the Cas13d binary complex

Experimental Data Snapshot

  • Resolution: 1.86 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 

Starting Model: experimental
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Two HEPN domains dictate CRISPR RNA maturation and target cleavage in Cas13d.

Zhang, B.Ye, Y.Ye, W.Perculija, V.Jiang, H.Chen, Y.Li, Y.Chen, J.Lin, J.Wang, S.Chen, Q.Han, Y.S.Ouyang, S.

(2019) Nat Commun 10: 2544-2544

  • DOI: https://doi.org/10.1038/s41467-019-10507-3
  • Primary Citation of Related Structures:  
    6IV8, 6IV9

  • PubMed Abstract: 

    Cas13d, the type VI-D CRISPR-Cas effector, is an RNA-guided ribonuclease that has been repurposed to edit RNA in a programmable manner. Here we report the detailed structural and functional analysis of the uncultured Ruminococcus sp. Cas13d (UrCas13d)-crRNA complex. Two hydrated Mg 2+ ions aid in stabilizing the conformation of the crRNA repeat region. Sequestration of divalent metal ions does not alter pre-crRNA processing, but abolishes target cleavage by UrCas13d. Notably, the pre-crRNA processing is executed by the HEPN-2 domain. Furthermore, both the structure and sequence of the nucleotides U(-8)-C(-1) within the repeat region are indispensable for target cleavage, and are specifically recognized by UrCas13d. Moreover, correct base pairings within two separate spacer regions (an internal and a 3'-end region) are essential for target cleavage. These findings provide a framework for the development of Cas13d into a tool for a wide range of applications.

  • Organizational Affiliation

    The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, 350117, Fuzhou, China.


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cas13d930uncultured Ruminococcus sp.Mutation(s): 2 
Gene Names: SAMEA3545300_02264
Find proteins for A0A1C5SD84 (uncultured Ruminococcus sp)
Explore A0A1C5SD84 
Go to UniProtKB:  A0A1C5SD84
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1C5SD84
Sequence Annotations
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
crRNA (50-MER)50uncultured Ruminococcus sp.
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.86 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.224α = 90
b = 136.481β = 90
c = 147.283γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
xia2data reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (China)China31770948

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-19
    Type: Initial release
  • Version 1.1: 2019-06-26
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description