8BD5

Cas12k-sgRNA-dsDNA-S15-TniQ-TnsC transposon recruitment complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 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

Structural basis for the assembly of the type V CRISPR-associated transposon complex.

Schmitz, M.Querques, I.Oberli, S.Chanez, C.Jinek, M.

(2022) Cell 185: 4999

  • DOI: https://doi.org/10.1016/j.cell.2022.11.009
  • Primary Citation of Related Structures:  
    8BD4, 8BD5, 8BD6

  • PubMed Abstract: 

    CRISPR-Cas systems have been co-opted by Tn7-like transposable elements to direct RNA-guided transposition. Type V-K CRISPR-associated transposons rely on the concerted activities of the pseudonuclease Cas12k, the AAA+ ATPase TnsC, the Zn-finger protein TniQ, and the transposase TnsB. Here we present a cryo-electron microscopic structure of a target DNA-bound Cas12k-transposon recruitment complex comprised of RNA-guided Cas12k, TniQ, a polymeric TnsC filament and, unexpectedly, the ribosomal protein S15. Complex assembly, mediated by a network of interactions involving the guide RNA, TniQ, and S15, results in R-loop completion. TniQ contacts two TnsC protomers at the Cas12k-proximal filament end, likely nucleating its polymerization. Transposition activity assays corroborate our structural findings, implying that S15 is a bona fide component of the type V crRNA-guided transposon machinery. Altogether, our work uncovers key mechanistic aspects underpinning RNA-mediated assembly of CRISPR-associated transposons to guide their development as programmable tools for site-specific insertion of large DNA payloads.


  • Organizational Affiliation

    Department of Biochemistry, University of Zurich, Zurich 8057, Switzerland. Electronic address: jinek@bioc.uzh.ch.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ShCas12k698Scytonema hofmanniiMutation(s): 0 
UniProt
Find proteins for A0A8X6EH11 (Scytonema hofmannii)
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Go to UniProtKB:  A0A8X6EH11
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8X6EH11
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
TnsC
E, F, G, H, I
E, F, G, H, I, J, K
276Scytonema hofmanniiMutation(s): 0 
UniProt
Find proteins for A0A8J0PCL3 (Scytonema hofmannii)
Explore A0A8J0PCL3 
Go to UniProtKB:  A0A8J0PCL3
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UniProt GroupA0A8J0PCL3
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  • Reference Sequence
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
TniQ (Homology model)L [auth Q]167Scytonema hofmanniiMutation(s): 0 
UniProt
Find proteins for A0A8J0PCL5 (Scytonema hofmannii)
Explore A0A8J0PCL5 
Go to UniProtKB:  A0A8J0PCL5
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UniProt GroupA0A8J0PCL5
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  • Reference Sequence
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15M [auth X]89Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsOsecCb3165JW3134
UniProt
Find proteins for P0ADZ4 (Escherichia coli (strain K12))
Explore P0ADZ4 
Go to UniProtKB:  P0ADZ4
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UniProt GroupP0ADZ4
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Entity ID: 2
MoleculeChains LengthOrganismImage
sgRNA256Scytonema hofmannii
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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA target strand49synthetic construct
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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA non-target strand49synthetic construct
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
N [auth E]
P [auth F]
R [auth G]
T [auth H]
V [auth I]
N [auth E],
P [auth F],
R [auth G],
T [auth H],
V [auth I],
X [auth J],
Z [auth K]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
BA [auth Q],
CA [auth Q]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
AA [auth K]
O [auth E]
Q [auth F]
S [auth G]
U [auth H]
AA [auth K],
O [auth E],
Q [auth F],
S [auth G],
U [auth H],
W [auth I],
Y [auth J]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1.2

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland31003A_182567
European Research Council (ERC)European UnionERC-CoG-820152
Howard Hughes Medical Institute (HHMI)United States55008735
European Molecular Biology Organization (EMBO)European UnionALTF 296-2020

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-28
    Type: Initial release
  • Version 1.1: 2023-01-04
    Changes: Database references
  • Version 1.2: 2023-02-01
    Changes: Database references, Structure summary