8K0J | pdb_00008k0j

Crystal structure of Cas7f

• PDB DOI: https://doi.org/10.2210/pdb8K0J/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Vibrio phage ICP1_2011_A
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-07-09 Released: 2024-07-10 
• Deposition Author(s): Feng, Y., Wang, H.
• Funding Organization(s): National Science Foundation (NSF, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free: 
  0.222 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

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

• PubMed: 38977786 
• DOI: https://doi.org/10.1038/s41589-024-01659-5
• Primary Citation 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.

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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.
Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China.
Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China. [e-mail].
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. [e-mail].
SUSTech Cryo-EM Facility Center, Southern University of Science and Technology, Shenzhen, China. [e-mail].
Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 33.4 kDa 
• Atom Count: 2,338 
• Modeled Residue Count: 299 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Csy3	A	306	Vibrio phage ICP1_2011_A	Mutation(s): 0  Gene Names: csy3, ICP12011A_086
UniProt
Find proteins for M1Q7R8 (Vibrio phage ICP1_2011_A) Explore M1Q7R8  Go to UniProtKB:  M1Q7R8

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free:  0.222 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.516	α = 90
b = 100.516	β = 90
c = 54.669	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-07-10 
Deposition Author(s): Feng, Y., Wang, H.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	32171274

Revision History  

• Version 1.0: 2024-07-10
  Type: Initial release
  
• Version 1.1: 2025-01-22
  Changes: Database references, Structure summary