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

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Basic information

Entry
Database: PDB / ID: 9mwy
TitleCrystal structure of the DNA binding domain of FLI1 in complex with a DNA containing four contiguous GGAA sites
Components
  • 25-mer DNA containing four contiguous GGAA sites, bottom strand
  • 25-mer DNA containing four contiguous GGAA sites, top strand
  • Friend leukemia integration 1 transcription factor
KeywordsDNA BINDING PROTEIN/DNA / transcription factor / Ewing sarcoma / leukemia / microsatellite / filament / TRANSCRIPTION-DNA complex / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
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: 3.28 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
D: Friend leukemia integration 1 transcription factor
C: Friend leukemia integration 1 transcription factor
L: Friend leukemia integration 1 transcription factor
G: 25-mer DNA containing four contiguous GGAA sites, bottom strand
H: 25-mer DNA containing four contiguous GGAA sites, top strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,2498
Polymers82,2036
Non-polymers462
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11540 Å2
ΔGint-93 kcal/mol
Surface area25760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.201, 78.201, 318.618
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 16710.762 Da / Num. of mol.: 4 / Fragment: DNA-binding domain (residues 259-399) / 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 25-mer DNA containing four contiguous GGAA sites, bottom strand


Mass: 7896.113 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain 25-mer DNA containing four contiguous GGAA sites, top strand


Mass: 7463.783 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
Has ligand of interestN
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: 2.96 Å3/Da / Density % sol: 58.49 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M Tris, pH 6.5, 0.7 M sodium acetate

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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: Jul 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.27→50 Å / Num. obs: 16164 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 10.1 % / CC1/2: 1 / Net I/σ(I): 14.4
Reflection shellResolution: 3.27→3.33 Å / Num. unique obs: 753 / CC1/2: 0.989

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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: 3.28→40 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.872 / SU B: 97.647 / SU ML: 0.616 / Cross valid method: THROUGHOUT / ESU R Free: 0.915 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28126 372 4.9 %RANDOM
Rwork0.21393 ---
obs0.21721 7168 46.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 100.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.15 Å2
Refinement stepCycle: 1 / Resolution: 3.28→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3097 1016 2 0 4115
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0124312
X-RAY DIFFRACTIONr_bond_other_d0.0160.0183485
X-RAY DIFFRACTIONr_angle_refined_deg1.0521.5086030
X-RAY DIFFRACTIONr_angle_other_deg1.4711.8268031
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2345376
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.20421.514185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.11615547
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9141525
X-RAY DIFFRACTIONr_chiral_restr0.0410.2536
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024212
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021067
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_it13.11311.3141522
X-RAY DIFFRACTIONr_mcbond_other13.11811.3111521
X-RAY DIFFRACTIONr_mcangle_it17.58716.9341892
X-RAY DIFFRACTIONr_mcangle_other17.58416.9381893
X-RAY DIFFRACTIONr_scbond_it7.98910.2642790
X-RAY DIFFRACTIONr_scbond_other7.99210.2642789
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.08115.3414138
X-RAY DIFFRACTIONr_rigid_bond_restr8.81337795
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.28→3.365 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.293 20 -
obs--1.76 %

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