4ELJ | pdb_00004elj

Crystal structure of the inactive retinoblastoma protein phosphorylated at T373

• PDB DOI: https://doi.org/10.2210/pdb4ELJ/pdb

• Classification: CELL CYCLE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-04-10 Released: 2012-05-23 
• Deposition Author(s): Burke, J.R., Rubin, S.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.266 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Literature

Structures of inactive retinoblastoma protein reveal multiple mechanisms for cell cycle control.

Burke, J.R., Hura, G.L., Rubin, S.M.

(2012) Genes Dev 26: 1156-1166

• PubMed: 22569856 
• DOI: https://doi.org/10.1101/gad.189837.112
• Primary Citation Related Structures: 
  4ELJ, 4ELL


• PubMed Abstract: 
  

  Cyclin-dependent kinase (Cdk) phosphorylation of the Retinoblastoma protein (Rb) drives cell proliferation through inhibition of Rb complexes with E2F transcription factors and other regulatory proteins. We present the first structures of phosphorylated Rb that reveal the mechanism of its inactivation. S608 phosphorylation orders a flexible "pocket" domain loop such that it mimics and directly blocks E2F transactivation domain (E2F(TD)) binding. T373 phosphorylation induces a global conformational change that associates the pocket and N-terminal domains (RbN). This first multidomain Rb structure demonstrates a novel role for RbN in allosterically inhibiting the E2F(TD)-pocket association and protein binding to the pocket "LxCxE" site. Together, these structures detail the regulatory mechanism for a canonical growth-repressive complex and provide a novel example of how multisite Cdk phosphorylation induces diverse structural changes to influence cell cycle signaling.

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Organizational Affiliation: 
• Department of Chemistry and Biochemistry, University of California at Santa Cruz, Santa Cruz, California 95064, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 76.37 kDa 
• Atom Count: 4,908 
• Modeled Residue Count: 590 
• Deposited Residue Count: 656 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Retinoblastoma-associated protein	A	656	Homo sapiens	Mutation(s): 0  Gene Names: RB1
UniProt & NIH Common Fund Data Resources
Find proteins for P06400 (Homo sapiens) Explore P06400  Go to UniProtKB:  P06400
PHAROS:  P06400 GTEx:  ENSG00000139687

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO	A	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.266 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.62	α = 90
b = 129.51	β = 90
c = 135.04	γ = 90

Software Package:

Software Name	Purpose
JBluIce-EPICS	data collection
PHASER	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-23 
Deposition Author(s): Burke, J.R., Rubin, S.M.

Revision History  

• Version 1.0: 2012-05-23
  Type: Initial release
  
• Version 1.1: 2012-08-15
  Changes: Database references
• Version 1.2: 2017-08-23
  Changes: Refinement description, Source and taxonomy
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary