8K0K | pdb_00008k0k

Crystal structure of Csy complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.238 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.1 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

  • 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_2011_AMutation(s): 0 
Gene Names: csy1ICP12011A_088
UniProt
Find proteins for M1R2X3 (Vibrio phage ICP1_2011_A)
Explore M1R2X3 
Go to UniProtKB:  M1R2X3
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UniProt GroupM1R2X3
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Csy2248Vibrio phage ICP1_2011_AMutation(s): 0 
Gene Names: csy2ICP12011A_087
UniProt
Find proteins for M1QWL5 (Vibrio phage ICP1_2011_A)
Explore M1QWL5 
Go to UniProtKB:  M1QWL5
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UniProt GroupM1QWL5
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Csy3
C, D, E, F, G
306Vibrio phage ICP1_2011_AMutation(s): 0 
Gene Names: csy3ICP12011A_086
UniProt
Find proteins for M1Q7R8 (Vibrio phage ICP1_2011_A)
Explore M1Q7R8 
Go to UniProtKB:  M1Q7R8
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UniProt GroupM1Q7R8
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Csy4168Vibrio phage ICP1_2011_AMutation(s): 0 
Gene Names: csy4ICP12011A_085
UniProt
Find proteins for M1R9H3 (Vibrio phage ICP1_2011_A)
Explore M1R9H3 
Go to UniProtKB:  M1R9H3
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UniProt GroupM1R9H3
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.238 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 238.853α = 90
b = 95.077β = 93.16
c = 204.031γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

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: 2024-07-10
    Type: Initial release
  • Version 1.1: 2025-01-22
    Changes: Database references, Structure summary