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- PDB-1cf7: STRUCTURAL BASIS OF DNA RECOGNITION BY THE HETERODIMERIC CELL CYC... -

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Basic information

Entry
Database: PDB / ID: 1cf7
TitleSTRUCTURAL BASIS OF DNA RECOGNITION BY THE HETERODIMERIC CELL CYCLE TRANSCRIPTION FACTOR E2F-DP
Components
  • DNA (5'-D(*AP*TP*TP*TP*TP*CP*GP*CP*GP*CP*GP*GP*TP*TP*TP*T)-3')
  • DNA (5'-D(*TP*AP*AP*AP*AP*CP*CP*GP*CP*GP*CP*GP*AP*AP*AP*A)-3')
  • PROTEIN (TRANSCRIPTION FACTOR DP-2)
  • PROTEIN (TRANSCRIPTION FACTOR E2F-4)
KeywordsTRANSCRIPTION/DNA / E2F / DP / WINGED-HELIX / DNA-BINDING DOMAIN / TRANSCRIPTION FACTOR / CELL CYCLE / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


multi-ciliated epithelial cell differentiation / centriole assembly / motile cilium assembly / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / Transcription of E2F targets under negative control by DREAM complex / Activation of NOXA and translocation to mitochondria / cell volume homeostasis / blood circulation / Activation of PUMA and translocation to mitochondria ...multi-ciliated epithelial cell differentiation / centriole assembly / motile cilium assembly / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / Transcription of E2F targets under negative control by DREAM complex / Activation of NOXA and translocation to mitochondria / cell volume homeostasis / blood circulation / Activation of PUMA and translocation to mitochondria / DNA-binding transcription activator activity / epithelial cell development / transcription factor binding / G1/S-Specific Transcription / Transcriptional Regulation by E2F6 / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / G0 and Early G1 / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / animal organ morphogenesis / promoter-specific chromatin binding / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Oncogene Induced Senescence / Pre-NOTCH Transcription and Translation / RNA polymerase II transcription regulator complex / Transcriptional regulation of granulopoiesis / sequence-specific double-stranded DNA binding / Cyclin D associated events in G1 / mitotic spindle / regulation of cell population proliferation / DNA-binding transcription activator activity, RNA polymerase II-specific / Oxidative Stress Induced Senescence / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of cell cycle / protein dimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Transcription factor DP, C-terminal / Transcription factor DP / Transcription factor DP, C-terminal domain superfamily / Transcription factor DP / Transcription factor DP / E2F transcription factor, CC-MB domain / E2F transcription factor CC-MB domain / E2F Family / E2F-DP heterodimerization region / E2F/DP family, winged-helix DNA-binding domain ...Transcription factor DP, C-terminal / Transcription factor DP / Transcription factor DP, C-terminal domain superfamily / Transcription factor DP / Transcription factor DP / E2F transcription factor, CC-MB domain / E2F transcription factor CC-MB domain / E2F Family / E2F-DP heterodimerization region / 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-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
DNA / DNA (> 10) / Transcription factor Dp-2 / Transcription factor E2F4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.6 Å
AuthorsZheng, N. / Fraenkel, E. / Pabo, C.O. / Pavletich, N.P.
CitationJournal: Genes Dev. / Year: 1999
Title: Structural basis of DNA recognition by the heterodimeric cell cycle transcription factor E2F-DP.
Authors: Zheng, N. / Fraenkel, E. / Pabo, C.O. / Pavletich, N.P.
History
DepositionMar 24, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 2, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
C: DNA (5'-D(*AP*TP*TP*TP*TP*CP*GP*CP*GP*CP*GP*GP*TP*TP*TP*T)-3')
D: DNA (5'-D(*TP*AP*AP*AP*AP*CP*CP*GP*CP*GP*CP*GP*AP*AP*AP*A)-3')
A: PROTEIN (TRANSCRIPTION FACTOR E2F-4)
B: PROTEIN (TRANSCRIPTION FACTOR DP-2)


Theoretical massNumber of molelcules
Total (without water)28,9844
Polymers28,9844
Non-polymers00
Water1,35175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.300, 101.300, 73.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Cell settingtrigonal
Space group name H-MP3121

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Components

#1: DNA chain DNA (5'-D(*AP*TP*TP*TP*TP*CP*GP*CP*GP*CP*GP*GP*TP*TP*TP*T)-3')


Mass: 4886.160 Da / Num. of mol.: 1 / Fragment: ADENOVIRUS TYPE 5 E2 PROMOTER E2F-BINDING SITE / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*TP*AP*AP*AP*AP*CP*CP*GP*CP*GP*CP*GP*AP*AP*AP*A)-3')


Mass: 4909.235 Da / Num. of mol.: 1 / Fragment: ADENOVIRUS TYPE 5 E2 PROMOTER E2F-BINDING SITE / Source method: obtained synthetically
#3: Protein PROTEIN (TRANSCRIPTION FACTOR E2F-4)


Mass: 8352.729 Da / Num. of mol.: 1 / Fragment: DNA-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEX-4T3 / Cell line (production host): BL21(DE3) / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / References: UniProt: Q16254
#4: Protein PROTEIN (TRANSCRIPTION FACTOR DP-2)


Mass: 10836.347 Da / Num. of mol.: 1 / Fragment: DNA-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEX-4T3 / Cell line (production host): BL21(DE3) / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / References: UniProt: Q14188
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 3.71 Å3/Da / Density % sol: 66.83 %
Crystal growTemperature: 277 K / pH: 6
Details: 14-16% PEG 400, 25MM NACL, 50MM MES, 10MM DTT, PH=6.0, 4 DEGREES C, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 40011
2NACL11
3MES11
4DTT11
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
127-32 %PEG4001reservoir
250 mM1reservoirNaCl
3100 mM1reservoir
420 mMdithiothreitol1reservoirpH6.0
50.3-0.6 mMternary complex1drop
620 mMBTP1drop
7100 mM1dropNaCl
85 mMdithiothreitol1drop
9300 mMammonium acetate1drop

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Data collection

DiffractionMean temperature: 127 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 1.1548
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1548 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 12901 / % possible obs: 96.5 % / Redundancy: 2.6 % / Rsym value: 5.4
Reflection
*PLUS
Num. measured all: 41452 / Rmerge(I) obs: 0.054

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Processing

SoftwareName: CNS / Version: 0.3A / Classification: refinement
RefinementMethod to determine structure: MIR / Resolution: 2.6→15 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.223 --
all-12057 -
obs-12057 96.5 %
Refinement stepCycle: LAST / Resolution: 2.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1185 615 0 75 1875
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.75
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Version: 0.3A / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 15 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.229 / Rfactor Rfree: 0.283
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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