4IG8

Structural basis for cytosolic double-stranded RNA surveillance by human OAS1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural basis for cytosolic double-stranded RNA surveillance by human oligoadenylate synthetase 1.

Donovan, J.Dufner, M.Korennykh, A.

(2013) Proc Natl Acad Sci U S A 110: 1652-1657

  • DOI: 10.1073/pnas.1218528110
  • Primary Citation of Related Structures:  
    4IG8

  • PubMed Abstract: 
  • The human sensor of double-stranded RNA (dsRNA) oligoadenylate synthetase 1 (hOAS1) polymerizes ATP into 2',5'-linked iso-RNA (2-5A) involved in innate immunity, cell cycle, and differentiation. We report the crystal structure of hOAS1 in complex with dsRNA and 2'-deoxy ATP at 2 ...

    The human sensor of double-stranded RNA (dsRNA) oligoadenylate synthetase 1 (hOAS1) polymerizes ATP into 2',5'-linked iso-RNA (2-5A) involved in innate immunity, cell cycle, and differentiation. We report the crystal structure of hOAS1 in complex with dsRNA and 2'-deoxy ATP at 2.7 Å resolution, which reveals the mechanism of cytoplasmic dsRNA recognition and activation of oligoadenylate synthetases. Human OAS1 recognizes dsRNA using a previously uncharacterized protein/RNA interface that forms via a conformational change induced by binding of dsRNA. The protein/RNA interface involves two minor grooves and has no sequence-specific contacts, with the exception of a single hydrogen bond between the -NH(2) group of nucleobase G17 and the carbonyl oxygen of serine 56. Using a biochemical readout, we show that hOAS1 undergoes more than 20,000-fold activation upon dsRNA binding and that canonical or GU-wobble substitutions produce dsRNA mutants that retain either full or partial activity, in agreement with the crystal structure. Ultimately, the binding of dsRNA promotes an elaborate conformational rearrangement in the N-terminal lobe of hOAS1, which brings residues D75, D77, and D148 into proximity and creates coordination geometry for binding of two catalytic Mg(2+) ions and ATP. The assembly of this critical active-site structure provides the gate that couples binding of dsRNA to the production and downstream functions of 2-5A.


    Organizational Affiliation

    Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
2'-5'-oligoadenylate synthase 1A349Homo sapiensMutation(s): 0 
Gene Names: OAS1OIAS
EC: 2.7.7 (PDB Primary Data), 2.7.7.84 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00973 (Homo sapiens)
Explore P00973 
Go to UniProtKB:  P00973
PHAROS:  P00973
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(*GP*GP*CP*UP*UP*UP*UP*GP*AP*CP*CP*UP*UP*UP*AP*UP*GP*C)-3')B18N/A
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      RNA (5'-R(*GP*CP*AP*UP*AP*AP*AP*GP*GP*UP*CP*AP*AP*AP*AP*GP*CP*C)-3')C18N/A
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      DTP (Subject of Investigation/LOI)
      Query on DTP

      Download Ideal Coordinates CCD File 
      F [auth A]2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
      C10 H16 N5 O12 P3
      SUYVUBYJARFZHO-RRKCRQDMSA-N
       Ligand Interaction
      MG
      Query on MG

      Download Ideal Coordinates CCD File 
      D [auth A], E [auth A]MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.70 Å
      • R-Value Free: 0.283 
      • R-Value Work: 0.229 
      • R-Value Observed: 0.231 
      • Space Group: P 21 21 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 71.2α = 90
      b = 93.2β = 90
      c = 98.6γ = 90
      Software Package:
      Software NamePurpose
      CBASSdata collection
      PHASERphasing
      PHENIXrefinement
      XDSdata reduction
      XDSdata scaling

      Structure Validation

      View Full Validation Report



      Ligand Structure Quality Assessment  



      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2013-01-16
        Type: Initial release
      • Version 1.1: 2013-01-30
        Changes: Database references
      • Version 1.2: 2013-02-13
        Changes: Database references