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- PDB-9cp6: Crystal structure of the DNA binding domain of FLI1 (residues 259-371) -

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Basic information

Entry
Database: PDB / ID: 9cp6
TitleCrystal structure of the DNA binding domain of FLI1 (residues 259-371)
ComponentsFriend leukemia integration 1 transcription factor
KeywordsDNA BINDING PROTEIN / transcription factor / Ewing sarcoma / ETS family
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
Friend leukemia integration 1 transcription factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsHou, C. / Tsodikov, O.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA243529 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
DepositionJul 17, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI ..._citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Friend leukemia integration 1 transcription factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4962
Polymers13,4731
Non-polymers231
Water1,11762
1
A: Friend leukemia integration 1 transcription factor
hetero molecules

A: Friend leukemia integration 1 transcription factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9924
Polymers26,9462
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/61
Buried area1950 Å2
ΔGint-39 kcal/mol
Surface area10240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.584, 44.584, 175.704
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-541-

HOH

21A-549-

HOH

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Components

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


Mass: 13473.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: human FLI1 (residues 259-371) / Source: (gene. exp.) Homo sapiens (human) / Gene: FLI1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q01543
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
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: 1.87 Å3/Da / Density % sol: 34.25 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M Hepes, pH 6.5, 1 M Na citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Jun 12, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.66→50 Å / Num. obs: 13210 / % possible obs: 100 % / Redundancy: 11.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Net I/σ(I): 48
Reflection shellResolution: 1.66→1.69 Å / Redundancy: 10.9 % / Num. unique obs: 632 / CC1/2: 0.939

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.66→35 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.936 / SU B: 1.878 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23542 691 5.3 %RANDOM
Rwork0.2024 ---
obs0.2041 12396 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.441 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20.06 Å2-0 Å2
2--0.12 Å2-0 Å2
3----0.4 Å2
Refinement stepCycle: 1 / Resolution: 1.66→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms801 0 1 62 864
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.013821
X-RAY DIFFRACTIONr_bond_other_d0.0010.018760
X-RAY DIFFRACTIONr_angle_refined_deg1.3681.6461105
X-RAY DIFFRACTIONr_angle_other_deg1.3761.5941743
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.934598
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.15221.70247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.67815143
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.289156
X-RAY DIFFRACTIONr_chiral_restr0.0710.299
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02937
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02211
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_it1.6152.095395
X-RAY DIFFRACTIONr_mcbond_other1.6152.089394
X-RAY DIFFRACTIONr_mcangle_it2.6483.131492
X-RAY DIFFRACTIONr_mcangle_other2.6453.138493
X-RAY DIFFRACTIONr_scbond_it2.3662.487425
X-RAY DIFFRACTIONr_scbond_other2.3642.493426
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8953.596613
X-RAY DIFFRACTIONr_long_range_B_refined6.45725.169983
X-RAY DIFFRACTIONr_long_range_B_other6.36924.796969
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.66→1.703 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 55 -
Rwork0.24 871 -
obs--100 %

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