1LJ2 | pdb_00001lj2

Recognition of eIF4G by Rotavirus NSP3 reveals a basis for mRNA circularization

• PDB DOI: https://doi.org/10.2210/pdb1LJ2/pdb

• Classification: Viral protein/ translation
• Organism(s): Simian rotavirus A/SA11, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-04-18 Released: 2002-07-05 
• Deposition Author(s): Groft, C.M., Burley, S.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 
  0.272 (Depositor) 
• R-Value Work: 
  0.221 (Depositor) 

Literature

Recognition of eIF4G by rotavirus NSP3 reveals a basis for mRNA circularization.

Groft, C.M., Burley, S.K.

(2002) Mol Cell 9: 1273-1283

• PubMed: 12086624 
• DOI: https://doi.org/10.1016/s1097-2765(02)00555-5
• Primary Citation Related Structures: 
  1LJ2


• PubMed Abstract: 
  

  Rotaviruses, segmented double-stranded RNA viruses, co-opt the eukaryotic translation machinery with the aid of nonstructural protein 3 (NSP3), a rotaviral functional homolog of the cellular poly(A) binding protein (PABP). NSP3 binds to viral mRNA 3' consensus sequences and circularizes mRNA via interactions with eIF4G. Here, we present the X-ray structure of the C-terminal domain of NSP3 (NSP3-C) recognizing a fragment of eIF4GI. Homodimerization of NSP3-C yields a symmetric, elongated, largely alpha-helical structure with two hydrophobic eIF4G binding pockets at the dimer interface. Site-directed mutagenesis and isothermal titration calorimetry documented that NSP3 and PABP use analogous eIF4G recognition strategies, despite marked differences in tertiary structure.

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Organizational Affiliation: 
• Laboratory of Molecular Biophysics, New York, NY 10021, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Macromolecule Content 

• Total Structure Weight: 32.68 kDa 
• Atom Count: 2,327 
• Modeled Residue Count: 265 
• Deposited Residue Count: 276 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NONSTRUCTURAL RNA-BINDING PROTEIN 34	A, B	110	Simian rotavirus A/SA11	Mutation(s): 0
UniProt
Find proteins for P03536 (Rotavirus A (strain RVA/SA11-Both/G3P5B[2])) Explore P03536  Go to UniProtKB:  P03536

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
eukaryotic protein synthesis initiation factor	C, D	28	N/A	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q04637 (Homo sapiens) Explore Q04637  Go to UniProtKB:  Q04637
PHAROS:  Q04637 GTEx:  ENSG00000114867

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AU	E [auth B], F [auth B], G [auth D]	GOLD ION Au ZBKIUFWVEIBQRT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free:  0.272 (Depositor) 
• R-Value Work:  0.221 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.69	α = 90
b = 74.04	β = 90
c = 77.46	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
TRUNCATE	data reduction
MLPHARE	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-07-05 
Deposition Author(s): Groft, C.M., Burley, S.K.

Revision History  

• Version 1.0: 2002-07-05
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references