8BD5 | pdb_00008bd5

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

Validation slider image for 8BD5

This is version 1.3 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 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.

Macromolecule Content 

  • Total Structure Weight: 444.84 kDa 
  • Atom Count: 28,398 
  • Modeled Residue Count: 2,999 
  • Deposited Residue Count: 3,240 
  • Unique protein chains: 4
  • Unique nucleic acid chains: 3

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ShCas12k698Scytonema hofmanniiMutation(s): 0 
UniProt
Find proteins for A0A8X6EH11 (Scytonema hofmannii)
Explore A0A8X6EH11 
Go to UniProtKB:  A0A8X6EH11
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8X6EH11
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
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
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8J0PCL3
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
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
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8J0PCL5
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
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
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ADZ4
Sequence Annotations
Expand
Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 2
MoleculeChains LengthOrganismImage
sgRNA256Scytonema hofmannii
Sequence Annotations
Expand
Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 3
MoleculeChains LengthOrganismImage
DNA target strand49synthetic construct
Sequence Annotations
Expand
Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 4
MoleculeChains LengthOrganismImage
DNA non-target strand49synthetic construct
Sequence Annotations
Expand
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
  • Version 1.3: 2024-07-24
    Changes: Data collection