8DZJ

Cryo-EM structure of Acidibacillus sulfuroxidans Cas12f in complex with sgRNA and target DNA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

An engineered hypercompact CRISPR-Cas12f system with boosted gene-editing activity.

Wu, T.Liu, C.Zou, S.Lyu, R.Yang, B.Yan, H.Zhao, M.Tang, W.

(2023) Nat Chem Biol 19: 1384-1393

  • DOI: https://doi.org/10.1038/s41589-023-01380-9
  • Primary Citation of Related Structures:  
    8DZJ

  • PubMed Abstract: 

    Compact CRISPR-Cas systems offer versatile treatment options for genetic disorders, but their application is often limited by modest gene-editing activity. Here we present enAsCas12f, an engineered RNA-guided DNA endonuclease up to 11.3-fold more potent than its parent protein, AsCas12f, and one-third of the size of SpCas9. enAsCas12f shows higher DNA cleavage activity than wild-type AsCas12f in vitro and functions broadly in human cells, delivering up to 69.8% insertions and deletions at user-specified genomic loci. Minimal off-target editing is observed with enAsCas12f, suggesting that boosted on-target activity does not impair genome-wide specificity. We determine the cryo-electron microscopy (cryo-EM) structure of the AsCas12f-sgRNA-DNA complex at a resolution of 2.9 Å, which reveals dimerization-mediated substrate recognition and cleavage. Structure-guided single guide RNA (sgRNA) engineering leads to sgRNA-v2, which is 33% shorter than the full-length sgRNA, but with on par activity. Together, the engineered hypercompact AsCas12f system enables robust and faithful gene editing in mammalian cells.


  • Organizational Affiliation

    Department of Chemistry, The University of Chicago, Chicago, IL, USA.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
OrfB_Zn_ribbon domain-containing protein
A, B
446Sulfoacidibacillus thermotoleransMutation(s): 0 
Gene Names: BM613_13600
UniProt
Find proteins for A0A2U3D0N8 (Sulfoacidibacillus thermotolerans)
Explore A0A2U3D0N8 
Go to UniProtKB:  A0A2U3D0N8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2U3D0N8
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
target DNA strand42Homo sapiens
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
Non-target DNA strand42Homo sapiens
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains LengthOrganismImage
sgRNA193Sulfoacidibacillus thermotolerans
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
F [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM143052

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-12
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references