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- PDB-5tuv: Crystal structure of the E2F5-DP1-p107 ternary complex -

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Basic information

Entry
Database: PDB / ID: 5tuv
TitleCrystal structure of the E2F5-DP1-p107 ternary complex
Components
  • Retinoblastoma-like protein 1
  • Transcription factor DP1
  • Transcription factor E2F5
KeywordsTRANSCRIPTION / Transcription factor / cell-cycle regulation
Function / homology
Function and homology information


Rb-E2F complex / regulation of lipid kinase activity / negative regulation of fat cell proliferation / regulation of DNA biosynthetic process / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / cell projection organization / 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 / anoikis / Activation of NOXA and translocation to mitochondria ...Rb-E2F complex / regulation of lipid kinase activity / negative regulation of fat cell proliferation / regulation of DNA biosynthetic process / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / cell projection organization / 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 / anoikis / Activation of NOXA and translocation to mitochondria / Activation of PUMA and translocation to mitochondria / DNA-binding transcription activator activity / negative regulation of G1/S transition of mitotic cell cycle / G1/S-Specific Transcription / Transcriptional Regulation by E2F6 / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / negative regulation of cellular senescence / transcription factor binding / G0 and Early G1 / epidermis development / positive regulation of G1/S transition of mitotic cell cycle / 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 / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Oncogene Induced Senescence / fibrillar center / Pre-NOTCH Transcription and Translation / positive regulation of DNA-binding transcription factor activity / Transcriptional regulation of granulopoiesis / RNA polymerase II transcription regulator complex / Cyclin D associated events in G1 / chromatin organization / Oxidative Stress Induced Senescence / DNA-binding transcription factor binding / transcription regulator complex / transcription by RNA polymerase II / cell differentiation / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of cell cycle / cell cycle / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / negative regulation of gene expression / intracellular membrane-bounded organelle / regulation of DNA-templated transcription / chromatin / nucleolus / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Transcription factor E2F5 / 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 E2F5 / 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 / Rb C-terminal domain / Retinoblastoma-associated protein, B-box / Retinoblastoma-associated protein, A-box / Retinoblastoma-associated protein, C-terminal / Retinoblastoma-associated protein, N-terminal / Retinoblastoma protein family / Retinoblastoma-associated protein B domain / Retinoblastoma-associated protein A domain / Domain of unknown function (DUF3452) / Domain of unknown function (DUF3452) / Retinoblastoma-associated protein A domain / Rb C-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Retinoblastoma-like protein 1 / Transcription factor Dp-1 / Transcription factor E2F5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsLiban, T.J. / Tripathi, S.M. / Rubin, 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 1.5Mar 6, 2024Group: 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
A: Transcription factor DP1
B: Transcription factor E2F5
C: Retinoblastoma-like protein 1
D: Transcription factor DP1
E: Transcription factor E2F5
F: Retinoblastoma-like protein 1


Theoretical massNumber of molelcules
Total (without water)70,4586
Polymers70,4586
Non-polymers00
Water00
1
A: Transcription factor DP1
B: Transcription factor E2F5
C: Retinoblastoma-like protein 1


Theoretical massNumber of molelcules
Total (without water)35,2293
Polymers35,2293
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7960 Å2
ΔGint-60 kcal/mol
Surface area14300 Å2
MethodPISA
2
D: Transcription factor DP1
E: Transcription factor E2F5
F: Retinoblastoma-like protein 1


Theoretical massNumber of molelcules
Total (without water)35,2293
Polymers35,2293
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6710 Å2
ΔGint-46 kcal/mol
Surface area12930 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17330 Å2
ΔGint-117 kcal/mol
Surface area24570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.980, 57.340, 99.198
Angle α, β, γ (deg.)90.00, 96.64, 90.00
Int Tables number4
Space group name H-MP1211

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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.: 2 / 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 E2F5 / E2F-5


