[English] 日本語
Yorodumi
- PDB-1eao: THE RUNX1 Runt domain at 1.4A resolution: a structural switch and... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1eao
TitleTHE RUNX1 Runt domain at 1.4A resolution: a structural switch and specifically bound chloride ions modulate DNA binding
ComponentsRUNT-RELATED TRANSCRIPTION FACTOR 1
KeywordsTRANSCRIPTION/DNA / ACUTE MYELOID LEUKEMIA / AML / RUNX1 / RUNT DOMAIN / CHLORIDE BINDING / TRANSCRIPTION FACTOR / IG FOLD / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


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 ...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 / positive regulation of cell maturation / negative regulation of CD4-positive, alpha-beta T cell differentiation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RUNX1 regulates transcription of genes involved in differentiation of HSCs / neuron fate commitment / Estrogen-dependent gene expression / myeloid progenitor cell differentiation / definitive hemopoiesis / regulation of T cell anergy / embryonic hemopoiesis / hair follicle morphogenesis / behavioral response to pain / regulation of cell differentiation / hemopoiesis / basement membrane / regulation of signal transduction / neuron development / chondrocyte differentiation / response to retinoic acid / cellular response to transforming growth factor beta stimulus / positive regulation of interleukin-2 production / ossification / liver development / skeletal system development / central nervous system development / promoter-specific chromatin binding / neuron differentiation / positive regulation of angiogenesis / sequence-specific double-stranded DNA binding / positive regulation of type II interferon production / DNA-binding transcription factor binding / in utero embryonic development / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / 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 / nucleus
Similarity search - Function
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. / Immunoglobulin-like - #720 / p53/RUNT-type transcription factor, DNA-binding domain superfamily ...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. / Immunoglobulin-like - #720 / p53/RUNT-type transcription factor, DNA-binding domain superfamily / p53-like transcription factor, DNA-binding / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
BROMIDE ION / Runt-related transcription factor 1
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsBackstrom, S. / Wolf-Watz, M. / Grundstrom, C. / Hard, T.H. / Grundstrom, T. / Sauer, U.H.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: The Runx1 Runt Domain at 1.25A Resolution: A Structural Switch and Specifically Bound Chloride Ions Modulate DNA Binding
Authors: Backstrom, S. / Wolf-Watz, M. / Grundstrom, C. / Hard, T. / Grundstrom, T. / Sauer, U.
History
DepositionJul 14, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 12, 2002Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RUNT-RELATED TRANSCRIPTION FACTOR 1
B: RUNT-RELATED TRANSCRIPTION FACTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3676
Polymers31,0472
Non-polymers3204
Water6,485360
1
A: RUNT-RELATED TRANSCRIPTION FACTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6833
Polymers15,5241
Non-polymers1602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: RUNT-RELATED TRANSCRIPTION FACTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6833
Polymers15,5241
Non-polymers1602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)91.066, 46.173, 62.904
Angle α, β, γ (deg.)90.00, 91.94, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.756729, -0.297093, -0.58232), (0.311672, -0.946973, 0.078115), (-0.574649, -0.122381, 0.809198)
Vector: 55.90745, 43.01644, 14.4855)

-
Components

#1: Protein RUNT-RELATED TRANSCRIPTION FACTOR 1 / ACUTE MYELOID LEUKEMIA 1 PROTEIN / ONCOGENE AML-1 / CORE-BINDING FACTOR / ALPHA B SUBUNIT / CBF- ...ACUTE MYELOID LEUKEMIA 1 PROTEIN / ONCOGENE AML-1 / CORE-BINDING FACTOR / ALPHA B SUBUNIT / CBF-ALPHA B / POLYOMAVIRUS ENHANCER BINDING PROTEIN 2 ALPHA B SUBUNIT / PEBP2-ALPHA B / PEA2-ALPHA B / SL3-3 ENHANCER FACTOR 1 ALPHA B SUBUNIT / SL3/AKV CORE-BINDING FACTOR ALPHA B SUBUNIT


Mass: 15523.550 Da / Num. of mol.: 2 / Fragment: RUNT DOMAIN RESIDUES 46-185 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: ENGINEERED MUTATION CYS 72 SER, CYS 81 SER / Source: (gene. exp.) MUS MUSCULUS (house mouse) / Description: REFOLDED FROM INCLUSION BODIES / Plasmid: PET11C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q03347
#2: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A ENGINEERED MUTATION CYS 72 SER, CYS 81 SER CBF BINDS TO THE CORE SITE, OF A NUMBER OF ...CHAIN A ENGINEERED MUTATION CYS 72 SER, CYS 81 SER CBF BINDS TO THE CORE SITE, OF A NUMBER OF ENHANCERS AND PROMOTERS, INCLUDING MURINE LEUKEMIA VIRUS, POLYOMAVIRUS ENHANCER, T-CELL RECEPTOR ENHANCERS, LCK, IL-3 AND GM-CSF PROMOTERS.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 34 %
Crystal growpH: 6.4
Details: 25 % PEG 3350, 16% GLYCEROL, 130 MM NA CACODYLATE, PH 6.4
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
11.6 M1dropNaCl
2100 mM1dropMgSO4
320 mMHEPES1droppH8.0
423 mg/mlprotein1drop
525 %(w/v)PEG33501reservoir
616 %(v/v)glycerol1reservoir
7130 mMsodium cacodylate1reservoirpH6.4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9195
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 15, 2000 / Details: MIRROR
RadiationMonochromator: SI(111), SI(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9195 Å / Relative weight: 1
ReflectionResolution: 1.4→24 Å / Num. obs: 50436 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 4.45 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 10.9
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 4 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 4 / % possible all: 96.4
Reflection
*PLUS
Lowest resolution: 24 Å / Num. measured all: 224261
Reflection shell
*PLUS
% possible obs: 97 %

-
Processing

Software
NameVersionClassification
REFMAC5.1.27refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: EBI-8233

Resolution: 1.4→24.77 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 0.698 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.173 2549 5.1 %RANDOM
Rwork0.141 ---
obs0.143 47744 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å2-0.01 Å2
2--0.03 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.4→24.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1900 0 4 360 2264
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221957
X-RAY DIFFRACTIONr_bond_other_d0.0020.021810
X-RAY DIFFRACTIONr_angle_refined_deg1.7121.9432666
X-RAY DIFFRACTIONr_angle_other_deg1.88334205
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3955246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.2080.2317
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022158
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02392
X-RAY DIFFRACTIONr_nbd_refined0.2160.2322
X-RAY DIFFRACTIONr_nbd_other0.2640.22077
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0880.21207
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2220
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1610.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3150.294
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.232
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.44 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.198 192
Rwork0.153 3396
Refinement
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 24 Å / Rfactor Rfree: 0.172 / Rfactor Rwork: 0.147
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.015
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.72

+
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