6IV9

the Cas13d binary complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 10.1038/s41467-019-10507-3
  • Primary Citation of Related Structures:  

  • 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 ...

    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

    Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, 350117, Fuzhou, China.,Institute of Fisheries Science, College of Life Science, National Taiwan University, 1, Sec. 4, Roosevelt Rd., 10617, Taipei, Taiwan.,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. ouyangsy@fjnu.edu.cn.,Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, 350117, Fuzhou, China. ouyangsy@fjnu.edu.cn.,National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China. ouyangsy@fjnu.edu.cn.,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.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), 266237, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), 266237, Qingdao, China. ouyangsy@fjnu.edu.cn.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cas13d
A
930uncultured Ruminococcus spMutation(s): 2 
Find proteins for A0A1C5SD84 (uncultured Ruminococcus sp)
Go to UniProtKB:  A0A1C5SD84
Entity ID: 2
MoleculeChainsLengthOrganism
crRNA (50-MER)B50uncultured Ruminococcus sp.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.170 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 72.224α = 90.00
b = 136.481β = 90.00
c = 147.283γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
REFMACrefinement
xia2data reduction
PDB_EXTRACTdata extraction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (China)China31770948

Revision History 

  • Version 1.0: 2019-06-19
    Type: Initial release
  • Version 1.1: 2019-06-26
    Type: Data collection, Database references