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- PDB-9mx8: Crystal structure of the DNA binding domain of FLI1 in complex wi... -

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Basic information

Entry
Database: PDB / ID: 9mx8
TitleCrystal structure of the DNA binding domain of FLI1 in complex with a DNA containing three contiguous GGAA sites
Components
  • DNA (5'-D(*CP*AP*CP*TP*TP*CP*CP*TP*TP*CP*CP*TP*TP*CP*CP*GP*GP*TP*C)-3')
  • DNA (5'-D(P*GP*AP*CP*CP*GP*GP*AP*AP*GP*GP*AP*AP*GP*GP*AP*AP*GP*TP*G)-3')
  • Friend leukemia integration 1 transcription factor
KeywordsDNA BINDING PROTEIN/DNA / oncogene / Ewing sarcoma / transcription factor / microsatellite / DNA BINDING PROTEIN-DNA complex / DNA BINDING PROTEIN
Function / homology
Function and homology information


hemostasis / blood circulation / megakaryocyte development / animal organ morphogenesis / Transcriptional regulation of granulopoiesis / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / transcription cis-regulatory region binding ...hemostasis / blood circulation / megakaryocyte development / animal organ morphogenesis / Transcriptional regulation of granulopoiesis / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / transcription cis-regulatory region binding / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / DNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Friend leukemia integration 1 transcription factor, pointed domain / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Ets-domain signature 1. / Ets-domain signature 2. / Ets domain / ETS family / Ets-domain ...Friend leukemia integration 1 transcription factor, pointed domain / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Ets-domain signature 1. / Ets-domain signature 2. / Ets domain / ETS family / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Sterile alpha motif/pointed domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Friend leukemia integration 1 transcription factor
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsHou, C. / Tsodikov, O.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA243529 United States
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: Structure and cooperative formation of a FLI1 filament on contiguous GGAA DNA sites.
Authors: Hou, C. / Tsodikov, O.V.
History
DepositionJan 17, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Friend leukemia integration 1 transcription factor
C: Friend leukemia integration 1 transcription factor
D: Friend leukemia integration 1 transcription factor
E: DNA (5'-D(P*GP*AP*CP*CP*GP*GP*AP*AP*GP*GP*AP*AP*GP*GP*AP*AP*GP*TP*G)-3')
F: DNA (5'-D(*CP*AP*CP*TP*TP*CP*CP*TP*TP*CP*CP*TP*TP*CP*CP*GP*GP*TP*C)-3')


Theoretical massNumber of molelcules
Total (without water)53,2395
Polymers53,2395
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8390 Å2
ΔGint-56 kcal/mol
Surface area19360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.539, 91.539, 180.728
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Friend leukemia integration 1 transcription factor / Proto-oncogene Fli-1 / Transcription factor ERGB


Mass: 13862.581 Da / Num. of mol.: 3 / Fragment: DNA-binding domain (residues 259-375) / Mutation: F362A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FLI1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q01543
#2: DNA chain DNA (5'-D(P*GP*AP*CP*CP*GP*GP*AP*AP*GP*GP*AP*AP*GP*GP*AP*AP*GP*TP*G)-3')


Mass: 5992.899 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*CP*AP*CP*TP*TP*CP*CP*TP*TP*CP*CP*TP*TP*CP*CP*GP*GP*TP*C)-3')


Mass: 5658.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Has protein modificationN

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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: 4.11 Å3/Da / Density % sol: 70.04 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium cacodylate, pH 7.0, 1.6 M sodium acetate, added cryoprotectant: 34% sucrose

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.15→50 Å / Num. obs: 10335 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 10 % / CC1/2: 1 / Net I/σ(I): 10.6
Reflection shellResolution: 3.15→3.2 Å / Num. unique obs: 775 / CC1/2: 0.996

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5JVT

5jvt


Resolution: 3.15→39.67 Å / Cor.coef. Fo:Fc: 0.879 / Cor.coef. Fo:Fc free: 0.833 / SU B: 20.466 / SU ML: 0.366 / Cross valid method: THROUGHOUT / ESU R Free: 0.59 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27833 552 5.4 %RANDOM
Rwork0.24978 ---
obs0.25133 9739 65.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.349 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20.24 Å20 Å2
2--0.49 Å20 Å2
3----1.58 Å2
Refinement stepCycle: 1 / Resolution: 3.15→39.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2415 775 0 0 3190
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0123349
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182711
X-RAY DIFFRACTIONr_angle_refined_deg1.0781.5134682
X-RAY DIFFRACTIONr_angle_other_deg1.1351.8176253
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1865295
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.65221.418141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.14915420
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0581519
X-RAY DIFFRACTIONr_chiral_restr0.0440.2417
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023273
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02820
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9236.91195
X-RAY DIFFRACTIONr_mcbond_other1.9226.8981194
X-RAY DIFFRACTIONr_mcangle_it3.4610.3261485
X-RAY DIFFRACTIONr_mcangle_other3.45910.3281486
X-RAY DIFFRACTIONr_scbond_it1.4335.5312154
X-RAY DIFFRACTIONr_scbond_other1.4325.5312153
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6288.2483197
X-RAY DIFFRACTIONr_long_range_B_refined5.26862.724022
X-RAY DIFFRACTIONr_long_range_B_other5.26762.7134023
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.15→3.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.219 20 -
Rwork0.185 193 -
obs--19.03 %

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