Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 45781.50 
• Atom Count: 2954 
• Residue Count: 389 
• Unique protein chains: 2

4YOO

p107 pocket domain in complex with LIN52 P29A peptide

• DOI: 10.2210/pdb4YOO/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG'


• Deposited: 2015-03-12 Released: 2015-05-13 
• Deposition Author(s): Guiley, K.Z., Liban, T.J., Felthousen, J.G., Ramanan, P., Tripathi, S., Litovchick, L., Rubin, S.M.
• Funding Organization(s): National Institutes of Health/National Cancer Institute 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.242 
• R-Value Work: 0.195 

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

• PubMed: 25917549 
• DOI: 10.1101/gad.257568.114
• Primary Citation of Related Structures:  
  4YOZ, 4YOS


• 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-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.

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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
Molecule	Chains	Sequence Length	Organism	Details
Retinoblastoma-like protein 1,Retinoblastoma-like protein 1	A	369	Homo sapiens	Mutation(s): 0  Gene Names: RBL1
Find proteins for P28749 (Homo sapiens) Go to Gene View: RBL1 Go to UniProtKB:  P28749

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
LIN52 peptide	X	20	Homo sapiens	Mutation(s): 0  Gene Names: LIN52 (C14orf46)
Find proteins for Q52LA3 (Homo sapiens) Go to Gene View: LIN52 Go to UniProtKB:  Q52LA3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	X	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.242 
• R-Value Work: 0.195 
• Space Group: C 2 2 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 74.815	α = 90.00
b = 100.530	β = 90.00
c = 142.790	γ = 90.00

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
Aimless	data scaling
iMOSFLM	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-03-12 
• Released Date: 2015-05-13 
• Deposition Author(s): Guiley, K.Z., Liban, T.J., Felthousen, J.G., Ramanan, P., Tripathi, S., Litovchick, L., Rubin, S.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute	United States	R01CA132685

Revision History 

• Version 1.0: 2015-05-13
  Type: Initial release
• Version 1.1: 2015-05-20
  Type: Database references
• Version 1.2: 2017-09-20
  Type: Author supporting evidence, Database references, Derived calculations, Refinement description, Source and taxonomy