5TUV

Crystal structure of the E2F5-DP1-p107 ternary complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Conservation and divergence of C-terminal domain structure in the retinoblastoma protein family.

Liban, T.J.Medina, E.M.Tripathi, S.Sengupta, S.Henry, R.W.Buchler, N.E.Rubin, S.M.

(2017) Proc. Natl. Acad. Sci. U.S.A. 114: 4942-4947

  • DOI: 10.1073/pnas.1619170114
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The retinoblastoma protein (Rb) and the homologous pocket proteins p107 and p130 negatively regulate cell proliferation by binding and inhibiting members of the E2F transcription factor family. The structural features that distinguish Rb from other p ...

    The retinoblastoma protein (Rb) and the homologous pocket proteins p107 and p130 negatively regulate cell proliferation by binding and inhibiting members of the E2F transcription factor family. The structural features that distinguish Rb from other pocket proteins have been unclear but are critical for understanding their functional diversity and determining why Rb has unique tumor suppressor activities. We describe here important differences in how the Rb and p107 C-terminal domains (CTDs) associate with the coiled-coil and marked-box domains (CMs) of E2Fs. We find that although CTD-CM binding is conserved across protein families, Rb and p107 CTDs show clear preferences for different E2Fs. A crystal structure of the p107 CTD bound to E2F5 and its dimer partner DP1 reveals the molecular basis for pocket protein-E2F binding specificity and how cyclin-dependent kinases differentially regulate pocket proteins through CTD phosphorylation. Our structural and biochemical data together with phylogenetic analyses of Rb and E2F proteins support the conclusion that Rb evolved specific structural motifs that confer its unique capacity to bind with high affinity those E2Fs that are the most potent activators of the cell cycle.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transcription factor DP1
A, D
155Homo sapiensMutation(s): 0 
Gene Names: TFDP1 (DP1)
Find proteins for Q14186 (Homo sapiens)
Go to Gene View: TFDP1
Go to UniProtKB:  Q14186
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Transcription factor E2F5
B, E
112Homo sapiensMutation(s): 0 
Gene Names: E2F5
Find proteins for Q15329 (Homo sapiens)
Go to Gene View: E2F5
Go to UniProtKB:  Q15329
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Retinoblastoma-like protein 1
C, F
41Homo sapiensMutation(s): 0 
Gene Names: RBL1
Find proteins for P28749 (Homo sapiens)
Go to Gene View: RBL1
Go to UniProtKB:  P28749
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.212 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 60.980α = 90.00
b = 57.340β = 96.64
c = 99.198γ = 90.00
Software Package:
Software NamePurpose
iMOSFLMdata reduction
PHENIXrefinement
AutoSolphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer InstituteUnited StatesR01CA132685

Revision History 

  • Version 1.0: 2017-05-03
    Type: Initial release
  • Version 1.1: 2017-05-10
    Type: Database references
  • Version 1.2: 2017-05-24
    Type: Database references
  • Version 1.3: 2017-09-27
    Type: Author supporting evidence