4S3N | pdb_00004s3n

Crystal structure of human OAS3 domain I in complex with dsRNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.211 (Depositor), 0.213 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 
    0.183 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Structural mechanism of sensing long dsRNA via a noncatalytic domain in human oligoadenylate synthetase 3.

Donovan, J.Whitney, G.Rath, S.Korennykh, A.

(2015) Proc Natl Acad Sci U S A 112: 3949-3954

  • DOI: https://doi.org/10.1073/pnas.1419409112
  • Primary Citation Related Structures: 
    4S3N

  • PubMed Abstract: 

    The mammalian innate immune system uses several sensors of double-stranded RNA (dsRNA) to develop the interferon response. Among these sensors are dsRNA-activated oligoadenylate synthetases (OAS), which produce signaling 2',5'-linked RNA molecules (2-5A) that activate regulated RNA decay in mammalian tissues. Different receptors from the OAS family contain one, two, or three copies of the 2-5A synthetase domain, which in several instances evolved into pseudoenzymes. The structures of the pseudoenzymatic domains and their roles in sensing dsRNA are unknown. Here we present the crystal structure of the first catalytically inactive domain of human OAS3 (hOAS3.DI) in complex with a 19-bp dsRNA, determined at 2.0-Å resolution. The conformation of hOAS3.DI is different from the apo- and the dsRNA-bound states of the catalytically active homolog, OAS1, reported previously. The unique conformation of hOAS3.DI disables 2-5A synthesis by placing the active site residues nonproductively, but favors the binding of dsRNA. Biochemical data show that hOAS3.DI is essential for activation of hOAS3 and serves as a dsRNA-binding module, whereas the C-terminal domain DIII carries out catalysis. The location of the dsRNA-binding domain (DI) and the catalytic domain (DIII) at the opposite protein termini makes hOAS3 selective for long dsRNA. This mechanism relies on the catalytic inactivity of domain DI, revealing a surprising role of pseudoenzyme evolution in dsRNA surveillance.


  • Organizational Affiliation
    • Department of Molecular Biology, Princeton University, Princeton, NJ 08544.

Macromolecule Content 

  • Total Structure Weight: 53.39 kDa 
  • Atom Count: 3,795 
  • Modeled Residue Count: 381 
  • Deposited Residue Count: 411 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 2

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
2'-5'-oligoadenylate synthase 3373Homo sapiensMutation(s): 1 
Gene Names: OAS3P/OKcl.4
EC: 2.7.7.84
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6K5 (Homo sapiens)
Explore Q9Y6K5 
Go to UniProtKB:  Q9Y6K5
PHAROS:  Q9Y6K5
GTEx:  ENSG00000111331 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y6K5
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (5'-R(*GP*GP*CP*UP*UP*UP*UP*GP*AP*CP*CP*UP*UP*UP*AP*UP*GP*AP*A)-3')19synthetic construct
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 3
MoleculeChains LengthOrganismImage
RNA (5'-R(*UP*UP*CP*AP*UP*AP*AP*AP*GP*GP*UP*CP*AP*AP*AP*AP*GP*CP*C)-3')19synthetic construct
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.211 (Depositor), 0.213 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 0.183 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.7α = 90
b = 104.7β = 97.8
c = 63.8γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-25
    Type: Initial release
  • Version 1.1: 2015-04-15
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Refinement description