8RKT | pdb_00008rkt

Conformational Landscape of the Type V-K CRISPR-associated TransposonIntegration Assembly CAST V-K Cas12k domain local-refinement map


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.35 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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Literature

Conformational landscape of the type V-K CRISPR-associated transposon integration assembly.

Tenjo-Castano, F.Sofos, N.Stutzke, L.S.Temperini, P.Fuglsang, A.Pape, T.Mesa, P.Montoya, G.

(2024) Mol Cell 84: 2353

  • DOI: https://doi.org/10.1016/j.molcel.2024.05.005
  • Primary Citation Related Structures: 
    8AXA, 8AXB, 8RDU, 8RKT, 8RKU, 8RKV

  • PubMed Abstract: 

    CRISPR-associated transposons (CASTs) are mobile genetic elements that co-opt CRISPR-Cas systems for RNA-guided DNA transposition. CASTs integrate large DNA cargos into the attachment (att) site independently of homology-directed repair and thus hold promise for eukaryotic genome engineering. However, the functional diversity and complexity of CASTs hinder an understanding of their mechanisms. Here, we present the high-resolution cryoelectron microscopy (cryo-EM) structure of the reconstituted ∼1 MDa post-transposition complex of the type V-K CAST, together with different assembly intermediates and diverse TnsC filament lengths, thus enabling the recapitulation of the integration complex formation. The results of mutagenesis experiments probing the roles of specific residues and TnsB-binding sites show that transposition activity can be enhanced and suggest that the distance between the PAM and att sites is determined by the lengths of the TnsB C terminus and the TnsC filament. This singular model of RNA-guided transposition provides a foundation for repurposing the system for genome-editing applications.


  • Organizational Affiliation
    • Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark.

Macromolecule Content 

  • Total Structure Weight: 256.27 kDa 
  • Atom Count: 13,794 
  • Modeled Residue Count: 1,165 
  • Deposited Residue Count: 1,429 
  • Unique protein chains: 3
  • Unique nucleic acid chains: 3

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
ShCas12kD [auth A]698Scytonema hofmanniiMutation(s): 0 
UniProt
Find proteins for A0A8M0FGU0 (Scytonema hofmannii)
Explore A0A8M0FGU0 
Go to UniProtKB:  A0A8M0FGU0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8M0FGU0
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS15E [auth B]90Scytonema hofmanniiMutation(s): 10 
Gene Names: rpsOrps15WA1_22700
UniProt
Find proteins for A0A139X9A4 (Scytonema hofmannii PCC 7110)
Explore A0A139X9A4 
Go to UniProtKB:  A0A139X9A4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A139X9A4
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
TniQF [auth C]179Scytonema hofmanniiMutation(s): 0 
UniProt
Find proteins for A0A8J0PCL5 (Scytonema hofmannii)
Explore A0A8J0PCL5 
Go to UniProtKB:  A0A8J0PCL5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8J0PCL5
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 1
MoleculeChains LengthOrganismImage
sgRNAA [auth 1]261Scytonema hofmannii
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 2
MoleculeChains LengthOrganismImage
Non-target strand - LEB [auth 2]68Scytonema hofmannii
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 3
MoleculeChains LengthOrganismImage
Target strand - LEC [auth 3]133Scytonema hofmannii
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.35 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.4
MODEL REFINEMENTISOLDE
MODEL REFINEMENTCoot
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Novo Nordisk FoundationDenmark--

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-19
    Type: Initial release
  • Version 1.1: 2024-07-03
    Changes: Data collection, Database references