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- PDB-5tuu: Crystal structure of the E2F4-DP1 coiled coil and marked-box domains -

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Basic information

Entry
Database: PDB / ID: 5tuu
TitleCrystal structure of the E2F4-DP1 coiled coil and marked-box domains
Components
  • Transcription factor DP1
  • Transcription factor E2F4
KeywordsTRANSCRIPTION / Transcription factor / cell-cycle regulation / coiled coil domian
Function / homology
Function and homology information


multi-ciliated epithelial cell differentiation / Rb-E2F complex / negative regulation of fat cell proliferation / regulation of DNA biosynthetic process / centriole assembly / motile cilium assembly / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / Transcription of E2F targets under negative control by DREAM complex / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / cell volume homeostasis ...multi-ciliated epithelial cell differentiation / Rb-E2F complex / negative regulation of fat cell proliferation / regulation of DNA biosynthetic process / centriole assembly / motile cilium assembly / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / Transcription of E2F targets under negative control by DREAM complex / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / cell volume homeostasis / blood circulation / Activation of NOXA and translocation to mitochondria / anoikis / Activation of PUMA and translocation to mitochondria / DNA-binding transcription activator activity / G1/S-Specific Transcription / epithelial cell development / Transcriptional Regulation by E2F6 / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / G0 and Early G1 / positive regulation of G1/S transition of mitotic cell cycle / epidermis development / cis-regulatory region sequence-specific DNA binding / 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 / promoter-specific chromatin binding / animal organ morphogenesis / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Oncogene Induced Senescence / Pre-NOTCH Transcription and Translation / Transcriptional regulation of granulopoiesis / RNA polymerase II transcription regulator complex / Cyclin D associated events in G1 / positive regulation of DNA-binding transcription factor activity / sequence-specific double-stranded DNA binding / regulation of cell population proliferation / DNA-binding transcription activator activity, RNA polymerase II-specific / Oxidative Stress Induced Senescence / DNA-binding transcription factor binding / transcription by RNA polymerase II / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / cell cycle / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Transcription factor DP / 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 ...Transcription factor DP / 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 / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcription factor Dp-1 / Transcription factor E2F4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.251 Å
AuthorsLiban, T.J. / Rubin, S.M. / Tripathi, S.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA132685 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Conservation and divergence of C-terminal domain structure in the retinoblastoma protein family.
Authors: Liban, T.J. / Medina, E.M. / Tripathi, S. / Sengupta, S. / Henry, R.W. / Buchler, N.E. / Rubin, S.M.
History
DepositionNov 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Database references
Revision 1.2May 24, 2017Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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: Transcription factor DP1
B: Transcription factor E2F4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3654
Polymers30,1802
Non-polymers1842
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6150 Å2
ΔGint-48 kcal/mol
Surface area14950 Å2
MethodPISA
2
A: Transcription factor DP1
B: Transcription factor E2F4
hetero molecules

A: Transcription factor DP1
B: Transcription factor E2F4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7298
Polymers60,3614
Non-polymers3684
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area16040 Å2
ΔGint-118 kcal/mol
Surface area26150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.575, 37.550, 109.942
Angle α, β, γ (deg.)90.00, 103.44, 90.00
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-513-

HOH

21A-523-

HOH

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Components

#1: Protein Transcription factor DP1 / DRTF1-polypeptide 1 / DRTF1 / E2F dimerization partner 1


Mass: 17603.086 Da / Num. of mol.: 1 / Fragment: UNP residues 199-350
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TFDP1, DP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q14186
#2: Protein Transcription factor E2F4 / E2F-4


Mass: 12577.285 Da / Num. of mol.: 1 / Fragment: UNP residues 91-198
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: E2F4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q16254
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.45 Å3/Da / Density % sol: 49.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M MES pH 6.5, 15% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.25→53.96 Å / Num. obs: 13407 / % possible obs: 94 % / Redundancy: 3.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.056 / Net I/σ(I): 20.3
Reflection shellResolution: 2.25→2.32 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.9 / CC1/2: 0.68 / % possible all: 93.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 2AZE

