5TUU

Crystal structure of the E2F4-DP1 coiled coil and marked-box domains


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.251 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.205 

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
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 E2F4
B
111Homo sapiensMutation(s): 0 
Gene Names: E2F4
Find proteins for Q16254 (Homo sapiens)
Go to Gene View: E2F4
Go to UniProtKB:  Q16254
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.251 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.205 
  • Space Group: I 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 73.575α = 90.00
b = 37.550β = 103.44
c = 109.942γ = 90.00
Software Package:
Software NamePurpose
iMOSFLMdata reduction
SCALAdata scaling
PHENIXrefinement
PHASERphasing

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