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 7EI1 | pdb_00007ei1

Structure of Pyrococcus furiosus Cas1Cas2 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 
    0.328 (Depositor), 0.333 (DCC) 
  • R-Value Work: 
    0.281 (Depositor), 0.280 (DCC) 
  • R-Value Observed: 
    0.281 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7EI1

This is version 1.1 of the entry. See complete history. 

Literature

A distinct structure of Cas1-Cas2 complex provides insights into the mechanism for the longer spacer acquisition in Pyrococcus furiosus.

Tang, D., Li, H., Wu, C., Jia, T., He, H., Yao, S., Yu, Y., Chen, Q.

(2021) Int J Biol Macromol 183: 379-386

  • DOI: https://doi.org/10.1016/j.ijbiomac.2021.04.074
  • Primary Citation Related Structures: 
    7EI1

  • PubMed Abstract: 

    In the adaptation stage of CRISPR-Cas systems, the Cas1-Cas2 integrase captures and integrates new invader-derived spacers into the CRISPR locus, serving as a molecular memory of prior infection. As of yet, the structural information of Cas1-Cas2 complex is available only for two species. Here we present the crystal structure of Cas1-Cas2 complex of Pyrococcus furiosus, which showed a distinct architecture from the known Cas1-Cas2 complexes. The shorter C-terminal tail of Pfu Cas2 directs the Cas1 dimers go in the opposite direction, resulting in a different prespacer binding mode. Based on our structural and mutagenesis results, we modeled a prespacer with a shorter duplex and longer 3' overhangs to bind Pfu Cas1-Cas2 complex. The prespacer preference was confirmed by EMSA, fluorescence polarization, and in vitro integration assays. This model provides a potential explanation for the longer spacer acquisition observed in P. furiosus when deleting both cas4 genes. Our study highlights the diversity of the CRISPR adaptation module.


  • Organizational Affiliation: 
    • State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, PR China.

Macromolecule Content 

  • Total Structure Weight: 680.57 kDa 
  • Atom Count: 46,274 
  • Modeled Residue Count: 5,622 
  • Deposited Residue Count: 5,832 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CRISPR-associated endonuclease Cas1322Pyrococcus furiosus COM1Mutation(s): 0 
Gene Names: cas1, PFC_04810
EC: 3.1
UniProt
Find proteins for I6TWX9 (Pyrococcus furiosus COM1)
Explore I6TWX9 
Go to UniProtKB:  I6TWX9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI6TWX9
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
CRISPR-associated endoribonuclease Cas285Pyrococcus furiosus COM1Mutation(s): 0 
Gene Names: cas2, PFC_04805
EC: 3.1
UniProt
Find proteins for I6V1H0 (Pyrococcus furiosus COM1)
Explore I6V1H0 
Go to UniProtKB:  I6V1H0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI6V1H0
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free:  0.328 (Depositor), 0.333 (DCC) 
  • R-Value Work:  0.281 (Depositor), 0.280 (DCC) 
  • R-Value Observed: 0.281 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.763α = 90
b = 180.473β = 94.428
c = 338.847γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-24
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description