4YOS

p107 pocket domain complexed with LIN52 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural mechanisms of DREAM complex assembly and regulation.

Guiley, K.Z.Liban, T.J.Felthousen, J.G.Ramanan, P.Litovchick, L.Rubin, S.M.

(2015) Genes Dev. 29: 961-974

  • DOI: 10.1101/gad.257568.114
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The DREAM complex represses cell cycle genes during quiescence through scaffolding MuvB proteins with E2F4/5 and the Rb tumor suppressor paralog p107 or p130. Upon cell cycle entry, MuvB dissociates from p107/p130 and recruits B-Myb and FoxM1 for up- ...

    The DREAM complex represses cell cycle genes during quiescence through scaffolding MuvB proteins with E2F4/5 and the Rb tumor suppressor paralog p107 or p130. Upon cell cycle entry, MuvB dissociates from p107/p130 and recruits B-Myb and FoxM1 for up-regulating mitotic gene expression. To understand the biochemical mechanisms underpinning DREAM function and regulation, we investigated the structural basis for DREAM assembly. We identified a sequence in the MuvB component LIN52 that binds directly to the pocket domains of p107 and p130 when phosphorylated on the DYRK1A kinase site S28. A crystal structure of the LIN52-p107 complex reveals that LIN52 uses a suboptimal LxSxExL sequence together with the phosphate at nearby S28 to bind the LxCxE cleft of the pocket domain with high affinity. The structure explains the specificity for p107/p130 over Rb in the DREAM complex and how the complex is disrupted by viral oncoproteins. Based on insights from the structure, we addressed how DREAM is disassembled upon cell cycle entry. We found that p130 and B-Myb can both bind the core MuvB complex simultaneously but that cyclin-dependent kinase phosphorylation of p130 weakens its association. Together, our data inform a novel target interface for studying MuvB and p130 function and the design of inhibitors that prevent tumor escape in quiescence.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California at Santa Cruz, Santa Cruz, California 95064, USA;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Retinoblastoma-like protein 1,Retinoblastoma-like protein 1
A
369Homo sapiensMutation(s): 0 
Gene Names: RBL1
Find proteins for P28749 (Homo sapiens)
Go to Gene View: RBL1
Go to UniProtKB:  P28749
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Protein lin-52 homolog
E
20Gallus gallusMutation(s): 0 
Gene Names: LIN52
Find proteins for Q5ZJQ3 (Gallus gallus)
Go to Gene View: LIN52
Go to UniProtKB:  Q5ZJQ3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
E
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.199 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 75.430α = 90.00
b = 101.060β = 90.00
c = 140.685γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
Aimlessdata scaling
iMOSFLMdata reduction

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: 2015-05-27
    Type: Initial release
  • Version 1.1: 2017-09-20
    Type: Author supporting evidence, Database references, Derived calculations, Refinement description, Source and taxonomy
  • Version 1.2: 2017-09-27
    Type: Data collection