2R7G

Structure of the retinoblastoma protein pocket domain in complex with adenovirus E1A CR1 domain

• PDB DOI: https://doi.org/10.2210/pdb2R7G/pdb

• Classification: TRANSCRIPTION REPRESSOR, CELL CYCLE
• Organism(s): Homo sapiens, Human adenovirus 5
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-09-07 Released: 2007-10-02 
• Deposition Author(s): Liu, X., Marmorstein, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free: 0.218 
• R-Value Work: 0.195 
• R-Value Observed: 0.198 

Literature

Structure of the retinoblastoma protein bound to adenovirus E1A reveals the molecular basis for viral oncoprotein inactivation of a tumor suppressor

Liu, X., Marmorstein, R.

(2007) Genes Dev 21: 2711-2716

• PubMed: 17974914 
• DOI: https://doi.org/10.1101/gad.1590607
• Primary Citation of Related Structures:  
  2R7G


• PubMed Abstract: 
  

  The adenovirus (Ad) E1A (Ad-E1A) oncoprotein mediates cell transformation, in part, by displacing E2F transcription factors from the retinoblastoma protein (pRb) tumor suppressor. In this study we determined the crystal structure of the pRb pocket domain in complex with conserved region 1 (CR1) of Ad5-E1A. The structure and accompanying biochemical studies reveal that E1A-CR1 binds at the interface of the A and B cyclin folds of the pRb pocket domain, and that both E1A-CR1 and the E2F transactivation domain use similar conserved nonpolar residues to engage overlapping sites on pRb, implicating a novel molecular mechanism for pRb inactivation by a viral oncoprotein.

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Organizational Affiliation: 

Program in Gene Expression and Regulation, The Wistar Institute, Philadelphia, Pennsylvania 19104, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A3B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A2B1C1D1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

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

Macromolecule Content

• Total Structure Weight: 85.24 kDa 
• Atom Count: 6,267 
• Modelled Residue Count: 702 
• Deposited Residue Count: 724 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Retinoblastoma-associated protein	A, C	347	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Early E1A 32 kDa protein	B, D, E	10	Human adenovirus 5	Mutation(s): 0
UniProt
Find proteins for P03255 (Human adenovirus C serotype 5) Explore P03255  Go to UniProtKB:  P03255

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	F [auth A], G [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free: 0.218 
• R-Value Work: 0.195 
• R-Value Observed: 0.198 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.713	α = 94.34
b = 57.706	β = 92.69
c = 92.268	γ = 105.79

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-02 
Deposition Author(s): Liu, X., Marmorstein, R.

Revision History  

• Version 1.0: 2007-10-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-07-26
  Changes: Refinement description, Source and taxonomy
• Version 1.3: 2017-10-25
  Changes: Refinement description
• Version 1.4: 2024-02-21
  Changes: Data collection, Database references, Derived calculations