Csf5, CRISPR-Cas type IV Cas6 crRNA endonuclease

Experimental Data Snapshot

  • Resolution: 1.75 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Type IV CRISPR RNA processing and effector complex formation in Aromatoleum aromaticum.

Ozcan, A.Pausch, P.Linden, A.Wulf, A.Schuhle, K.Heider, J.Urlaub, H.Heimerl, T.Bange, G.Randau, L.

(2019) Nat Microbiol 4: 89-96

  • DOI: https://doi.org/10.1038/s41564-018-0274-8
  • Primary Citation of Related Structures:  
    6H9H, 6H9I

  • PubMed Abstract: 

    Type IV CRISPR-Cas modules belong to class 1 prokaryotic adaptive immune systems, which are defined by the presence of multisubunit effector complexes. They usually lack the known Cas proteins involved in adaptation and target cleavage, and their function has not been experimentally addressed. To investigate RNA and protein components of this CRISPR-Cas type, we located a complete type IV cas gene locus and an adjacent CRISPR array on a megaplasmid of Aromatoleum aromaticum EbN1, which contains an additional type I-C system on its chromosome. RNA sequencing analyses verified CRISPR RNA (crRNA) production and maturation for both systems. Type IV crRNAs were shown to harbour unusually short 7 nucleotide 5'-repeat tags and stable 3' hairpin structures. A unique Cas6 variant (Csf5) was identified that generates crRNAs that are specifically incorporated into type IV CRISPR-ribonucleoprotein (crRNP) complexes. Structures of RNA-bound Csf5 were obtained. Recombinant production and purification of the type IV Cas proteins, together with electron microscopy, revealed that Csf2 acts as a helical backbone for type IV crRNPs that include Csf5, Csf3 and a large subunit (Csf1). Mass spectrometry analyses identified protein-protein and protein-RNA contact sites. These results highlight evolutionary connections between type IV and type I CRISPR-Cas systems and demonstrate that type IV CRISPR-Cas systems employ crRNA-guided effector complexes.

  • Organizational Affiliation

    Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Csf5A [auth B],
B [auth A]
266Aromatoleum aromaticum EbN1Mutation(s): 0 
Gene Names: p1B372
Find proteins for Q5NWP0 (Aromatoleum aromaticum (strain EbN1))
Explore Q5NWP0 
Go to UniProtKB:  Q5NWP0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5NWP0
Sequence Annotations
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
crRNAC [auth D],
D [auth E]
26Aromatoleum aromaticum EbN1
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.75 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.563α = 90
b = 100.989β = 90
c = 101.933γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-26
    Type: Initial release
  • Version 1.1: 2018-11-14
    Changes: Data collection, Database references
  • Version 1.2: 2018-12-26
    Changes: Data collection, Database references
  • Version 1.3: 2024-05-15
    Changes: Data collection, Database references, Derived calculations