6EXP

Crystal structure of the SIRV3 AcrID1 (gp02) anti-CRISPR protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Anti-CRISPR proteins encoded by archaeal lytic viruses inhibit subtype I-D immunity.

He, F.Bhoobalan-Chitty, Y.Van, L.B.Kjeldsen, A.L.Dedola, M.Makarova, K.S.Koonin, E.V.Brodersen, D.E.Peng, X.

(2018) Nat Microbiol 3: 461-469

  • DOI: 10.1038/s41564-018-0120-z

  • PubMed Abstract: 
  • Viruses employ a range of strategies to counteract the prokaryotic adaptive immune system, clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas), including mutational escape and physical blocking of enz ...

    Viruses employ a range of strategies to counteract the prokaryotic adaptive immune system, clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas), including mutational escape and physical blocking of enzymatic function using anti-CRISPR proteins (Acrs). Acrs have been found in many bacteriophages but so far not in archaeal viruses, despite the near ubiquity of CRISPR-Cas systems in archaea. Here, we report the functional and structural characterization of two archaeal Acrs from the lytic rudiviruses, SIRV2 and SIRV3. We show that a 4 kb deletion in the SIRV2 genome dramatically reduces infectivity in Sulfolobus islandicus LAL14/1 that carries functional CRISPR-Cas subtypes I-A, I-D and III-B. Subsequent insertion of a single gene from SIRV3, gp02 (AcrID1), which is conserved in the deleted fragment, successfully restored infectivity. We demonstrate that AcrID1 protein inhibits the CRISPR-Cas subtype I-D system by interacting directly with Cas10d protein, which is required for the interference stage. Sequence and structural analysis of AcrID1 show that it belongs to a conserved family of compact, dimeric αβ-sandwich proteins characterized by extreme pH and temperature stability and a tendency to form protein fibres. We identify about 50 homologues of AcrID1 in four archaeal viral families demonstrating the broad distribution of this group of anti-CRISPR proteins.


    Organizational Affiliation

    Danish Archaea Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SIRV3 AcrID1 (gp02) anti-CRISPR protein
A, B, C, D, E, F
104Sulfolobus islandicus rudivirus 3Mutation(s): 0 
Find proteins for A0A1B3SN05 (Sulfolobus islandicus rudivirus 3)
Go to UniProtKB:  A0A1B3SN05
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.235 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 54.750α = 90.00
b = 80.440β = 101.23
c = 106.320γ = 90.00
Software Package:
Software NamePurpose
SHELXDphasing
XSCALEdata scaling
XDSdata reduction
PHENIXrefinement
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Danish National Research FoundationDenmarkDNRF120

Revision History 

  • Version 1.0: 2018-01-31
    Type: Initial release
  • Version 1.1: 2018-05-16
    Type: Data collection, Database references