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 7TR6 | pdb_00007tr6

Cascade complex from type I-A CRISPR-Cas system


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7TR6

This is version 1.2 of the entry. See complete history. 

Literature

Allosteric control of type I-A CRISPR-Cas3 complexes and establishment as effective nucleic acid detection and human genome editing tools.

Hu, C., Ni, D., Nam, K.H., Majumdar, S., McLean, J., Stahlberg, H., Terns, M.P., Ke, A.

(2022) Mol Cell 82: 2754-2768.e5

  • DOI: https://doi.org/10.1016/j.molcel.2022.06.007
  • Primary Citation Related Structures: 
    7TR6, 7TR8, 7TR9, 7TRA

  • PubMed Abstract: 

    Type I CRISPR-Cas systems typically rely on a two-step process to degrade DNA. First, an RNA-guided complex named Cascade identifies the complementary DNA target. The helicase-nuclease fusion enzyme Cas3 is then recruited in trans for processive DNA degradation. Contrary to this model, here, we show that type I-A Cascade and Cas3 function as an integral effector complex. We provide four cryoelectron microscopy (cryo-EM) snapshots of the Pyrococcus furiosus (Pfu) type I-A effector complex in different stages of DNA recognition and degradation. The HD nuclease of Cas3 is autoinhibited inside the effector complex. It is only allosterically activated upon full R-loop formation, when the entire targeted region has been validated by the RNA guide. The mechanistic insights inspired us to convert Pfu Cascade-Cas3 into a high-sensitivity, low-background, and temperature-activated nucleic acid detection tool. Moreover, Pfu CRISPR-Cas3 shows robust bi-directional deletion-editing activity in human cells, which could find usage in allele-specific inactivation of disease-causing mutations.


  • Organizational Affiliation: 
    • Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA.

Macromolecule Content 

  • Total Structure Weight: 402.29 kDa 
  • Atom Count: 27,449 
  • Modeled Residue Count: 3,428 
  • Deposited Residue Count: 3,534 
  • Unique protein chains: 4
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cas8aA [auth C]341Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: PF0637
UniProt
Find proteins for Q8U338 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8U338 
Go to UniProtKB:  Q8U338
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8U338
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Cas11aB [auth D],
C [auth E],
D [auth F],
E [auth G],
F [auth H]
108Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: PF0643
UniProt
Find proteins for Q8U332 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8U332 
Go to UniProtKB:  Q8U332
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8U332
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Cas7a336Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: PF0642
UniProt
Find proteins for Q8U333 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8U333 
Go to UniProtKB:  Q8U333
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8U333
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Cas5aN [auth P]256Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: cas5a, PFDSM3638_03200
UniProt
Find proteins for A0A5C0XNV9 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore A0A5C0XNV9 
Go to UniProtKB:  A0A5C0XNV9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A5C0XNV9
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 5
MoleculeChains LengthOrganismImage
crRNA (45-MER)O [auth R]45Escherichia coli
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM118117
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM118160
Swiss National Science FoundationSwitzerlandNCCR

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-10
    Type: Initial release
  • Version 1.1: 2022-08-17
    Changes: Database references
  • Version 1.2: 2024-11-13
    Changes: Data collection, Structure summary