5WQE

Crystal structure of Alicyclobacillus acidoterrestris C2c1 in complex with single-guide RNA at 3.1 Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.13 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.239 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

C2c1-sgRNA Complex Structure Reveals RNA-Guided DNA Cleavage Mechanism

Liu, L.Chen, P.Wang, M.Li, X.Wang, J.Yin, M.Wang, Y.

(2017) Mol Cell 65: 310-322

  • DOI: https://doi.org/10.1016/j.molcel.2016.11.040
  • Primary Citation of Related Structures:  
    5WQE

  • PubMed Abstract: 

    C2c1 is a type V-B CRISPR-Cas system dual-RNA-guided DNA endonuclease. Here, we report the crystal structure of Alicyclobacillus acidoterrestris C2c1 in complex with a chimeric single-molecule guide RNA (sgRNA). AacC2c1 exhibits a bi-lobed architecture consisting of a REC and NUC lobe. The sgRNA scaffold forms a tetra-helical structure, distinct from previous predictions. The crRNA is located in the central channel of C2c1, and the tracrRNA resides in an external surface groove. Although AacC2c1 lacks a PAM-interacting domain, our analysis revealed that the PAM duplex has a similar binding position found in Cpf1. Importantly, C2c1-sgRNA system is highly sensitive to single-nucleotide mismatches between guide RNA and target DNA. The resulting reduction in off-target cleavage renders C2c1 a valuable addition to the current arsenal of genome-editing tools. Together, our findings indicate that sgRNA assembly is achieved through a mechanism distinct from that reported previously for Cas9 or Cpf1 endonucleases.


  • Organizational Affiliation

    Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR-associated endonuclease C2c11,137Alicyclobacillus acidoterrestris ATCC 49025Mutation(s): 0 
Gene Names: c2c1N007_06525
EC: 3.1
UniProt
Find proteins for T0D7A2 (Alicyclobacillus acidoterrestris (strain ATCC 49025 / DSM 3922 / CIP 106132 / NCIMB 13137 / GD3B))
Explore T0D7A2 
Go to UniProtKB:  T0D7A2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupT0D7A2
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (60-MER)112Alicyclobacillus acidoterrestris ATCC 49025
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.13 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.239 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 194.554α = 90
b = 129.836β = 110
c = 84.001γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHENIXphasing
HKL-2000data processing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina91440201
National Natural Science Foundation of ChinaChina31571335
National Natural Science Foundation of ChinaChina31400640
Ministry of Science and Technology (China)China2014CB910102
Strategic Priority Research Program of the Chinese Academy of SciencesChinaXDB08010203

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-25
    Type: Initial release
  • Version 1.1: 2017-02-01
    Changes: Database references
  • Version 1.2: 2017-10-18
    Changes: Author supporting evidence
  • Version 1.3: 2024-10-16
    Changes: Data collection, Database references, Structure summary