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- PDB-1hjc: CRYSTAL STRUCTURE OF RUNX-1/AML1/CBFALPHA RUNT DOMAIN BOUND TO A ... -

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Basic information

Entry
Database: PDB / ID: 1hjc
TitleCRYSTAL STRUCTURE OF RUNX-1/AML1/CBFALPHA RUNT DOMAIN BOUND TO A DNA FRAGMENT FROM THE CSF-1R PROMOTER
Components
  • DNA (5'-(*GP*AP*AP*CP*TP*CP*TP*GP*TP*GP*GP* TP*TP*GP*CP*G)-3')
  • DNA (5'-(CP*CP*GP*CP*AP*AP*CP*CP*AP*CP*AP* GP*AP*GP*TP*T)-3')
  • RUNT-RELATED TRANSCRIPTION FACTOR 1
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / TRANSCRIPTION FACTOR / BZIP / RUNX / RUNT / C/EBP / CBF / CORE BINDING FACTOR / AML1 / AML / ONCOPROTEIN / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


regulation of hair follicle cell proliferation / SLC-mediated transport of organic cations / 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) / core-binding factor complex ...regulation of hair follicle cell proliferation / SLC-mediated transport of organic cations / 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) / 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 / central nervous system neuron differentiation / embryonic hemopoiesis / hair follicle morphogenesis / behavioral response to pain / hemopoiesis / basement membrane / regulation of signal transduction / response to retinoic acid / neuron development / cellular response to transforming growth factor beta stimulus / positive regulation of interleukin-2 production / central nervous system development / skeletal system development / liver development / positive regulation of type II interferon production / positive regulation of angiogenesis / neuron differentiation / 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
DNA / DNA (> 10) / Runt-related transcription factor 1
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsTahirov, T.H. / Ogata, K.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 2001
Title: Structural Analyses of DNA Recognition by the Aml1/Runx-1 Runt Domain and its Allosteric Control by Cbfbeta
Authors: Tahirov, T.H. / Inoue-Bungo, T. / Morii, H. / Fujikawa, A. / Sasaki, M. / Kimura, K. / Shiina, M. / Sato, K. / Kumasaka, T. / Yamamoto, M. / Ishii, S. / Ogata, K.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Crystallization and Preliminary X-Ray Analyses of Quaternary, Ternary and Binary Protein-DNA Complexes with Involvement of Aml1/Runx-1/Cbfalpha Runt Domain, Cbfbeta and the C/Ebpbeta bZIP Region
Authors: Tahirov, T.H. / Inoue-Bungo, T. / Sasaki, M. / Shiina, M. / Kimura, K. / Sato, K. / Kumasaka, T. / Yamamoto, M. / Kamiya, N. / Ogata, K.
History
DepositionJan 11, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 9, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.4Dec 13, 2023Group: 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

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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: DNA (5'-(*GP*AP*AP*CP*TP*CP*TP*GP*TP*GP*GP* TP*TP*GP*CP*G)-3')
C: DNA (5'-(CP*CP*GP*CP*AP*AP*CP*CP*AP*CP*AP* GP*AP*GP*TP*T)-3')
D: RUNT-RELATED TRANSCRIPTION FACTOR 1
E: DNA (5'-(*GP*AP*AP*CP*TP*CP*TP*GP*TP*GP*GP* TP*TP*GP*CP*G)-3')
F: DNA (5'-(CP*CP*GP*CP*AP*AP*CP*CP*AP*CP*AP* GP*AP*GP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)47,0266
Polymers47,0266
Non-polymers00
Water1,04558
1
A: RUNT-RELATED TRANSCRIPTION FACTOR 1
B: DNA (5'-(*GP*AP*AP*CP*TP*CP*TP*GP*TP*GP*GP* TP*TP*GP*CP*G)-3')
C: DNA (5'-(CP*CP*GP*CP*AP*AP*CP*CP*AP*CP*AP* GP*AP*GP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)23,5133
Polymers23,5133
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
D: RUNT-RELATED TRANSCRIPTION FACTOR 1
E: DNA (5'-(*GP*AP*AP*CP*TP*CP*TP*GP*TP*GP*GP* TP*TP*GP*CP*G)-3')
F: DNA (5'-(CP*CP*GP*CP*AP*AP*CP*CP*AP*CP*AP* GP*AP*GP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)23,5133
Polymers23,5133
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)51.094, 104.073, 116.185
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsCHAIN AND DNA DUPLEX

