8K28 | pdb_00008k28

ICP1 Csy-dsDNA complex (form 1)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.54 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.2 of the entry. See complete history


Literature

Cas1 mediates the interference stage in a phage-encoded CRISPR-Cas system.

Zhang, L.Wang, H.Zeng, J.Cao, X.Gao, Z.Liu, Z.Li, F.Wang, J.Zhang, Y.Yang, M.Feng, Y.

(2024) Nat Chem Biol 20: 1471-1481

  • DOI: https://doi.org/10.1038/s41589-024-01659-5
  • Primary Citation of Related Structures:  
    8K0H, 8K0J, 8K0K, 8K28

  • PubMed Abstract: 

    Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems are prokaryotic adaptive immune systems against invading phages and other mobile genetic elements. Notably, some phages, including the Vibrio cholerae-infecting ICP1 (International Center for Diarrheal Disease Research, Bangladesh cholera phage 1), harbor CRISPR-Cas systems to counteract host defenses. Nevertheless, ICP1 Cas8f lacks the helical bundle domain essential for recruitment of helicase-nuclease Cas2/3 during target DNA cleavage and how this system accomplishes the interference stage remains unknown. Here, we found that Cas1, a highly conserved component known to exclusively work in the adaptation stage, also mediates the interference stage through connecting Cas2/3 to the DNA-bound CRISPR-associated complex for antiviral defense (Cascade; CRISPR system yersinia, Csy) of the ICP1 CRISPR-Cas system. A series of structures of Csy, Csy-dsDNA (double-stranded DNA), Cas1-Cas2/3 and Csy-dsDNA-Cas1-Cas2/3 complexes reveal the whole process of Cas1-mediated target DNA cleavage by the ICP1 CRISPR-Cas system. Together, these data support an unprecedented model in which Cas1 mediates the interference stage in a phage-encoded CRISPR-Cas system and the study also sheds light on a unique model of primed adaptation.


  • Organizational Affiliation
    • Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Csy1179Vibrio phage ICP1_2004_AMutation(s): 0 
Gene Names: TUST1-10_00450
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Csy2248Vibrio phage ICP1_2004_AMutation(s): 0 
Gene Names: TUST1-10_00445
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Csy3
C,
D,
E,
F,
G,
L [auth H]
306Vibrio phage ICP1_2004_AMutation(s): 0 
Gene Names: TUST1-10_00440
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Csy4H [auth I]168Vibrio phage ICP1_2004_AMutation(s): 0 
Gene Names: TUST1-10_00435
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (33-MER)I [auth Q]33Vibrio phage ICP1_2004_A
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (27-MER)J [auth R]27Vibrio phage ICP1_2004_A
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Entity ID: 7
MoleculeChains LengthOrganismImage
RNA (59-MER)K [auth P]59Vibrio phage ICP1_2004_A
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.54 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China32171274

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-17
    Type: Initial release
  • Version 1.1: 2025-07-23
    Changes: Data collection, Structure summary
  • Version 1.2: 2026-01-28
    Changes: Data collection, Database references