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- PDB-2j6w: R164N mutant of the RUNX1 Runt domain -

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Basic information

Entry
Database: PDB / ID: 2j6w
TitleR164N mutant of the RUNX1 Runt domain
ComponentsRUNT-RELATED TRANSCRIPTION FACTOR 1
KeywordsTRANSCRIPTION / TRANSCRIPTION FACTOR / TRANSCRIPTION/DNA / CHLORIDE BINDING / ACUTE MYELOID LEUKEMIA / TRANSCRIPTION REGULATION / NUCLEAR PROTEIN / PHOSPHORYLATION / AML / RUNX1 / IG FOLD / RUNT DOMAIN / DNA-BINDING
Function / homology
Function and homology information


regulation of hair follicle cell proliferation / SLC-mediated transport of organic cations / 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 interacts with co-factors whose precise effect on RUNX1 targets is not known / positive regulation of granulocyte differentiation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) ...regulation of hair follicle cell proliferation / SLC-mediated transport of organic cations / 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 interacts with co-factors whose precise effect on RUNX1 targets is not known / positive regulation of granulocyte differentiation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / core-binding factor complex / positive regulation of CD8-positive, alpha-beta T cell differentiation / positive regulation of cell maturation / myeloid leukocyte differentiation / negative regulation of CD4-positive, alpha-beta T cell differentiation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / negative regulation of granulocyte differentiation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / neuron fate commitment / Estrogen-dependent gene expression / myeloid progenitor cell differentiation / myeloid cell differentiation / definitive hemopoiesis / regulation of T cell anergy / embryonic hemopoiesis / hair follicle morphogenesis / hemopoiesis / regulation of cell differentiation / basement membrane / behavioral response to pain / regulation of signal transduction / chondrocyte differentiation / response to retinoic acid / cellular response to transforming growth factor beta stimulus / neuron development / positive regulation of interleukin-2 production / ossification / transcription corepressor binding / central nervous system development / skeletal system development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / promoter-specific chromatin binding / liver development / transcription coactivator binding / positive regulation of type II interferon production / neuron differentiation / positive regulation of angiogenesis / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / gene expression / in utero embryonic development / 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 / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / calcium ion binding / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / 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: 2.6 Å
AuthorsGrembecka, J. / Zhe, L. / Lukasik, S.M. / Liu, Y. / Bielnicka, I. / Bushweller, J.H. / Speck, N.A.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: A Mutation in the S-Switch Region of the Runt Domain Alters the Dynamics of an Allosteric Network Responsible for Cbfbeta Regulation.
Authors: Li, Z. / Lukasik, S.M. / Liu, Y. / Grembecka, J. / Bielnicka, I. / Bushweller, J.H. / Speck, N.A.
History
DepositionOct 4, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 10, 2011Group: Database references / Derived calculations
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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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)31,1036
Polymers30,9612
Non-polymers1424
Water88349
1
A: RUNT-RELATED TRANSCRIPTION FACTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5513
Polymers15,4801
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)15,5513
Polymers15,4801
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)91.948, 46.497, 63.552
Angle α, β, γ (deg.)90.00, 90.66, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein RUNT-RELATED TRANSCRIPTION FACTOR 1 / CORE-BINDING FACTOR ALPHA 2 SUBUNIT / CBF-ALPHA 2 / ACUTE MYELOID LEUKEMIA 1 PROTEIN / ONCOGENE AML- ...CORE-BINDING FACTOR ALPHA 2 SUBUNIT / CBF-ALPHA 2 / ACUTE MYELOID LEUKEMIA 1 PROTEIN / ONCOGENE AML-1 / 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 / R164N MUTANT OF THE RUNX1 RUNT DOMAIN


Mass: 15480.460 Da / Num. of mol.: 2 / Fragment: RUNT DOMAIN, RESIDUES 46-185 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PET3C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)PLYS / 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.: 49 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 72 TO SER ENGINEERED RESIDUE IN CHAIN A, CYS 81 TO SER ...ENGINEERED RESIDUE IN CHAIN A, CYS 72 TO SER ENGINEERED RESIDUE IN CHAIN A, CYS 81 TO SER ENGINEERED RESIDUE IN CHAIN A, ARG 164 TO ASN ENGINEERED RESIDUE IN CHAIN B, CYS 72 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 81 TO SER ENGINEERED RESIDUE IN CHAIN B, ARG 164 TO ASN
Sequence detailsR164N

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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: 2.1 Å3/Da / Density % sol: 42 % / Description: NONE
Crystal growpH: 6.5
Details: 22% PEG 8000, 0.1M SODIUM CACODYLATE PH=6.5, 0.2M AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794
DetectorType: BUILT IN ANL / Detector: CCD / Date: Jun 18, 2005
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 7962 / % possible obs: 94.5 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 19.6
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.3 / % possible all: 73.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKLdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EAO

1eao


Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.889 / SU B: 26.087 / SU ML: 0.272 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.383 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.268 776 9.7 %RANDOM
Rwork0.209 ---
obs0.214 7186 94.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20 Å2-1.01 Å2
2---1.95 Å20 Å2
3---1.22 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1894 0 4 49 1947
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221934
X-RAY DIFFRACTIONr_bond_other_d0.0050.021774
X-RAY DIFFRACTIONr_angle_refined_deg2.2381.952638
X-RAY DIFFRACTIONr_angle_other_deg1.77434114
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.7695246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.47923.65982
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.07115304
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.0511514
X-RAY DIFFRACTIONr_chiral_restr0.0450.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.022156
X-RAY DIFFRACTIONr_gen_planes_other00.02384
X-RAY DIFFRACTIONr_nbd_refined0.1180.2259
X-RAY DIFFRACTIONr_nbd_other0.0940.21512
X-RAY DIFFRACTIONr_nbtor_refined0.1250.2871
X-RAY DIFFRACTIONr_nbtor_other0.060.21062
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0680.264
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0410.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.0810.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0580.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.0811.51595
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.09522016
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.133797
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.2154.5622
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: 2.6→2.67 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.387 43
Rwork0.273 384
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.09340.2526-0.24085.99791.90866.27810.0708-0.04950.04430.0567-0.16050.0784-0.0006-0.08060.0897-0.2292-0.05380.05340.11090.0164-0.33477.94517.21815.525
22.2661.2688-0.20822.80490.18946.0319-0.0423-0.03440.0615-0.04950.04020.1474-0.18390.05390.0021-0.2214-0.03760.06970.11370.0108-0.258329.848-17.09718.747
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A50 - 173
2X-RAY DIFFRACTION2B50 - 173

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