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- PDB-6vg2: Crystal structure of the DNA binding domain of human transcriptio... -

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Basic information

Entry
Database: PDB / ID: 6vg2
TitleCrystal structure of the DNA binding domain of human transcription factor FLI1 in complex with 16-mer DNA CAGAGGATGTGGCTTC
Components
  • DNA (5'-D(*GP*AP*AP*GP*CP*CP*AP*CP*TP*TP*CP*CP*GP*GP*TP*C)-3')
  • DNA (5'-D(*GP*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP*GP*CP*TP*TP*C)-3')
  • Friend leukemia integration 1 transcription factor
KeywordsTRANSCRIPTION / DNA binding / Ewing sarcoma / Leukemia / Oncogenesis / 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 / nuclear body / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific ...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 / nuclear body / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / 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 family / Ets-domain signature 2. / Ets domain / 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 family / Ets-domain signature 2. / Ets domain / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 Å
AuthorsHou, C. / Tsodikov, O.V.
Funding support United States, 2items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)PC150300P1 United States
Department of Defense (DOD, United States)PC150300P2 United States
CitationJournal: Structure / Year: 2021
Title: Allosteric interference in oncogenic FLI1 and ERG transactions by mithramycins.
Authors: Hou, C. / Mandal, A. / Rohr, J. / Tsodikov, O.V.
History
DepositionJan 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 19, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
B: DNA (5'-D(*GP*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP*GP*CP*TP*TP*C)-3')
C: DNA (5'-D(*GP*AP*AP*GP*CP*CP*AP*CP*TP*TP*CP*CP*GP*GP*TP*C)-3')
D: Friend leukemia integration 1 transcription factor
E: DNA (5'-D(*GP*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP*GP*CP*TP*TP*C)-3')
F: DNA (5'-D(*GP*AP*AP*GP*CP*CP*AP*CP*TP*TP*CP*CP*GP*GP*TP*C)-3')


Theoretical massNumber of molelcules
Total (without water)43,7926
Polymers43,7926
Non-polymers00
Water0
1
A: Friend leukemia integration 1 transcription factor
B: DNA (5'-D(*GP*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP*GP*CP*TP*TP*C)-3')
C: DNA (5'-D(*GP*AP*AP*GP*CP*CP*AP*CP*TP*TP*CP*CP*GP*GP*TP*C)-3')


Theoretical massNumber of molelcules
Total (without water)21,8963
Polymers21,8963
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-23 kcal/mol
Surface area10210 Å2
MethodPISA
2
D: Friend leukemia integration 1 transcription factor
E: DNA (5'-D(*GP*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP*GP*CP*TP*TP*C)-3')
F: DNA (5'-D(*GP*AP*AP*GP*CP*CP*AP*CP*TP*TP*CP*CP*GP*GP*TP*C)-3')


Theoretical massNumber of molelcules
Total (without water)21,8963
Polymers21,8963
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-23 kcal/mol
Surface area10260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.422, 90.732, 165.204
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121

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Components

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


Mass: 12098.655 Da / Num. of mol.: 2 / Fragment: DNA binding domain
Source method: isolated from a genetically manipulated source
Details: Region GPHM at the N-terminus is a leftover from the affinity tag.
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*TP*GP*GP*CP*TP*TP*C)-3')


Mass: 4954.214 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Enhancer DNA / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*GP*AP*AP*GP*CP*CP*AP*CP*TP*TP*CP*CP*GP*GP*TP*C)-3')


Mass: 4843.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Enhancer DNA / Source: (synth.) Homo sapiens (human)

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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: 3.59 Å3/Da / Density % sol: 65.74 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 1.6 M ammonium sulfate

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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: RAYONIX MX300-HS / Detector: CCD / Date: Oct 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.65→50 Å / Num. obs: 6615 / % possible obs: 95.8 % / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 8.1
Reflection shellResolution: 3.65→3.71 Å / Num. unique obs: 287 / CC1/2: 0.493

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JVT

5jvt


Resolution: 3.9→35 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.895 / SU B: 74.53 / SU ML: 0.949 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.856 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2943 260 4.7 %RANDOM
Rwork0.2474 ---
obs0.2495 5326 97.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 273.76 Å2 / Biso mean: 125.421 Å2 / Biso min: 75.31 Å2
Baniso -1Baniso -2Baniso -3
1--11.96 Å20 Å20 Å2
2--24.57 Å20 Å2
3----12.61 Å2
Refinement stepCycle: final / Resolution: 3.9→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1525 1299 0 0 2824
Num. residues----249
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0123019
X-RAY DIFFRACTIONr_bond_other_d0.0150.0182121
X-RAY DIFFRACTIONr_angle_refined_deg1.0631.4014345
X-RAY DIFFRACTIONr_angle_other_deg1.5442.0744947
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9225183
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.01321.70294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.40415274
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1091512
X-RAY DIFFRACTIONr_chiral_restr0.0570.2381
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022526
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02698
LS refinement shellResolution: 3.9→4 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 20 -
Rwork0.353 341 -
all-361 -
obs--89.58 %

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