1KNZ | pdb_00001knz

Recognition of the rotavirus mRNA 3' consensus by an asymmetric NSP3 homodimer

• PDB DOI: https://doi.org/10.2210/pdb1KNZ/pdb
• NAKB: 1KNZ

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


• Deposited: 2001-12-19 Released: 2002-01-17 
• Deposition Author(s): Deo, R.C., Groft, C.M., Rajashankar, K.R., Burley, S.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 
  0.280 (Depositor) 
• R-Value Work: 
  0.228 (Depositor) 

Literature

Recognition of the rotavirus mRNA 3' consensus by an asymmetric NSP3 homodimer.

Deo, R.C., Groft, C.M., Rajashankar, K.R., Burley, S.K.

(2002) Cell 108: 71-81

• PubMed: 11792322 
• DOI: https://doi.org/10.1016/s0092-8674(01)00632-8
• Primary Citation Related Structures: 
  1KNZ


• PubMed Abstract: 
  

  Rotaviruses, the cause of life-threatening diarrhea in humans and cattle, utilize a functional homolog of poly(A) binding protein (PABP) known as nonstructural protein 3 (NSP3) for translation of viral mRNAs. NSP3 binds to viral mRNA 3' consensus sequences and circularizes the mRNA via interactions with eIF4G. The X-ray structure of the NSP3 RNA binding domain bound to a rotaviral mRNA 3' end has been determined. NSP3 is a novel, heart-shaped homodimer with a medial RNA binding cleft. The homodimer is asymmetric, and contains two similar N-terminal segments plus two structurally different C-terminal segments that intertwine to create a tunnel enveloping the mRNA 3' end. Biophysical studies demonstrate high affinity binding leading to increased thermal stability and slow dissociation kinetics, consistent with NSP3 function.

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Organizational Affiliation: 
• Laboratories of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 153.22 kDa 
• Atom Count: 9,555 
• Modeled Residue Count: 1,188 
• Deposited Residue Count: 1,332 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nonstructural RNA-binding Protein 34	E [auth A], F [auth B], G [auth C], H [auth D], I, J, K [auth M], L [auth N]	164	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: 1
Molecule	Chains	Length	Organism	Image
5'-R(*UP*GP*AP*CP*C)-3'	A [auth W], B [auth X], C [auth Y], D [auth Z]	5	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.280 (Depositor) 
• R-Value Work:  0.228 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.275	α = 89.99
b = 85.359	β = 90
c = 96.051	γ = 90.05

Software Package:

Software Name	Purpose
MLPHARE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-01-17 
Deposition Author(s): Deo, R.C., Groft, C.M., Rajashankar, K.R., Burley, S.K.

Revision History  

• Version 1.0: 2002-01-17
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-02-03
  Changes: Database references, Structure summary
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references