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- PDB-1hjb: CRYSTAL STRUCTURE OF RUNX-1/AML1/CBFALPHA RUNT DOMAIN AND C/EBPBE... -

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


granuloma formation / regulation of odontoblast differentiation / regulation of hair follicle cell proliferation / positive regulation of sodium-dependent phosphate transport / Organic cation transport / CHOP-C/EBP complex / C/EBP complex / positive regulation of progesterone secretion / RUNX1 regulates estrogen receptor mediated transcription / RUNX1 regulates transcription of genes involved in BCR signaling ...granuloma formation / regulation of odontoblast differentiation / regulation of hair follicle cell proliferation / positive regulation of sodium-dependent phosphate transport / Organic cation transport / CHOP-C/EBP complex / C/EBP complex / 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 / positive regulation of biomineral tissue development / myeloid cell development / integrated stress response signaling / T-helper 1 cell activation / 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 / hepatocyte proliferation / Response of EIF2AK1 (HRI) to heme deficiency / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RUNX1 regulates transcription of genes involved in differentiation of HSCs / ATF4 activates genes in response to endoplasmic reticulum stress / neuron fate commitment / regulation of osteoclast differentiation / Estrogen-dependent gene expression / mammary gland epithelial cell differentiation / myeloid progenitor cell differentiation / condensed chromosome, centromeric region / regulation of dendritic cell differentiation / definitive hemopoiesis / regulation of T cell anergy / regulation of interleukin-6 production / embryonic hemopoiesis / hair follicle morphogenesis / mammary gland epithelial cell proliferation / histone acetyltransferase binding / regulation of cell differentiation / positive regulation of interleukin-4 production / behavioral response to pain / ubiquitin-like protein ligase binding / hemopoiesis / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / Response of EIF2AK4 (GCN2) to amino acid deficiency / Transcriptional Regulation by VENTX / basement membrane / regulation of signal transduction / neuron development / embryonic placenta development / positive regulation of fat cell differentiation / RNA polymerase II core promoter sequence-specific DNA binding / chondrocyte differentiation / positive regulation of osteoblast differentiation / brown fat cell differentiation / Nuclear events stimulated by ALK signaling in cancer / negative regulation of T cell proliferation / response to retinoic acid / ovarian follicle development / cellular response to transforming growth factor beta stimulus / response to endoplasmic reticulum stress / positive regulation of interleukin-2 production / ossification / liver development / skeletal system development / acute-phase response / central nervous system development / promoter-specific chromatin binding / liver regeneration / cellular response to amino acid stimulus / RNA polymerase II transcription regulatory region sequence-specific DNA binding / neuron differentiation / kinase binding / chromatin DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / histone deacetylase binding / Transcriptional regulation of white adipocyte differentiation / nuclear matrix / positive regulation of inflammatory response / Transcriptional regulation of granulopoiesis / RNA polymerase II transcription regulator complex / positive regulation of type II interferon production / positive regulation of angiogenesis / sequence-specific double-stranded DNA binding / positive regulation of cold-induced thermogenesis / Senescence-Associated Secretory Phenotype (SASP) / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / in utero embryonic development / negative regulation of neuron apoptotic process / response to lipopolysaccharide / transcription by RNA polymerase II / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / defense response to bacterium
Similarity search - Function
CCAAT/enhancer-binding protein, chordates / : / 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. ...CCAAT/enhancer-binding protein, chordates / : / 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 / Basic region leucine zipper / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Basic-leucine zipper domain superfamily / p53/RUNT-type transcription factor, DNA-binding domain superfamily / p53-like transcription factor, DNA-binding / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / CCAAT/enhancer-binding protein beta / Runt-related transcription factor 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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 / struct_biol
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: CCAAT/ENHANCER BINDING PROTEIN BETA
B: CCAAT/ENHANCER BINDING PROTEIN BETA
C: RUNT-RELATED TRANSCRIPTION FACTOR 1
D: CCAAT/ENHANCER BINDING PROTEIN BETA
E: CCAAT/ENHANCER BINDING PROTEIN BETA
F: RUNT-RELATED TRANSCRIPTION FACTOR 1
G: DNA (5'-(*GP*AP*AP*GP*AP*TP*TP*TP*CP*CP* AP*AP*AP*CP*TP*CP*TP*GP*TP*GP*GP*TP*TP*GP*CP*G)-3')
H: DNA (5'-(*CP*CP*GP*CP*AP*AP*CP*CP*AP*CP* AP*GP*AP*GP*TP*TP*TP*GP*GP*AP*AP*AP*TP*CP*TP*T)-3')
I: DNA (5'-(*GP*AP*AP*GP*AP*TP*TP*TP*CP*CP* AP*AP*AP*CP*TP*CP*TP*GP*TP*GP*GP*TP*TP*GP*CP*G)-3')
J: DNA (5'-(*CP*CP*GP*CP*AP*AP*CP*CP*AP*CP* AP*GP*AP*GP*TP*TP*TP*GP*GP*AP*AP*AP*TP*CP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)100,37610
Polymers100,37610
Non-polymers00
Water00
1
A: CCAAT/ENHANCER BINDING PROTEIN BETA
B: CCAAT/ENHANCER BINDING PROTEIN BETA
C: RUNT-RELATED TRANSCRIPTION FACTOR 1
G: DNA (5'-(*GP*AP*AP*GP*AP*TP*TP*TP*CP*CP* AP*AP*AP*CP*TP*CP*TP*GP*TP*GP*GP*TP*TP*GP*CP*G)-3')
H: DNA (5'-(*CP*CP*GP*CP*AP*AP*CP*CP*AP*CP* AP*GP*AP*GP*TP*TP*TP*GP*GP*AP*AP*AP*TP*CP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)50,1885
Polymers50,1885
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
D: CCAAT/ENHANCER BINDING PROTEIN BETA
E: CCAAT/ENHANCER BINDING PROTEIN BETA
F: RUNT-RELATED TRANSCRIPTION FACTOR 1
I: DNA (5'-(*GP*AP*AP*GP*AP*TP*TP*TP*CP*CP* AP*AP*AP*CP*TP*CP*TP*GP*TP*GP*GP*TP*TP*GP*CP*G)-3')
J: DNA (5'-(*CP*CP*GP*CP*AP*AP*CP*CP*AP*CP* AP*GP*AP*GP*TP*TP*TP*GP*GP*AP*AP*AP*TP*CP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)50,1885
Polymers50,1885
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)102.165, 109.273, 127.405
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
CCAAT/ENHANCER BINDING PROTEIN BETA / C/EBP BETA / NFIL-6


