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- PDB-1ljm: DNA recognition is mediated by conformational transition and by D... -

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Basic information

Entry
Database: PDB / ID: 1ljm
TitleDNA recognition is mediated by conformational transition and by DNA bending
ComponentsRUNX1 transcription factor
KeywordsTRANSCRIPTION / immunoglobulin fold / beta-sandwich
Function / homology
Function and homology information


regulation of connective tissue replacement / peripheral nervous system neuron development / positive regulation of granulocyte differentiation / RUNX1 regulates transcription of genes involved in BCR signaling / SLC-mediated transport of organic cations / RUNX1 regulates transcription of genes involved in interleukin signaling / core-binding factor complex / RUNX1 regulates expression of components of tight junctions / positive regulation of CD8-positive, alpha-beta T cell differentiation / myeloid leukocyte differentiation ...regulation of connective tissue replacement / peripheral nervous system neuron development / positive regulation of granulocyte differentiation / RUNX1 regulates transcription of genes involved in BCR signaling / SLC-mediated transport of organic cations / RUNX1 regulates transcription of genes involved in interleukin signaling / core-binding factor complex / RUNX1 regulates expression of components of tight junctions / positive regulation of CD8-positive, alpha-beta T cell differentiation / myeloid leukocyte differentiation / regulation of cardiac muscle cell proliferation / cardiac muscle tissue regeneration / negative regulation of CD4-positive, alpha-beta T cell differentiation / negative regulation of granulocyte differentiation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / positive regulation of extracellular matrix organization / RUNX2 regulates genes involved in differentiation of myeloid cells / regulation of plasminogen activation / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / myeloid cell differentiation / Regulation of RUNX1 Expression and Activity / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / hematopoietic stem cell proliferation / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / regulation of cell differentiation / positive regulation of collagen biosynthetic process / hemopoiesis / RUNX3 regulates p14-ARF / chondrocyte differentiation / positive regulation of interleukin-2 production / ossification / transcription corepressor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Pre-NOTCH Transcription and Translation / transcription coactivator binding / Transcriptional regulation of granulopoiesis / positive regulation of angiogenesis / neuron differentiation / SARS-CoV-1 activates/modulates innate immune responses / RUNX1 regulates transcription of genes involved in differentiation of HSCs / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / Estrogen-dependent gene expression / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein heterodimerization activity / intracellular membrane-bounded organelle / calcium ion binding / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBartfeld, D. / Shimon, L. / Couture, G.C. / Rabinovich, D. / Frolow, F. / Levanon, D. / Groner, Y. / Shakked, Z.
CitationJournal: Structure
Title: DNA Recognition by the RUNX1 Transcription Factor Is Mediated by an Allosteric Transition in the RUNT Domain and by DNA Bending.
Authors: Bartfeld, D. / Shimon, L. / Couture, G. / Rabinovich, D. / Frolow, F. / Levanon, D. / Groner, Y. / Shakked, Z.
History
DepositionApr 22, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
A: RUNX1 transcription factor
B: RUNX1 transcription factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3377
Polymers29,1592
Non-polymers1775
Water3,621201
1
A: RUNX1 transcription factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6152
Polymers14,5801
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RUNX1 transcription factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7215
Polymers14,5801
Non-polymers1424
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: RUNX1 transcription factor
B: RUNX1 transcription factor
hetero molecules

A: RUNX1 transcription factor
B: RUNX1 transcription factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,67314
Polymers58,3194
Non-polymers35510
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_455y-1/3,x+1/3,-z+1/31
Buried area5810 Å2
ΔGint-119 kcal/mol
Surface area20950 Å2
MethodPISA
4
B: RUNX1 transcription factor
hetero molecules

B: RUNX1 transcription factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,44310
Polymers29,1592
Non-polymers2848
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_455y-1/3,x+1/3,-z+1/31
Buried area1860 Å2
ΔGint-88 kcal/mol
Surface area11440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.230, 121.230, 186.330
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-3114-

HOH

21B-3112-

HOH

31B-3148-

HOH

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Components

#1: Protein RUNX1 transcription factor / Runt-related transcription factor 1 / Acute myeloid leukemia 1 protein / Core-binding factor / alpha 2 subunit


Mass: 14579.675 Da / Num. of mol.: 2 / Fragment: Runt domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: human / Plasmid: RUNT-PV-8 / Production host: Escherichia coli (E. coli) / Strain (production host): PHS2 / References: UniProt: Q01196
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 4.52 Å3/Da / Density % sol: 72.76 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Ethanol, Sodium Chloride, Tris-HCl, Hepes, DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
18-12 mg/mlprotein1drop
26 %ethanol1reservoir
31.4-1.5 M1reservoirNaCl
4100 mMTris1reservoirpH7.5
520 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 18, 2000 / Details: mirrors
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→43 Å / Num. all: 17501 / Num. obs: 17379 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 13.9 % / Biso Wilson estimate: 31.5 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 17.2
Reflection shellResolution: 2.5→2.54 Å / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.295 / % possible all: 99.3
Reflection
*PLUS
Num. all: 17379 / Num. obs: 15686 / Num. measured all: 243124 / Rmerge(I) obs: 0.071
Reflection shell
*PLUS
Highest resolution: 2.5 Å / % possible obs: 99.8 % / Rmerge(I) obs: 0.295

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MTF/ULTIMAmodel building
CNSrefinement
MTFphasing
ULTIMAphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E50

1e50


Resolution: 2.5→43 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 842 -RANDOM
Rwork0.193 ---
all0.1947 17501 --
obs0.1947 17379 99.3 %-
Displacement parametersBiso mean: 40.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.29 Å
Luzzati d res low-43 Å
Luzzati sigma a0.39 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.5→43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1759 0 5 201 1965
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_scbond_it3.8
X-RAY DIFFRACTIONc_dihedral_angle_d26.5
X-RAY DIFFRACTIONc_improper_angle_d0.78
Refinement
*PLUS
Lowest resolution: 43 Å / % reflection Rfree: 5 % / Rfactor obs: 0.1947 / Rfactor Rfree: 0.249 / Rfactor Rwork: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78

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