[English] 日本語
Yorodumi
- PDB-1io4: CRYSTAL STRUCTURE OF RUNX-1/AML1/CBFALPHA RUNT DOMAIN-CBFBETA COR... -

+
Open data


ID or keywords:

Loading...

-
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 / Nuclear events stimulated by ALK signaling in cancer / positive regulation of osteoblast differentiation / 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 / Transcriptional regulation of granulopoiesis / osteoblast differentiation / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
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