6KQR

A pre-assembled molecular-helical Cascade backbone of Csy3 subunits from Zymomonas mobilis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A CRISPR RNA Is Closely Related With the Size of the Cascade Nucleoprotein Complex.

Gu, D.H.Ha, S.C.Kim, J.S.

(2019) Front Microbiol 10: 2458-2458

  • DOI: https://doi.org/10.3389/fmicb.2019.02458
  • Primary Citation of Related Structures:  
    6KQR

  • PubMed Abstract: 

    The currently known prokaryotic adaptive immune system against mobile genetic elements is based on clustered regularly interspaced short palindromic repeats (CRISPR). CRISPR-associated (Cas) proteins and the transcribed short CRISPR RNA (crRNA) molecule form a heterologous ribonucleoprotein complex that neutralizes invading foreign nucleic acids, wherein the crRNA molecule base-pairs with the exogenous genetic elements. In the ribonucleoprotein complexes of the type I CRISPR system, a helical backbone of six identical subunits is commonly found. However, it is not clear how this ribonucleoprotein complex is assembled and what is the determinant factor for its size. We elucidated the crystal structure of the Csy3 subunit of the type I-F ribonucleoprotein complex from Zymomonas mobilis (ZmCsy3), in which seven ZmCsy3 protomers in the asymmetric unit form a molecular helix that is part of a filamentous structure in the entire crystal system. This ZmCsy3 helical structure is remarkably similar to the crRNA-bound hexameric Csy3 backbone from Pseudomonas aeruginosa , with conserved interactions between neighboring subunits. The monomeric ZmCsy3 in solution is transformed into different oligomeric states depending on the added crRNAs. These results suggest that a crRNA and Csy3 subunit play a determinant role in the stepwise formation of the functional Cascade ribonucleoprotein complex and the recruitment of other subunits, and crRNA functions as a molecular ruler for determining the size of the Cascade silencing complex.


  • Organizational Affiliation

    Department of Chemistry, Chonnam National University, Gwangju, South Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR-associated protein Csy3 family
A, B, C, D, E
A, B, C, D, E, F, G
348Zymomonas mobilis subsp. mobilisMutation(s): 0 
Gene Names: ZMO2_ZMO0684ZMO3_ZMO0684
UniProt
Find proteins for Q5NPQ2 (Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4))
Explore Q5NPQ2 
Go to UniProtKB:  Q5NPQ2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5NPQ2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.181α = 99.37
b = 116.163β = 103.12
c = 115.937γ = 103.35
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic Of2017R1D1A3B03032278

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-13
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description