Structure of R354_WT

Experimental Data Snapshot

  • Resolution: 2.81 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Structural and Mechanistic Analyses Reveal a Unique Cas4-like Protein in the Mimivirus Virophage Resistance Element System.

Dou, C.Yu, M.Gu, Y.Wang, J.Yin, K.Nie, C.Zhu, X.Qi, S.Wei, Y.Cheng, W.

(2018) iScience 3: 1-10

  • DOI: https://doi.org/10.1016/j.isci.2018.04.001
  • Primary Citation of Related Structures:  
    5YET, 5YEU

  • PubMed Abstract: 

    A clustered regularly interspaced short palindromic repeats (CRISPR)-like "mimivirus virophage resistance element" (MIMIVIRE) system, which contains specific cascade genes and a CRISPR array against virophages, was reported in mimiviruses. An essential component of the MIMIVIRE system is R354, encoding a nuclease and a likely functional homolog of Cas4. Here we show that R354 is a dual nuclease with both exonuclease and endonuclease activities. Structural analysis revealed that the catalytic core domain of R354 is similar to those of Cas4 and ? exonuclease despite their low sequence identity. R354 forms a homodimer that is important for its exonuclease but not endonuclease activity. Structural comparisons between the active and semi-active states of R354 demonstrated that an activation loop adjacent to the catalytic site is critical for enzymatic activity. Overall, the results suggest that R354 belongs to a novel MIMIVIRE system involved in innate virus immunity and provides a template for the identification of new CRISPR systems in other species.

  • Organizational Affiliation

    Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, 17th, 3rd Section, Southern Renmin Road, Chengdu, 610041, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein R354
A, B
399Acanthamoeba polyphaga mimivirusMutation(s): 0 
Gene Names: MIMI_R354
Find proteins for Q5UQV1 (Acanthamoeba polyphaga mimivirus)
Explore Q5UQV1 
Go to UniProtKB:  Q5UQV1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5UQV1
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.81 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.846α = 90
b = 57.809β = 108.39
c = 99.948γ = 90
Software Package:
Software NamePurpose
PHENIXdata reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-20
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Database references
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references