8HUD | pdb_00008hud

Cryo-EM structure of the EvCas9-sgRNA-target DNA ternary complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.43 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Molecular Basis and Genome Editing Applications of a Compact Eubacterium ventriosum CRISPR-Cas9 System.

Tang, N.Wu, Z.Gao, Y.Chen, W.Wang, Z.Su, M.Ji, W.Ji, Q.

(2024) ACS Synth Biol 13: 269-281

  • DOI: https://doi.org/10.1021/acssynbio.3c00501
  • Primary Citation of Related Structures:  
    8HUD

  • PubMed Abstract: 

    CRISPR-Cas9 systems have been widely harnessed for diverse genome editing applications because of their ease of use and high efficiency. However, the large molecular sizes and strict PAM requirements of commonly used CRISPR-Cas9 systems restrict their broad applications in therapeutics. Here, we report the molecular basis and genome editing applications of a novel compact type II-A Eubacterium ventriosum CRISPR-Cas9 system (EvCas9) with 1107 residues and distinct 5'-NNGDGN-3' (where D represents A, T, or G) PAM specificity. We determine the cryo-EM structure of EvCas9 in a complex with an sgRNA and a target DNA, revealing the detailed PAM recognition and sgRNA and target DNA association mechanisms. Additionally, we demonstrate the robust genome editing capacity of EvCas9 in bacteria and human cells with superior fidelity compared to SaCas9 and SpCas9, and we engineer it to be efficient base editors by fusing a cytidine or adenosine deaminase. Collectively, our results facilitate further understanding of CRISPR-Cas9 working mechanisms and expand the compact CRISPR-Cas9 toolbox.


  • Organizational Affiliation
    • School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China.

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR-associated endonuclease Cas91,107Eubacterium ventriosum ATCC 27560Mutation(s): 0 
Gene Names: csn1cas9EUBVEN_00141
EC: 3.1
UniProt
Find proteins for A5Z395 (Eubacterium ventriosum ATCC 27560)
Explore A5Z395 
Go to UniProtKB:  A5Z395
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5Z395
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
sgRNA75synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains LengthOrganismImage
Target DNA strand28synthetic construct
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 4
MoleculeChains LengthOrganismImage
Non-target DNA strand8synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.43 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China21922705
National Natural Science Foundation of China (NSFC)China22277078

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-27
    Type: Initial release
  • Version 1.1: 2024-08-07
    Changes: Data collection, Database references
  • Version 1.2: 2024-10-09
    Changes: Data collection, Structure summary