1KNZ

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


Experimental Data Snapshot

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

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This is version 1.3 of the entry. See complete history


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

  • DOI: 10.1016/s0092-8674(01)00632-8
  • Primary Citation of 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 ...

    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.


    Organizational Affiliation

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



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nonstructural RNA-binding Protein 34164Simian rotavirus A/SA11Mutation(s): 0 
UniProt
Find proteins for P03536 (Rotavirus A (strain RVA/SA11-Both/G3P5B[2]))
Explore P03536 
Go to UniProtKB:  P03536
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03536
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-R(*UP*GP*AP*CP*C)-3'A [auth W],
B [auth X],
C [auth Y],
D [auth Z]
5N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
RNA PDBBind:  1KNZ Kd: 79 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.228 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.275α = 89.99
b = 85.359β = 90
c = 96.051γ = 90.05
Software Package:
Software NamePurpose
MLPHAREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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