Mass: 12962.745 Da / Num. of mol.: 2 / Fragment: UNP residues 124-232
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: E2F5 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15329
#3: Protein/peptide Retinoblastoma-like protein 1 / 107 kDa retinoblastoma-associated protein / p107 / pRb1


Mass: 4663.346 Da / Num. of mol.: 2 / Fragment: UNP residues 994-1031
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBL1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P28749

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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: 2.44 Å3/Da / Density % sol: 49.69 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 100mM Hepes pH 7.0, 7% PEG 5000, 5% 1-propanol, 2% 2-propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→60.57 Å / Num. obs: 15301 / % possible obs: 99 % / Redundancy: 10.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.6
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 5.5 / CC1/2: 0.921 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
SCALAdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.9→49.266 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.68
RfactorNum. reflection% reflection
Rfree0.2601 802 5.24 %
Rwork0.2122 --
obs0.2147 15296 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.9→49.266 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3532 0 0 0 3532
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033584
X-RAY DIFFRACTIONf_angle_d0.8164856
X-RAY DIFFRACTIONf_dihedral_angle_d13.9681303
X-RAY DIFFRACTIONf_chiral_restr0.03565
X-RAY DIFFRACTIONf_plane_restr0.004640
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.08170.32811440.27342383X-RAY DIFFRACTION100
3.0817-3.31960.28961320.24642386X-RAY DIFFRACTION100
3.3196-3.65360.28671160.2262436X-RAY DIFFRACTION100
3.6536-4.1820.25971430.20172396X-RAY DIFFRACTION100
4.182-5.26790.22311370.18692426X-RAY DIFFRACTION100
5.2679-49.2730.25121300.20712467X-RAY DIFFRACTION99
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)
16.3441-0.1487-2.0961.3457-0.14881.6695-0.07250.5562-0.8543-0.30230.1834-0.19650.0470.0971-0.17010.6570.01460.02070.6619-0.27770.428724.273346.5872-30.3637
21.2855-0.6191-0.02370.32920.17050.6976-0.4664-0.24040.15620.50250.3043-0.1157-0.9955-1.0676-0.11220.57130.1718-0.0810.6170.10830.50271.966246.6903-11.2564
32.4837-0.62350.05592.85430.09581.71270.25790.0717-0.1754-0.0715-0.11910.34780.62860.0415-0.16570.36310.00330.02090.22930.00770.420917.803841.4381-5.7618
45.83420.0862-2.84461.2175-0.07182.10380.26281.5106-0.153-0.4542-0.0678-0.0971-0.4149-0.3661-0.20380.62280.2062-0.06111.1547-0.17080.532.863153.428-36.7363
56.746-0.668-1.16025.10410.053.52450.38760.47081.20330.01630.0067-0.0154-1.15920.466-0.20960.59380.06310.00890.27780.09350.56972.386255.7824-19.9058
64.635-2.9505-0.85042.8621-1.56954.7149-0.1255-0.1363-0.5494-0.24-0.17090.41640.8282-0.3443-0.79750.33080.051-0.26290.387-0.08590.58914.943438.8373-14.7329
75.10823.4461-0.41348.47150.54346.2593-0.31720.0941-1.2017-0.4377-0.0282-0.68780.4733-0.499-0.01320.35470.0433-0.07470.3032-0.05490.352912.17636.8571-7.7729
83.8231-3.86661.80537.5143-3.17422.2944-0.0468-0.59950.29580.36010.3175-1.0298-0.21930.58140.26890.27370.1807-0.14510.236-0.09270.405526.944543.2501-2.8826
