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Basic information

Entry
Database: PDB / ID: 5jvt
TitleCrystal structure of the DNA binding domain of transcription factor FLI1 in complex with an 11-mer DNA GACCGGAAGTG
Components
  • DNA (5'-D(*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*G)-3')
  • Friend leukemia integration 1 transcription factor
Keywordstranscription/dna / transcription / DNA binding / cancer / Ewing sarcoma / transcription-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 / 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-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / DNA / DNA (> 10) / Friend leukemia integration 1 transcription factor
Similarity search - Component
Biological speciesHomo sapiens (human)
Endothia gyrosa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsHou, C. / Tsodikov, O.V.
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Structures of mithramycin analogues bound to DNA and implications for targeting transcription factor FLI1.
Authors: Hou, C. / Weidenbach, S. / Cano, K.E. / Wang, Z. / Mitra, P. / Ivanov, D.N. / Rohr, J. / Tsodikov, O.V.
History
DepositionMay 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2016Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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*G)-3')
C: DNA (5'-D(*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*G)-3')
F: DNA (5'-D(*CP*AP*CP*TP*TP*CP*CP*GP*GP*TP*C)-3')
G: Friend leukemia integration 1 transcription factor
H: DNA (5'-D(*GP*AP*CP*CP*GP*GP*AP*AP*GP*TP*G)-3')
I: DNA (5'-D(*CP*AP*CP*TP*TP*CP*CP*GP*GP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,60811
Polymers56,4219
Non-polymers1872
Water362
1
A: Friend leukemia integration 1 transcription factor
B: DNA (5'-D(*GP*AP*CP*CP*GP*GP*AP*AP*GP*TP*G)-3')
C: DNA (5'-D(*CP*AP*CP*TP*TP*CP*CP*GP*GP*TP*C)-3')


Theoretical massNumber of molelcules
Total (without water)18,8073
Polymers18,8073
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-23 kcal/mol
Surface area8770 Å2
MethodPISA
2
D: Friend leukemia integration 1 transcription factor
E: DNA (5'-D(*GP*AP*CP*CP*GP*GP*AP*AP*GP*TP*G)-3')
F: DNA (5'-D(*CP*AP*CP*TP*TP*CP*CP*GP*GP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9024
Polymers18,8073
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-26 kcal/mol
Surface area8460 Å2
MethodPISA
3
G: Friend leukemia integration 1 transcription factor
H: DNA (5'-D(*GP*AP*CP*CP*GP*GP*AP*AP*GP*TP*G)-3')
I: DNA (5'-D(*CP*AP*CP*TP*TP*CP*CP*GP*GP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8994
Polymers18,8073
Non-polymers921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-20 kcal/mol
Surface area8410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)191.845, 191.845, 87.556
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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Protein , 1 types, 3 molecules ADG

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


Mass: 12098.655 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FLI1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: Q01543

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DNA chain , 2 types, 6 molecules BEHCFI

#2: DNA chain DNA (5'-D(*GP*AP*CP*CP*GP*GP*AP*AP*GP*TP*G)-3')


Mass: 3423.248 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Endothia gyrosa (fungus)
#3: DNA chain DNA (5'-D(*CP*AP*CP*TP*TP*CP*CP*GP*GP*TP*C)-3')


Mass: 3285.148 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Endothia gyrosa (fungus)

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Non-polymers , 3 types, 4 molecules

#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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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: 4.12 Å3/Da / Density % sol: 70.16 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 1.6 M ammonium sulphate, 0.1 M sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 17757 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 19

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5E8I

5e8i


Resolution: 3.1→40 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.933 / SU ML: 0.323 / Cross valid method: THROUGHOUT / ESU R: 0.814 / ESU R Free: 0.35 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23716 885 5 %RANDOM
Rwork0.19414 ---
obs0.19629 16790 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.92 Å2-0.46 Å20 Å2
2---0.92 Å20 Å2
3---3 Å2
Refinement stepCycle: 1 / Resolution: 3.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2334 1330 11 2 3677
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0163894
X-RAY DIFFRACTIONr_bond_other_d0.0060.022963
X-RAY DIFFRACTIONr_angle_refined_deg1.1281.6165529
X-RAY DIFFRACTIONr_angle_other_deg1.14136849
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9055279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.53623.492126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.54815421
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4561518
X-RAY DIFFRACTIONr_chiral_restr0.0710.2518
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023510
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02951
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_it1.274.961125
X-RAY DIFFRACTIONr_mcbond_other1.274.9571124
X-RAY DIFFRACTIONr_mcangle_it2.2927.4261401
X-RAY DIFFRACTIONr_mcangle_other2.2927.431402
X-RAY DIFFRACTIONr_scbond_it1.0234.5132768
X-RAY DIFFRACTIONr_scbond_other0.9924.5012764
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8086.7144123
X-RAY DIFFRACTIONr_long_range_B_refined3.71940.3884903
X-RAY DIFFRACTIONr_long_range_B_other3.71440.3894903
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 61 -
Rwork0.257 1203 -
obs--100 %
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)
14.5865-0.842-0.13465.5972-0.13693.19810.36240.2013-0.50380.21540.15390.36420.07230.6572-0.51630.2032-0.0321-0.23460.5065-0.02020.4116139.32766.1427.566
25.43643.1572-0.346.58913.821510.75430.20490.7109-0.8746-0.27430.19630.52260.02610.615-0.40120.31640.2778-0.35150.8184-0.25610.904145.15956.803-4.414
34.00380.7948-3.01945.1201-0.72962.77530.53940.3409-0.8977-1.021-0.61290.2829-0.20860.30460.07340.5550.3264-0.47861.2108-0.49380.9873146.77556.768-3.588
42.61420.46141.6777.81831.13232.78810.53950.4356-0.174-0.45120.0626-0.5106-0.4007-0.0013-0.60210.46730.31150.22840.7941-0.06130.6467177.31874.63611.027
58.52681.1174-0.24814.9247-2.37095.3070.69210.0183-1.3383-0.19560.173-0.26790.3042-0.2742-0.86510.18430.1072-0.36860.8078-0.24110.9146177.59658.55513.246
69.8734-1.3907-4.53798.58110.39042.88820.47821.0679-1.2299-0.5993-0.0238-0.63710.1597-0.4168-0.45440.28770.142-0.5090.9353-0.14971.4442176.44158.512.273
74.3976-1.9626-1.04716.32392.22026.22880.80320.13690.2735-0.40410.1013-0.77-0.27140.0906-0.90450.31680.07070.4170.4547-0.02070.9329175.47792.66728.856
87.5974-0.66540.2835.5159-0.48785.39350.35870.42971.0871-0.3070.034-0.2419-0.43290.1041-0.39280.59970.14080.7290.54970.05411.0946175.877108.85827.337
98.6278-1.98590.51765.3642-2.3573.78140.378-0.30850.8822-0.80030.23-0.5865-0.555-0.0013-0.6080.7285-0.06540.64510.5823-0.08161.2545174.713109.01728.254
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A279 - 374
2X-RAY DIFFRACTION2B1 - 11
3X-RAY DIFFRACTION3C14 - 24
4X-RAY DIFFRACTION4D279 - 371
5X-RAY DIFFRACTION5E1 - 11
6X-RAY DIFFRACTION6F14 - 24
7X-RAY DIFFRACTION7G279 - 371
8X-RAY DIFFRACTION8H1 - 11
9X-RAY DIFFRACTION9I14 - 24

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