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- PDB-9mxa: Crystal structure of the DNA binding domain of FLI1 (wild-type) i... -

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Basic information

Entry
Database: PDB / ID: 9mxa
TitleCrystal structure of the DNA binding domain of FLI1 (wild-type) in complex with a DNA containing two contiguous GGAA sites
Components
  • DNA (5'-D(*CP*AP*CP*TP*TP*CP*CP*TP*TP*CP*CP*GP*GP*TP*C)-3')
  • DNA (5'-D(*GP*AP*CP*CP*GP*GP*AP*AP*GP*GP*AP*AP*GP*TP*G)-3')
  • Friend leukemia integration 1 transcription factor
KeywordsDNA BINDING PROTEIN/DNA / Ewing sarcoma / transcription factor / oncogenesis / bone tumor / drug target / deregulation / 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 / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / 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 / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / 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: 2.59 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
E: DNA (5'-D(*GP*AP*CP*CP*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*GP*GP*TP*C)-3')


Theoretical massNumber of molelcules
Total (without water)42,7544
Polymers42,7544
Non-polymers00
Water905
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-44 kcal/mol
Surface area13900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.949, 96.949, 185.748
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

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


Mass: 16786.859 Da / Num. of mol.: 2 / Fragment: DNA-binding domain (residues 259-399)
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(*GP*AP*CP*CP*GP*GP*AP*AP*GP*GP*AP*AP*GP*TP*G)-3')


Mass: 4708.073 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*GP*GP*TP*C)-3')


Mass: 4471.897 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
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: 2.55 Å3/Da / Density % sol: 51.81 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris, pH 8.5, 2 M ammonium phosphate

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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: Dec 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. obs: 13984 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 13.6 % / CC1/2: 1 / Rmerge(I) obs: 0.071 / Net I/σ(I): 47
Reflection shellResolution: 2.59→2.63 Å / Num. unique obs: 699 / CC1/2: 0.899

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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: 2.59→40 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.922 / SU B: 42.066 / SU ML: 0.376 / Cross valid method: THROUGHOUT / ESU R: 0.465 / ESU R Free: 0.306 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28738 674 4.8 %RANDOM
Rwork0.26048 ---
obs0.26179 13295 98.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 98.744 Å2
Baniso -1Baniso -2Baniso -3
1--1.71 Å20 Å2-0 Å2
2---1.71 Å2-0 Å2
3---3.42 Å2
Refinement stepCycle: 1 / Resolution: 2.59→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1531 608 0 5 2144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0122250
X-RAY DIFFRACTIONr_bond_other_d0.0030.0181780
X-RAY DIFFRACTIONr_angle_refined_deg1.3761.4913161
X-RAY DIFFRACTIONr_angle_other_deg1.2931.8654105
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5495186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.72321.09991
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.1615270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6391513
X-RAY DIFFRACTIONr_chiral_restr0.0620.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022137
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02556
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_it3.1864.464753
X-RAY DIFFRACTIONr_mcbond_other3.1884.47752
X-RAY DIFFRACTIONr_mcangle_it5.3996.672936
X-RAY DIFFRACTIONr_mcangle_other5.3966.665937
X-RAY DIFFRACTIONr_scbond_it2.4753.3481494
X-RAY DIFFRACTIONr_scbond_other2.4763.351493
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2864.9312225
X-RAY DIFFRACTIONr_long_range_B_refined8.43637.0232744
X-RAY DIFFRACTIONr_long_range_B_other8.43437.0122745
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.594→2.661 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.41 46 -
Rwork0.433 960 -
obs--99.51 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0025-0.01430.03310.1328-0.07890.7174-0.06730.02880.00590.0728-0.33930.0490.02860.09790.40650.2782-0.0361-0.32540.6755-0.43781.236525.91157.399139.2095
20.9160.0789-0.19532.8591-1.90871.4462-0.0530.14210.26250.25550.1403-0.2470.0624-0.3-0.08730.647-0.1543-0.15060.8049-0.12970.972512.091-5.886415.611
32.9909-1.50640.49051.8214-0.45692.9343-0.0161-0.5050.6163-0.1734-0.59-0.8487-0.1809-0.40960.60610.66390.1268-0.21690.691-0.23321.389724.48610.634322.7908
40.51470.49460.45270.80560.9683.6165-0.1363-0.24560.1362-0.2413-0.3134-0.2187-0.37790.32890.44970.6272-0.0702-0.07120.6537-0.07161.180625.8663-0.838524.6583
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A281 - 369
2X-RAY DIFFRACTION2D268 - 373
3X-RAY DIFFRACTION3E1 - 15
4X-RAY DIFFRACTION4F1 - 15

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