8YHA

Type I-EHNH Cascade-ssDNA complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Mechanisms for HNH-mediated target DNA cleavage in type I CRISPR-Cas systems.

Zhang, C.Chen, F.Wang, F.Xu, H.Xue, J.Li, Z.

(2024) Mol Cell 

  • DOI: https://doi.org/10.1016/j.molcel.2024.06.033
  • Primary Citation of Related Structures:  
    8YB6, 8YDB, 8YEO, 8YH9, 8YHA

  • PubMed Abstract: 

    The metagenome-derived type I-E and type I-F variant CRISPR-associated complex for antiviral defense (Cascade) complexes, fused with HNH domains, precisely cleave target DNA, representing recently identified genome editing tools. However, the underlying working mechanisms remain unknown. Here, structures of type I-F HNH and I-E HNH Cascade complexes at different states are reported. In type I-F HNH Cascade, Cas8f HNH loosely attaches to Cascade head and is adjacent to the 5' end of the target single-stranded DNA (ssDNA). Formation of the full R-loop drives the Cascade head to move outward, allowing Cas8f HNH to detach and rotate ∼150° to accommodate target ssDNA for cleavage. In type I-E HNH Cascade, Cas5e HNH domain is adjacent to the 5' end of the target ssDNA. Full crRNA-target pairing drives the lift of the Cascade head, widening the substrate channel for target ssDNA entrance. Altogether, these analyses into both complexes revealed that crRNA-guided positioning of target DNA and target DNA-induced HNH unlocking are two key factors for their site-specific cleavage of target DNA.


  • Organizational Affiliation

    State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, Hubei, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR system Cascade subunit CasD388Candidatus Cloacimonetes bacterium ADurb.Bin088Mutation(s): 0 
Gene Names: casDBWX75_00750
UniProt
Find proteins for A0A1V6F8C5 (Candidatus Cloacimonetes bacterium ADurb.Bin088)
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Go to UniProtKB:  A0A1V6F8C5
Entity Groups  
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UniProt GroupA0A1V6F8C5
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR-associated endoribonuclease Cse3272Candidatus Cloacimonetes bacterium ADurb.Bin088Mutation(s): 0 
Gene Names: cse3BWX75_00751
EC: 3.1
UniProt
Find proteins for A0A1V6F8C4 (Candidatus Cloacimonetes bacterium ADurb.Bin088)
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UniProt GroupA0A1V6F8C4
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR system Cascade subunit CasC
D, E, F, G, H
D, E, F, G, H, I
378Candidatus Cloacimonetes bacterium ADurb.Bin088Mutation(s): 0 
Gene Names: casCBWX75_00749
UniProt
Find proteins for A0A1V6F8B5 (Candidatus Cloacimonetes bacterium ADurb.Bin088)
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UniProt GroupA0A1V6F8B5
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR-associated protein Cse1 (CRISPR_cse1)535Candidatus Cloacimonetes bacterium ADurb.Bin088Mutation(s): 0 
Gene Names: BWX75_00747
UniProt
Find proteins for A0A1V6F8D1 (Candidatus Cloacimonetes bacterium ADurb.Bin088)
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UniProt GroupA0A1V6F8D1
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR-associated protein Cse2 (CRISPR_cse2)174Candidatus Cloacimonetes bacterium ADurb.Bin088Mutation(s): 0 
Gene Names: BWX75_00748
UniProt
Find proteins for A0A1V6F8C9 (Candidatus Cloacimonetes bacterium ADurb.Bin088)
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UniProt GroupA0A1V6F8C9
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Entity ID: 3
MoleculeChains LengthOrganismImage
61-nt crRNA61Candidatus Cloacimonadota bacterium
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Entity ID: 7
MoleculeChains LengthOrganismImage
DNA/RNA (47-MER)L [auth T]56Candidatus Cloacimonadota bacterium
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2024-07-31 
  • Deposition Author(s): Li, Z.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-31
    Type: Initial release
  • Version 1.1: 2024-08-07
    Changes: Data collection, Database references