93.57610.01021.03296.66391.24073.944-0.24910.22230.3372-0.8128-0.13960.2289-0.0313-0.07170.04720.32920.02340.02080.2946-0.05040.208613.07148.324-4.0771
105.2573-1.60570.52876.8993-1.25284.0740.20481.17090.0397-1.283-0.2778-0.69570.39080.6827-0.09980.46510.04270.00140.3018-0.04210.259326.488842.7592-12.9145
112.9038-1.66722.38860.9637-1.37911.96750.76510.30740.70420.24080.40911.0071-0.5584-0.59910.76820.86780.6719-0.4241-0.21370.08891.023840.634232.0536-6.6723
124.6148-2.3063-2.40593.01530.54822.44150.1074-0.53250.39670.57650.03640.1972-0.5012-0.4701-0.12620.57790.0180.10890.8791-0.06340.40295.764539.759733.5201
132.0872-0.6623-0.09162.2364-0.92691.9010.15520.09390.2031-0.1855-0.0973-0.27380.53570.5614-0.01480.3321-0.06330.09670.4593-0.01990.477714.527433.429113.2935
144.09142.0388-0.68473.9503-1.20092.73190.3053-0.15330.06940.0853-0.24440.5668-0.5019-0.18630.00830.2671-0.04650.03450.3414-0.02010.32856.496348.55073.6307
151.9425-3.06493.80655.0015-5.68518.03160.2075-0.85520.0710.28050.25740.50320.1897-0.697-0.19790.2987-0.12610.03610.4944-0.05650.48815.589433.520620.6965
162.8089-2.0839-1.34792.0219-0.05781.85220.2374-0.30680.1530.5917-0.25620.0213-0.26490.16380.20380.99870.01160.17331.04120.01660.6487-0.763450.344845.2871
173.8040.73961.89452.16570.31262.504-0.4195-0.52640.57590.0349-0.28470.3206-0.29950.77720.23860.4248-0.057-0.00890.82130.12220.4119.229531.548621.4323
182.5897-1.1945-1.21973.4987-1.0531.944-0.0564-0.150.06720.24380.17780.387-0.0472-0.0266-0.0710.3059-0.06740.03260.3278-0.01620.43585.970243.71399.7195
194.275-0.78090.99224.8042-1.52190.9536-0.2599-0.5354-0.50491.14250.29450.3811-0.5796-0.271-0.19560.95460.04040.23720.737-0.02610.67612.457146.560121.2429
206.5538-1.22652.08697.4882-3.06549.38490.4941-1.0803-0.52530.39170.45611.58310.5333-0.7922-0.33680.36390.07540.11580.86120.07630.7397-6.992140.677115.9863
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 198 through 246 )
2X-RAY DIFFRACTION2chain 'A' and (resid 247 through 261 )
3X-RAY DIFFRACTION3chain 'A' and (resid 262 through 305 )
4X-RAY DIFFRACTION4chain 'B' and (resid 124 through 162 )
5X-RAY DIFFRACTION5chain 'B' and (resid 163 through 170 )
6X-RAY DIFFRACTION6chain 'B' and (resid 171 through 181 )
7X-RAY DIFFRACTION7chain 'B' and (resid 182 through 191 )
8X-RAY DIFFRACTION8chain 'B' and (resid 192 through 215 )
9X-RAY DIFFRACTION9chain 'B' and (resid 216 through 230 )
10X-RAY DIFFRACTION10chain 'C' and (resid 1000 through 1023 )
11X-RAY DIFFRACTION11chain 'C' and (resid 1024 through 1028 )
12X-RAY DIFFRACTION12chain 'D' and (resid 208 through 243 )
13X-RAY DIFFRACTION13chain 'D' and (resid 244 through 271 )
14X-RAY DIFFRACTION14chain 'D' and (resid 272 through 290 )
15X-RAY DIFFRACTION15chain 'D' and (resid 291 through 306 )
16X-RAY DIFFRACTION16chain 'E' and (resid 125 through 162 )
17X-RAY DIFFRACTION17chain 'E' and (resid 163 through 181 )
18X-RAY DIFFRACTION18chain 'E' and (resid 182 through 231 )
19X-RAY DIFFRACTION19chain 'F' and (resid 1001 through 1014 )
20X-RAY DIFFRACTION20chain 'F' and (resid 1015 through 1024 )

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