAVELENGTH FROM GOLD DERIVATIVE / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. all: 66989 / Num. obs: 21113 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.173 % / Biso Wilson estimate: 45.1 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 6.2 / Net I/σ(I): 15.5
Reflection shellResolution: 3→3.05 Å / Redundancy: 3.246 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 1.7 / Rsym value: 37.2 / % possible all: 90.8
Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 20 Å / Num. measured all: 66989

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Processing

Software
NameVersionClassification
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS0.9phasing
RefinementMethod to determine structure: MAD / Resolution: 3→19.95 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 461658.95 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.299 1038 4.9 %RANDOM
Rwork0.247 ---
all-21111 --
obs-21111 95.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 25 Å2 / ksol: 0.198 e/Å3
Displacement parametersBiso mean: 82.1 Å2
Baniso -1Baniso -2Baniso -3
1-29.96 Å20 Å20 Å2
2---15.3 Å20 Å2
3----14.66 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.57 Å0.45 Å
Luzzati d res low-20 Å
Luzzati sigma a0.64 Å0.64 Å
Refinement stepCycle: LAST / Resolution: 3→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3126 1060 3 8 4197
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.2
X-RAY DIFFRACTIONc_improper_angle_d1.1
X-RAY DIFFRACTIONc_mcbond_it14.091.5
X-RAY DIFFRACTIONc_mcangle_it18.82
X-RAY DIFFRACTIONc_scbond_it20.262
X-RAY DIFFRACTIONc_scangle_it23.662.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.464 150 4.6 %
Rwork0.447 3090 -
obs--88.9 %
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
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 4.9 % / Rfactor obs: 0.247
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 82.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.1
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.464 / % reflection Rfree: 4.6 % / Rfactor Rwork: 0.447

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