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- PDB-3jtg: Crystal structure of mouse Elf3 C-terminal DNA-binding domain in ... -

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Basic information

Entry
Database: PDB / ID: 3jtg
TitleCrystal structure of mouse Elf3 C-terminal DNA-binding domain in complex with type II TGF-beta receptor promoter DNA
Components
  • DNA (5'-D(*CP*AP*AP*AP*CP*AP*GP*GP*AP*AP*AP*CP*TP*CP*CP*T)-3')
  • DNA (5'-D(*GP*AP*GP*GP*AP*GP*TP*TP*TP*CP*CP*TP*GP*TP*TP*T)-3')
  • ETS-related transcription factor Elf-3
KeywordsTRANSCRIPTION / Elf3 / protein-dna complex / type II TGF-beta receptor / Activator / Alternative splicing / Cytoplasm / Developmental protein / Differentiation / DNA-binding / Inflammatory response / Nucleus / Repressor / Transcription regulation
Function / homology
Function and homology information


Pre-NOTCH Transcription and Translation / mammary gland involution / blastocyst development / anatomical structure morphogenesis / extracellular matrix organization / DNA-binding transcription activator activity, RNA polymerase II-specific / cell differentiation / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity ...Pre-NOTCH Transcription and Translation / mammary gland involution / blastocyst development / anatomical structure morphogenesis / extracellular matrix organization / DNA-binding transcription activator activity, RNA polymerase II-specific / cell differentiation / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / Golgi apparatus / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
ETS-related transcription factor Elf-3, pointed domain / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Ets domain / ETS family / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain ...ETS-related transcription factor Elf-3, pointed domain / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Ets domain / ETS family / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Sterile alpha motif/pointed domain superfamily / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / ETS-related transcription factor Elf-3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsTahirov, T.H. / Babayeva, N.D. / Agarkar, V.B. / Rizzino, A.
Citation
Journal: J.Mol.Biol. / Year: 2010
Title: Crystal structure of mouse Elf3 C-terminal DNA-binding domain in complex with type II TGF-beta receptor promoter DNA.
Authors: Agarkar, V.B. / Babayeva, N.D. / Wilder, P.J. / Rizzino, A. / Tahirov, T.H.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Preliminary crystallographic analysis of mouse Elf3 C-terminal DNA-binding domain in complex with type II TGF-beta receptor promoter DNA
Authors: Agarkar, V.B. / Babayeva, N.D. / Rizzino, A. / Tahirov, T.H.
History
DepositionSep 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ETS-related transcription factor Elf-3
B: DNA (5'-D(*GP*AP*GP*GP*AP*GP*TP*TP*TP*CP*CP*TP*GP*TP*TP*T)-3')
C: DNA (5'-D(*CP*AP*AP*AP*CP*AP*GP*GP*AP*AP*AP*CP*TP*CP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)22,2683
Polymers22,2683
Non-polymers00
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-27 kcal/mol
Surface area10130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.660, 52.005, 99.783
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ETS-related transcription factor Elf-3 / E74-like factor 3 / Epithelium-specific Ets transcription factor 1 / ESE-1 / Epithelium-restricted ...E74-like factor 3 / Epithelium-specific Ets transcription factor 1 / ESE-1 / Epithelium-restricted Ets protein ESX / Epithelial-restricted with serine box


Mass: 12472.242 Da / Num. of mol.: 1 / Fragment: residues 289-391
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Elf3, Ert, Esx, Jen / Plasmid: pET-28b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) E.coli / References: UniProt: Q3UPW2
#2: DNA chain DNA (5'-D(*GP*AP*GP*GP*AP*GP*TP*TP*TP*CP*CP*TP*GP*TP*TP*T)-3')


Mass: 4935.198 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: sequences obtained from type II TGF-beta receptor promoter DNA
#3: DNA chain DNA (5'-D(*CP*AP*AP*AP*CP*AP*GP*GP*AP*AP*AP*CP*TP*CP*CP*T)-3')


Mass: 4860.196 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: sequences obtained from type II TGF-beta receptor promoter DNA
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.49 Å3/Da / Density % sol: 50.51 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M ammonium acetate, 0.01 M magnesium acetate tetrahydrate, 0.05 M sodium cacodylate trihydrate pH 6.5, 25% w/v PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 17, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 11575 / Num. obs: 11575 / % possible obs: 97.6 % / Observed criterion σ(I): -1 / Redundancy: 5.8 % / Biso Wilson estimate: 31.2 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 53.45
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 6 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 9.9 / Num. unique all: 587 / % possible all: 97.5

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Processing

Software
NameClassification
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→36 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1294278.67 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.263 585 5.1 %RANDOM
Rwork0.234 ---
obs0.234 11365 96.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.0553 Å2 / ksol: 0.333095 e/Å3
Displacement parametersBiso mean: 45.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20 Å20 Å2
2---0.53 Å20 Å2
3----0.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.61 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.2→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms818 650 0 54 1522
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.02
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.056 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.536 91 5.1 %
Rwork0.403 1688 -
obs--92.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramwater.top
X-RAY DIFFRACTION3water_rep.paramdna-rna.top

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