6YES | pdb_00006yes

Crystal structure of type I-D CRISPR-Cas nuclease Cas10d


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.10 Å
  • R-Value Free: 
    0.370 (Depositor), 0.371 (DCC) 
  • R-Value Work: 
    0.343 (Depositor), 0.346 (DCC) 
  • R-Value Observed: 
    0.345 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.5 of the entry. See complete history

Literature

Structural basis for inhibition of an archaeal CRISPR-Cas type I-D large subunit by an anti-CRISPR protein.

Manav, M.C.Van, L.B.Lin, J.Fuglsang, A.Peng, X.Brodersen, D.E.

(2020) Nat Commun 11: 5993-5993

  • DOI: https://doi.org/10.1038/s41467-020-19847-x
  • Primary Citation Related Structures: 
    6THH, 6YES

  • PubMed Abstract: 

    A hallmark of type I CRISPR-Cas systems is the presence of Cas3, which contains both the nuclease and helicase activities required for DNA cleavage during interference. In subtype I-D systems, however, the histidine-aspartate (HD) nuclease domain is encoded as part of a Cas10-like large effector complex subunit and the helicase activity in a separate Cas3' subunit, but the functional and mechanistic consequences of this organisation are not currently understood. Here we show that the Sulfolobus islandicus type I-D Cas10d large subunit exhibits an unusual domain architecture consisting of a Cas3-like HD nuclease domain fused to a degenerate polymerase fold and a C-terminal domain structurally similar to Cas11. Crystal structures of Cas10d both in isolation and bound to S. islandicus rod-shaped virus 3 AcrID1 reveal that the anti-CRISPR protein sequesters the large subunit in a non-functional state unable to form a cleavage-competent effector complex. The architecture of Cas10d suggests that the type I-D effector complex is similar to those found in type III CRISPR-Cas systems and that this feature is specifically exploited by phages for anti-CRISPR defence.


  • Organizational Affiliation
    • Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10c, DK-8000, Aarhus C, Denmark.

Macromolecule Content 

  • Total Structure Weight: 195.11 kDa 
  • Atom Count: 12,534 
  • Modeled Residue Count: 1,567 
  • Deposited Residue Count: 1,710 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CRISPR-associated protein, CscA
A, B
855Saccharolobus islandicus LAL14/1Mutation(s): 0 
Gene Names: SiL_0609
UniProt
Find proteins for M9U4Y8 (Saccharolobus islandicus LAL14/1)
Explore M9U4Y8 
Go to UniProtKB:  M9U4Y8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupM9U4Y8
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.10 Å
  • R-Value Free:  0.370 (Depositor), 0.371 (DCC) 
  • R-Value Work:  0.343 (Depositor), 0.346 (DCC) 
  • R-Value Observed: 0.345 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.43α = 90
b = 141.43β = 90
c = 223.87γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
LundbeckfondenDenmarkR-287-2018-1555
Novo Nordisk FoundationDenmarkNNF17OC0028072

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-28
    Type: Initial release
  • Version 1.1: 2020-12-02
    Changes: Database references
  • Version 1.2: 2020-12-09
    Changes: Database references
  • Version 1.3: 2021-06-30
    Changes: Refinement description, Source and taxonomy, Structure summary
  • Version 1.4: 2024-01-24
    Changes: Data collection, Database references, Refinement description
  • Version 1.5: 2024-11-13
    Changes: Structure summary