8FYB

Cryo-EM structure of Cas1:Cas2-DEDDh:half-site integration complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Genome expansion by a CRISPR trimmer-integrase.

Wang, J.Y.Tuck, O.T.Skopintsev, P.Soczek, K.M.Li, G.Al-Shayeb, B.Zhou, J.Doudna, J.A.

(2023) Nature 618: 855-861

  • DOI: https://doi.org/10.1038/s41586-023-06178-2
  • Primary Citation of Related Structures:  
    8FY9, 8FYA, 8FYB, 8FYC, 8FYD

  • PubMed Abstract: 

    CRISPR-Cas adaptive immune systems capture DNA fragments from invading mobile genetic elements and integrate them into the host genome to provide a template for RNA-guided immunity 1 . CRISPR systems maintain genome integrity and avoid autoimmunity by distinguishing between self and non-self, a process for which the CRISPR/Cas1-Cas2 integrase is necessary but not sufficient 2-5 . In some microorganisms, the Cas4 endonuclease assists CRISPR adaptation 6,7 , but many CRISPR-Cas systems lack Cas4 8 . Here we show here that an elegant alternative pathway in a type I-E system uses an internal DnaQ-like exonuclease (DEDDh) to select and process DNA for integration using the protospacer adjacent motif (PAM). The natural Cas1-Cas2/exonuclease fusion (trimmer-integrase) catalyses coordinated DNA capture, trimming and integration. Five cryo-electron microscopy structures of the CRISPR trimmer-integrase, visualized both before and during DNA integration, show how asymmetric processing generates size-defined, PAM-containing substrates. Before genome integration, the PAM sequence is released by Cas1 and cleaved by the exonuclease, marking inserted DNA as self and preventing aberrant CRISPR targeting of the host. Together, these data support a model in which CRISPR systems lacking Cas4 use fused or recruited 9,10 exonucleases for faithful acquisition of new CRISPR immune sequences.


  • Organizational Affiliation

    Department of Chemistry, University of California, Berkeley, CA, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cas2-DEDDh
A, D
289MegasphaeraMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cas1
B, C, E, F
316MegasphaeraMutation(s): 0 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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  • Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (52-MER)64Megasphaera
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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (31-MER)33Megasphaera
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (36-MER)I [auth J]78Megasphaera
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (17-MER)J [auth I]44Megasphaera
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2-4158
RECONSTRUCTIONcryoSPARC4.1.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesDGE 1752814
National Science Foundation (NSF, United States)United StatesDGE 2146752
Swiss National Science FoundationSwitzerlandP2EZP3_195621

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-03
    Type: Initial release
  • Version 1.1: 2023-06-14
    Changes: Database references
  • Version 1.2: 2023-06-28
    Changes: Database references
  • Version 1.3: 2023-07-05
    Changes: Database references
  • Version 1.4: 2024-06-19
    Changes: Data collection