Mass: 10248.872 Da / Num. of mol.: 4 / Fragment: RESIDUES 259-345
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PAR2156 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P17676
#2: Protein RUNT-RELATED TRANSCRIPTION FACTOR 1 / CORE BINDING FACTOR ALPHA / 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
#3: DNA chain DNA (5'-(*GP*AP*AP*GP*AP*TP*TP*TP*CP*CP* AP*AP*AP*CP*TP*CP*TP*GP*TP*GP*GP*TP*TP*GP*CP*G)-3')


Mass: 8018.176 Da / Num. of mol.: 2 / Fragment: FRAGMENT FROM CSF-1R PROMOTER / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human)
#4: DNA chain DNA (5'-(*CP*CP*GP*CP*AP*AP*CP*CP*AP*CP* AP*GP*AP*GP*TP*TP*TP*GP*GP*AP*AP*AP*TP*CP*TP*T)-3')


Mass: 7956.156 Da / Num. of mol.: 2 / Fragment: FRAGMENT FROM CSF-1R PROMOTER / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human)
Compound detailsC/EBP BETA IS IMPORTANT TRANSCRIPTIONAL ACTIVATOR IN THE REGULATION OF GENES INVOLVED IN IMMUNE AND ...C/EBP BETA IS IMPORTANT TRANSCRIPTIONAL ACTIVATOR IN THE REGULATION OF GENES INVOLVED IN IMMUNE AND INFLAMMATORY RESPONSES. SPECIFICALL THE CORE BINDING FACTOR ALPHA SUBUNIT BINDS DNA AND APPEARS TO HAVE A ROLE IN THE DEVELOPMENT OF NORMAL HEMATOPOIESIS.

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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: 3.54 Å3/Da / Density % sol: 64.4 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 5 MM MGSO4, 3% W/V PEG 4000, 1% V/V DIOXANE, 50 MM MES BUFFER, PH 5.6 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: BL41XU / Wavelength: 0.7085
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7085 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 26407 / % possible obs: 91.3 % / Observed criterion σ(I): 0 / Redundancy: 4.456 % / Biso Wilson estimate: 46 Å2 / Rsym value: 0.066 / Net I/σ(I): 13.1
Reflection shellResolution: 3→3.05 Å / Redundancy: 1.91 % / Mean I/σ(I) obs: 1.4 / Rsym value: 0.302 / % possible all: 71.9
Reflection
*PLUS
Num. measured all: 117670 / Rmerge(I) obs: 0.006

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Processing

Software
NameVersionClassification
CNS0.9refinement
HKL-2000data reduction
HKL-2000data scaling
CNS0.9phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IO4

1io4


Resolution: 3→30 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 173187.84 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT MODEL USED, BSOL IS DETERMINED MANUALLY AND FIXED. ATOMS C, O, N, AND CA ARE HARMONICALLY RESTRAINED DURING REFINEMENT WITH HARMONIC RESTRAINT CONSTANT OF 20
RfactorNum. reflection% reflectionSelection details
Rfree0.313 1264 4.8 %RANDOM
Rwork0.244 ---
obs0.244 26157 89.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 19 Å2 / ksol: 0.197986 e/Å3
Displacement parametersBiso mean: 72.9 Å2
Baniso -1Baniso -2Baniso -3
1-23.49 Å20 Å20 Å2
2---38.31 Å20 Å2
3---14.82 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.6 Å0.44 Å
Luzzati d res low-20 Å
Luzzati sigma a0.63 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4150 2120 0 0 6270
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.6
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_it21.581.5
X-RAY DIFFRACTIONc_mcangle_it26.382
X-RAY DIFFRACTIONc_scbond_it32.322
X-RAY DIFFRACTIONc_scangle_it35.122.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.425 170 5.1 %
Rwork0.36 3154 -
obs--69.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.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_deg20.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.13
LS refinement shell
*PLUS
Rfactor Rwork: 0.36

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