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- PDB-1ean: THE RUNX1 Runt domain at 1.70A resolution: A structural switch an... -

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Entry
Database: PDB / ID: 1ean
TitleTHE RUNX1 Runt domain at 1.70A resolution: A structural switch and specifically bound chloride ions modulate DNA binding
ComponentsRUNT-RELATED TRANSCRIPTION FACTOR 1
KeywordsTRANSCRIPTION/DNA / TRANSCRIPTION-DNA COMPLEX / ACUTE MYELOID LEUKEMIA / AML / RUNX1 / RUNT DOMAIN / CHLORIDE BINDING / TRANSCRIPTION FACTOR / IG FOLD
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
Runt-related transcription factor 1
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBackstrom, S. / Wolf-Watz, M. / Grundstrom, C. / Hard, T. / Grundstrom, T. / Sauer, U.H.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: The Runx1 Runt Domain at 1.25 A 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.H.
History
DepositionJul 13, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 12, 2002Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 29, 2017Group: Structure summary
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)15,5943
Polymers15,5241
Non-polymers712
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)110.696, 110.696, 117.293
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-2101-

HOH

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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.: 1 / Fragment: RUNT DOMAIN RESIDUES 46-185 / Mutation: YES
Source method: isolated from a genetically manipulated source
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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A ENGINEERED MUTATION CYS72SER, CYS81SER CBF BINDS TO THE CORE SITE, OF A NUMBER OF ENHANCERS ...CHAIN A ENGINEERED MUTATION CYS72SER, CYS81SER 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.

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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: 4.46 Å3/Da / Density % sol: 72 %
Crystal growpH: 6.5
Details: 30% MPEG 350, 5-10% PEG 3350, 70 MM NA CACODYLATE, PH 6.5
Crystal grow
*PLUS
Temperature: 293 K / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
116 mg/mlprotein1drop
21.1 M1dropNaCl
330 %(v/v)MPEG3501reservoir
45-10 %(w/v)PEG33501reservoir
570 mMHEPES1reservoirpH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9315
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 6, 1999 / Details: MIRROR
RadiationMonochromator: SI(111), SI(113) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9315 Å / Relative weight: 1
ReflectionResolution: 1.7→19.7 Å / Num. obs: 28866 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 11.3
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 4 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.5 / % possible all: 99
Reflection
*PLUS
Num. measured all: 357303 / Rmerge(I) obs: 0.04
Reflection shell
*PLUS
% possible obs: 99 %

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Processing

Software
NameVersionClassification
REFMAC5.0.36refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB CODE 1EAQ

1eaq


Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.072 / SU ML: 0.069 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1519 5 %RANDOM
Rwork0.204 ---
obs-28868 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 21.44 Å2
Baniso -1Baniso -2Baniso -3
1-1.56 Å20.78 Å20 Å2
2--1.56 Å20 Å2
3----2.34 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms875 0 2 119 996
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d
X-RAY DIFFRACTIONr_bond_other_d0.0010.02841
X-RAY DIFFRACTIONr_angle_refined_deg1.5861.9441231
X-RAY DIFFRACTIONr_angle_other_deg1.50131950
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0173113
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.47815156
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1030.2148
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.02994
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02185
X-RAY DIFFRACTIONr_nbd_refined0.2060.3143
X-RAY DIFFRACTIONr_nbd_other0.2040.3743
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.596
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1130.31
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2170.316
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.8120.58
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4331.5571
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.8092935
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.133332
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.8544.5296
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: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.279 101
Rwork0.276 2114
Refinement TLS params.Method: refined / Origin x: -29.621 Å / Origin y: 18.482 Å / Origin z: -85.696 Å
111213212223313233
T0.0513 Å2-0.0154 Å20.0478 Å2-0.0186 Å2-0.0133 Å2--0.0491 Å2
L2.3371 °21.1573 °2-0.288 °2-1.9631 °20.3192 °2--2.1668 °2
S-0.0571 Å °0.0172 Å °-0.0083 Å °0.02 Å °0.1317 Å °-0.0617 Å °0.0473 Å °-0.0903 Å °-0.0747 Å °
Software
*PLUS
Name: REFMAC / Version: '5.0.36 18/01/2001' / Classification: refinement
Refinement
*PLUS
Lowest resolution: 19.7 Å / Rfactor Rfree: 0.223 / Rfactor Rwork: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.014
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.14

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