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- PDB-1eaq: The RUNX1 Runt domain at 1.25A resolution: A structural switch an... -

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Basic information

Entry
Database: PDB / ID: 1eaq
TitleThe RUNX1 Runt domain at 1.25A 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 / 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 ...regulation of hair follicle cell proliferation / Organic cation transport / 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 / hemopoiesis / basement membrane / regulation of signal transduction / neuron development / response to retinoic acid / cellular response to transforming growth factor beta stimulus / positive regulation of interleukin-2 production / liver development / central nervous system development / skeletal system development / neuron differentiation / positive regulation of type II interferon production / positive regulation of angiogenesis / gene expression / DNA-binding transcription factor binding / in utero embryonic development / 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 / 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 / MAD / Resolution: 1.25 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 14, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 12, 2002Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag
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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)31,4706
Polymers31,3282
Non-polymers1424
Water6,467359
1
A: RUNT-RELATED TRANSCRIPTION FACTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7353
Polymers15,6641
Non-polymers712
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)15,7353
Polymers15,6641
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)91.300, 46.400, 63.000
Angle α, β, γ (deg.)90.00, 92.30, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.756045, -0.282533, -0.590399), (0.299867, -0.951317, 0.07125), (-0.581787, -0.123172, 0.80396)
Vector: 56.00146, 42.96741, 14.74166)

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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: 15664.235 Da / Num. of mol.: 2 / Fragment: RUNT DOMAIN RESIDUES 36-185 / 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: SE-MET LABELLED, REFOLDED FROM INCLUSION BODIES
Plasmid: PET11C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q03347
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A ENGINEERED MUTATION CYS 72 SER, CYS 81 SER CHAIN B ENGINEERED MUTATION CYS 72 SER, CYS 81 ...CHAIN A ENGINEERED MUTATION CYS 72 SER, CYS 81 SER CHAIN B 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.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9315,0.9793,0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 6, 1999 / Details: MIRROR
RadiationMonochromator: SI(111), SI(113) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.93151
20.97931
30.97951
ReflectionResolution: 1.25→37 Å / Num. obs: 71531 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 8.48 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.3
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 2 / % possible all: 78
Reflection
*PLUS
Lowest resolution: 37 Å / Num. measured all: 606863 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 78 %

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Processing

Software
NameVersionClassification
REFMAC5.1.27refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.25→25 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.494 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.04 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.167 1047 1.5 %RANDOM
Rwork0.149 ---
obs0.149 70348 97.9 %-
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: 16.45 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20.22 Å2
2--0.55 Å20 Å2
3----0.76 Å2
Refinement stepCycle: LAST / Resolution: 1.25→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1911 0 4 359 2274
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0221967
X-RAY DIFFRACTIONr_bond_other_d0.0020.021814
X-RAY DIFFRACTIONr_angle_refined_deg2.091.9452675
X-RAY DIFFRACTIONr_angle_other_deg2.51434217
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1445247
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_restr0.1490.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022171
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02401
X-RAY DIFFRACTIONr_nbd_refined0.2390.2309
X-RAY DIFFRACTIONr_nbd_other0.2760.22039
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0950.21247
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2181
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3380.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3340.2101
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1270.234
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1961.51244
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.24222032
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.8183723
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.4054.5642
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: 1.25→1.28 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.228 57
Rwork0.183 4262
Refinement
*PLUS
Lowest resolution: 37 Å / Rfactor Rfree: 0.171 / Rfactor Rwork: 0.153
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.021
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.15

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