2aze


Resolution: 2.251→53.466 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 28.76
RfactorNum. reflection% reflection
Rfree0.2386 643 4.8 %
Rwork0.2054 --
obs0.2072 13401 94.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.251→53.466 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1928 0 12 42 1982
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051967
X-RAY DIFFRACTIONf_angle_d0.742662
X-RAY DIFFRACTIONf_dihedral_angle_d17.461218
X-RAY DIFFRACTIONf_chiral_restr0.043308
X-RAY DIFFRACTIONf_plane_restr0.006352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2506-2.42440.32421120.27392499X-RAY DIFFRACTION93
2.4244-2.66840.30231160.2542515X-RAY DIFFRACTION94
2.6684-3.05440.29661310.24492524X-RAY DIFFRACTION94
3.0544-3.84810.23841440.20312579X-RAY DIFFRACTION96
3.8481-53.48080.20531400.17662641X-RAY DIFFRACTION95
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)
12.5633-0.4135-4.63392.03310.47886.8511-0.1499-0.4365-0.21210.0655-0.19740.369-0.25470.0760.20710.27710.0966-0.07850.83680.00920.5168-24.0549-1.75233.4772
23.9352-2.2117-0.22783.4081-1.00013.4205-0.09140.18950.1219-0.2538-0.0221-0.0672-0.2016-0.00430.13120.3457-0.06150.00330.1873-0.01210.2794-1.5884-5.8331-11.5785
31.5922-0.58390.91453.08830.45686.2302-0.0213-0.54481.201-0.6596-0.16961.5883-1.0992-1.35690.2060.83360.4013-0.11290.9058-0.12980.8988-24.41988.3038-5.3435
46.24210.79144.34082.4459-0.7543.98570.28020.5883-0.0145-1.2896-0.0671-1.1641.14480.5738-1.17311.29340.22180.28570.6367-0.1470.5956-43.81125.704231.1238
52.7514-0.6455-3.9911.0899-0.27746.57630.00830.6123-0.6882-0.0117-0.37350.5016-0.3825-1.28760.29070.3720.0259-0.04421.0683-0.09030.6793-32.7665-3.9784.919
61.6556-0.5575-1.4274.1951-0.80182.72570.16150.3009-1.036-0.6123-0.64040.47510.4521-1.98690.04730.6354-0.0371-0.11021.0249-0.16280.4727-17.0068-5.9521-20.736
79.44413.18645.1548.2576-1.30074.54820.1918-0.14790.9244-0.1624-0.1325-0.7971-0.54240.1811-0.0890.5206-0.01860.08650.32510.02020.533-1.29932.8129-15.3602
82.6457-1.6012-0.70394.43230.12291.6635-0.41370.1985-0.0943-0.40330.5286-0.18880.09010.06320.13530.4237-0.02880.01940.26660.02410.3642-0.5411-10.7578-9.7139
91.37670.19151.17822.94681.23915.0742-0.26770.03690.31220.4884-0.0334-0.58220.56370.92450.04740.4664-0.0005-0.030.52870.03360.417211.9616-13.48693.62
103.52560.58982.24572.57610.12745.6131-0.3313-0.18-0.82940.1396-0.19930.19070.75550.0693-0.02120.5206-0.02330.18490.373-0.00240.5071-2.1224-22.672-11.0941
113.22133.3661-3.95713.4825-4.20757.0432-0.66670.67780.3384-0.20520.1806-0.1685-0.92391.01030.15650.502-0.077-0.0080.4461-0.00720.35412.8972-8.7389-17.2773
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 197 through 246 )
2X-RAY DIFFRACTION2chain 'A' and (resid 247 through 316 )
3X-RAY DIFFRACTION3chain 'A' and (resid 317 through 339 )
4X-RAY DIFFRACTION4chain 'B' and (resid 91 through 96 )
5X-RAY DIFFRACTION5chain 'B' and (resid 97 through 128 )
6X-RAY DIFFRACTION6chain 'B' and (resid 129 through 141 )
7X-RAY DIFFRACTION7chain 'B' and (resid 142 through 148 )
8X-RAY DIFFRACTION8chain 'B' and (resid 149 through 166 )
9X-RAY DIFFRACTION9chain 'B' and (resid 167 through 181 )
10X-RAY DIFFRACTION10chain 'B' and (resid 182 through 190 )
11X-RAY DIFFRACTION11chain 'B' and (resid 191 through 196 )

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