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Components

#1: Protein RUNT-RELATED TRANSCRIPTION FACTOR 1 / CORE-BINDING FACTOR / ALPHA B SUBUNIT / RUNX-1 / AML1 / PEBP2ALPHAB / CBFA2


Mass: 13715.696 Da / Num. of mol.: 2 / Fragment: RESIDUES 60-182
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PAR2156 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q03347
#2: DNA chain DNA (5'-(*GP*AP*AP*CP*TP*CP*TP*GP*TP*GP*GP* TP*TP*GP*CP*G)-3')


Mass: 4945.200 Da / Num. of mol.: 2 / Fragment: FRAGMENT FROM CSF-1R PROMOTER / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human)
#3: DNA chain DNA (5'-(CP*CP*GP*CP*AP*AP*CP*CP*AP*CP*AP* GP*AP*GP*TP*T)-3')


Mass: 4852.170 Da / Num. of mol.: 2 / Fragment: FRAGMENT FROM CSF-1R PROMOTER / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 3.28 Å3/Da / Density % sol: 61.3 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M AMMONIUM ACETATE, 0.15 M MAGNESIUM ACETATE, 5% W/V PEG 4000, 50 MM HEPES BUFFER, PH 7.0 AT 24 DEGREES C
Crystal grow
*PLUS
Temperature: 297 K / Method: vapor diffusion, sitting drop / Details: Tahirov, T.H., (2001) Acta Crystallogr., D57, 850.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein-DNA solution1drop
20.1 M1reservoirKCl
30.01 M1reservoirMgCl2
410 %(v/v)PEG4001reservoir
50.05 MMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1
DetectorType: RIGAKU RAXIS4 / Detector: IMAGE PLATE / Date: Jun 10, 2000 / Details: MIRRORS
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→20 Å / Num. obs: 17550 / % possible obs: 94.5 % / Observed criterion σ(I): 0 / Redundancy: 3.436 % / Biso Wilson estimate: 40.9 Å2 / Rsym value: 0.047 / Net I/σ(I): 26.6
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 2.91 % / Mean I/σ(I) obs: 10.9 / Rsym value: 0.092 / % possible all: 88.9
Reflection
*PLUS
Num. measured all: 61764 / Rmerge(I) obs: 0.047

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Processing

Software
NameVersionClassification
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS0.9phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IO4

1io4


Resolution: 2.65→18.01 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1305275.52 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT MODEL USED, ATOMS C, O, N, CA AND CB ARE HARMONICALLY RESTRAINED DURING REFINEMENT WITH HARMONIC RESTRAINT CONSTANT OF 50
RfactorNum. reflection% reflectionSelection details
Rfree0.263 876 5 %RANDOM
Rwork0.223 ---
obs0.223 17550 94.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.9964 Å2 / ksol: 0.298698 e/Å3
Displacement parametersBiso mean: 52.4 Å2
Baniso -1Baniso -2Baniso -3
1--25.93 Å20 Å20 Å2
2---21.77 Å20 Å2
3---47.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.38 Å
Luzzati d res low-20 Å
Luzzati sigma a0.7 Å0.58 Å
Refinement stepCycle: LAST / Resolution: 2.65→18.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1826 1300 0 58 3184
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.13
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.431.5
X-RAY DIFFRACTIONc_mcangle_it6.552
X-RAY DIFFRACTIONc_scbond_it5.892
X-RAY DIFFRACTIONc_scangle_it8.142.5
LS refinement shellResolution: 2.65→2.82 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.409 127 4.7 %
Rwork0.416 2561 -
obs--88.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.13

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