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

Experimental Data Snapshot

  • Resolution: 1.93 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.236 

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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: https://doi.org/10.1038/s41564-018-0120-z
  • Primary Citation of Related Structures:  

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SIRV3 AcrID1 (gp02) anti-CRISPR protein
A, B, C, D, E
A, B, C, D, E, F
104Sulfolobus islandicus rudivirus 3Mutation(s): 0 
Find proteins for A0A1B3SN05 (Sulfolobus islandicus rod-shaped virus 3)
Explore A0A1B3SN05 
Go to UniProtKB:  A0A1B3SN05
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1B3SN05
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.93 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.236 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.75α = 90
b = 80.44β = 101.23
c = 106.32γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
Cootmodel building

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Danish National Research FoundationDenmarkDNRF120

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-31
    Type: Initial release
  • Version 1.1: 2018-05-16
    Changes: Data collection, Database references
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references, Refinement description