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- PDB-4yo2: Structure of E2F8, an atypical member of E2F family of transcript... -

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Basic information

Entry
Database: PDB / ID: 4yo2
TitleStructure of E2F8, an atypical member of E2F family of transcription factors
Components
  • DNA (5'-D(P*TP*TP*TP*TP*CP*CP*CP*GP*CP*CP*AP*AP*AP*AP*A)-3')
  • DNA (5'-D(P*TP*TP*TP*TP*TP*GP*GP*CP*GP*GP*GP*AP*AP*AP*A)-3')
  • Transcription factor E2F8
KeywordsTRANSCRIPTION / transcription factor / E2F family / DNA-complex / fusion protein
Function / homology
Function and homology information


cell cycle comprising mitosis without cytokinesis / positive regulation of DNA endoreduplication / negative regulation of cytokinesis / chorionic trophoblast cell differentiation / trophoblast giant cell differentiation / chromatin => GO:0000785 / hepatocyte differentiation / sprouting angiogenesis / DNA-binding transcription repressor activity / transcription factor binding ...cell cycle comprising mitosis without cytokinesis / positive regulation of DNA endoreduplication / negative regulation of cytokinesis / chorionic trophoblast cell differentiation / trophoblast giant cell differentiation / chromatin => GO:0000785 / hepatocyte differentiation / sprouting angiogenesis / DNA-binding transcription repressor activity / transcription factor binding / cis-regulatory region sequence-specific DNA binding / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / placenta development / DNA-binding transcription repressor activity, RNA polymerase II-specific / RNA polymerase II transcription regulator complex / sequence-specific double-stranded DNA binding / cell population proliferation / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of cell cycle / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / nucleolus / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
E2F Family / E2F/DP family, winged-helix DNA-binding domain / E2F/DP family winged-helix DNA-binding domain / E2F/DP family winged-helix DNA-binding domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Transcription factor E2F8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.073 Å
AuthorsMorgunova, E. / Yin, Y. / Jolma, A. / Dave, K. / Schmierer, B. / Popov, A. / Eremina, N. / Nilsson, L. / Taipale, J.
CitationJournal: Nat Commun / Year: 2015
Title: Structural insights into the DNA-binding specificity of E2F family transcription factors.
Authors: Morgunova, E. / Yin, Y. / Jolma, A. / Dave, K. / Schmierer, B. / Popov, A. / Eremina, N. / Nilsson, L. / Taipale, J.
History
DepositionMar 11, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: 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: Transcription factor E2F8
C: DNA (5'-D(P*TP*TP*TP*TP*CP*CP*CP*GP*CP*CP*AP*AP*AP*AP*A)-3')
D: DNA (5'-D(P*TP*TP*TP*TP*TP*GP*GP*CP*GP*GP*GP*AP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)36,0803
Polymers36,0803
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-28 kcal/mol
Surface area15330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.830, 98.830, 121.690
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Transcription factor E2F8 / E2F-8


Mass: 26903.115 Da / Num. of mol.: 1 / Fragment: UNP residues 110-341
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: E2F8 / Plasmid: pETG20A / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 pLysS / References: UniProt: A0AVK6
#2: DNA chain DNA (5'-D(P*TP*TP*TP*TP*CP*CP*CP*GP*CP*CP*AP*AP*AP*AP*A)-3')


Mass: 4512.963 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(P*TP*TP*TP*TP*TP*GP*GP*CP*GP*GP*GP*AP*AP*AP*A)-3')


Mass: 4664.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / 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: 4.63 Å3/Da / Density % sol: 73 % / Description: half of hexagonal plate
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.09 / Details: Hepes, PEG 4000, ammonium sulfate, PEG 400 / PH range: 7.0 - 7.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97628 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 21, 2013
RadiationMonochromator: bent cylindrical mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97628 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.22
ReflectionResolution: 3.073→49.591 Å / Num. all: 77733 / Num. obs: 12768 / % possible obs: 97 % / Redundancy: 6.5 % / Biso Wilson estimate: 123 Å2 / Rmerge(I) obs: 0.169 / Net I/σ(I): 8.67
Reflection shellResolution: 3.07→3.182 Å / % possible all: 89.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameClassification
PHASERphasing
PHENIXrefinement
XSCALEdata scaling
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CF7

1cf7


Resolution: 3.073→14.918 Å / FOM work R set: 0.5314 / Cross valid method: THROUGHOUT / σ(F): 2.02 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2968 632 5 %random
Rwork0.2716 11989 --
obs0.272 12641 96.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 539.43 Å2 / Biso mean: 153.7 Å2 / Biso min: 69.31 Å2
Refinement stepCycle: final / Resolution: 3.073→14.918 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1515 615 0 0 2130
Num. residues----216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032225
X-RAY DIFFRACTIONf_angle_d0.6613118
X-RAY DIFFRACTIONf_chiral_restr0.03355
X-RAY DIFFRACTIONf_plane_restr0.003289
X-RAY DIFFRACTIONf_dihedral_angle_d22.53903
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0726-3.30722287X-RAY DIFFRACTION89
3.3072-3.6350.32741270.3082409X-RAY DIFFRACTION93
3.635-4.14970.35961270.32532414X-RAY DIFFRACTION93
4.1497-5.18620.31141270.30722415X-RAY DIFFRACTION92
5.1862-14.28190.26311300.21552464X-RAY DIFFRACTION91
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)DetailsOrigin x (Å)Origin y (Å)Origin z (Å)
12.0263-0.9628-0.88952.24841.61293.48460.5564-0.54251.33270.2353-0.38420.1302-0.23260.58710.00310.6918-0.17960.09791.23810.06521.0604Chain A DBD183.803153.482835.0096
20.7575-0.7037-0.6941.89020.85220.5151-0.61760.0013-0.35460.1614-1.15970.7585-1.58891.3951-0.58591.2116-0.1994-0.28511.470.62171.4905Chain B DBD277.959559.938622.9192
31.3827-0.6634-1.50122.26460.6251.49640.35020.72960.0225-0.645-0.44110.0363-0.0330.65830.0950.6008-0.01040.24252.11070.15420.6669DNA83.369144.911520.0478
43.55580.18740.30451.948-1.50751.11621.14660.64650.2202-0.3505-0.7648-0.19920.30810.60350.71650.6602-0.15710.09651.79440.14390.8922DNA84.066142.774520.5193
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'D' and (resid 1 through 15 )D1 - 15
2X-RAY DIFFRACTION2chain 'B' and (resid 259 through 341 )B0
3X-RAY DIFFRACTION3chain 'C' and (resid 1 through 15 )C0
4X-RAY DIFFRACTION4chain 'D' and (resid 1 through 15 )D0

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