3POM

Crystal Structure of the Unliganded Retinoblastoma Protein Pocket Domain

• PDB DOI: https://doi.org/10.2210/pdb3POM/pdb

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


• Deposited: 2010-11-23 Released: 2011-04-27 
• Deposition Author(s): Balog, E.R.M., Burke, J.R., Rubin, S.M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.262 
• R-Value Work: 0.213 
• R-Value Observed: 0.213 

Literature

Crystal structure of the unliganded retinoblastoma protein pocket domain.

Balog, E.R., Burke, J.R., Hura, G.L., Rubin, S.M.

(2011) Proteins 79: 2010-2014

• PubMed: 21491492 
• DOI: https://doi.org/10.1002/prot.23007
• Primary Citation of Related Structures:  
  3POM


• PubMed Abstract: 
  

  The retinoblastoma protein (Rb) regulates cell proliferation through its association with E2F transcription factors and other proteins. The Rb “pocket” domain primarily facilitates protein-protein interactions, and several structures of the pocket bound to E2F and tumorigenic viral proteins have been reported. We report here the first crystal structure of the pocket domain without bound ligand. We find that ligand association results in observable structural changes at the binding sites but no significant changes to the overall conformation of the domain. These data support models for regulation of Rb-E2F binding that do not require considerable structural changes in the pocket domain.

---

Organizational Affiliation: 

Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, CA 95064, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 82.43 kDa 
• Atom Count: 5,731 
• Modelled Residue Count: 674 
• Deposited Residue Count: 704 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Retinoblastoma-associated protein	A, B	352	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.262 
• R-Value Work: 0.213 
• R-Value Observed: 0.213 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.282	α = 90
b = 111.164	β = 90
c = 138.93	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-27 
Deposition Author(s): Balog, E.R.M., Burke, J.R., Rubin, S.M.

Revision History  

• Version 1.0: 2011-04-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-08-09
  Changes: Refinement description, Source and taxonomy
• Version 1.3: 2017-11-08
  Changes: Refinement description
• Version 1.4: 2024-11-06
  Changes: Data collection, Database references, Structure summary