8GAF | pdb_00008gaf

Exploiting Activation and Inactivation Mechanisms in Type I-C CRISPR-Cas3 for Genome Editing Applications


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.64 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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Literature

Exploiting activation and inactivation mechanisms in type I-C CRISPR-Cas3 for genome-editing applications.

Hu, C.Myers, M.T.Zhou, X.Hou, Z.Lozen, M.L.Nam, K.H.Zhang, Y.Ke, A.

(2024) Mol Cell 84: 463-475.e5

  • DOI: https://doi.org/10.1016/j.molcel.2023.12.034
  • Primary Citation Related Structures: 
    8G9S, 8G9T, 8G9U, 8GAF, 8GAM, 8GAN

  • PubMed Abstract: 

    Type I CRISPR-Cas systems utilize the RNA-guided Cascade complex to identify matching DNA targets and the nuclease-helicase Cas3 to degrade them. Among the seven subtypes, type I-C is compact in size and highly active in creating large-sized genome deletions in human cells. Here, we use four cryoelectron microscopy snapshots to define its RNA-guided DNA binding and cleavage mechanisms in high resolution. The non-target DNA strand (NTS) is accommodated by I-C Cascade in a continuous binding groove along the juxtaposed Cas11 subunits. Binding of Cas3 further traps a flexible bulge in NTS, enabling NTS nicking. We identified two anti-CRISPR proteins AcrIC8 and AcrIC9 that strongly inhibit Neisseria lactamica I-C function. Structural analysis showed that AcrIC8 inhibits PAM recognition through allosteric inhibition, whereas AcrIC9 achieves so through direct competition. Both Acrs potently inhibit I-C-mediated genome editing and transcriptional modulation in human cells, providing the first off-switches for type I CRISPR eukaryotic genome engineering.


  • Organizational Affiliation
    • Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA; Department of Biological Sciences, Faculty of Science; Department of Biochemistry, Precision Medicine Translational Research Programme (TRP), Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore.

Macromolecule Content 

  • Total Structure Weight: 421.07 kDa 
  • Atom Count: 24,582 
  • Modeled Residue Count: 3,004 
  • Deposited Residue Count: 3,641 
  • Unique protein chains: 4
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cas7
A,
B,
C,
D,
E,
F,
L [auth M]
283Neisseria lactamicaMutation(s): 0 
Gene Names: NCTC10618_01084
UniProt
Find proteins for D0W8X6 (Neisseria lactamica ATCC 23970)
Explore D0W8X6 
Go to UniProtKB:  D0W8X6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0W8X6
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Cas8
G, H
582Neisseria lactamicaMutation(s): 0 
Gene Names: B2G52_10005
UniProt
Find proteins for D0W8X5 (Neisseria lactamica ATCC 23970)
Explore D0W8X5 
Go to UniProtKB:  D0W8X5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0W8X5
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Cas11
I, J
124Neisseria lactamicaMutation(s): 0 
Gene Names: NCTC10618_01085
UniProt
Find proteins for D0W8X5 (Neisseria lactamica ATCC 23970)
Explore D0W8X5 
Go to UniProtKB:  D0W8X5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0W8X5
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Cas5M [auth N]205Neisseria lactamicaMutation(s): 0 
Gene Names: cas5d
EC: 3.1
UniProt
Find proteins for D0W8X4 (Neisseria lactamica ATCC 23970)
Explore D0W8X4 
Go to UniProtKB:  D0W8X4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0W8X4
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 4
MoleculeChains LengthOrganismImage
crRNA (43-MER)43Neisseria lactamica
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.64 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 Center for Research Resources (NIH/NCRR)United StatesGM118174

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-06
    Type: Initial release