8EX9

ISDra2 TnpB in complex with reRNA and cognate DNA, conformation 2 (RuvC domain unresolved)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.96 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

TnpB structure reveals minimal functional core of Cas12 nuclease family.

Sasnauskas, G.Tamulaitiene, G.Druteika, G.Carabias, A.Silanskas, A.Kazlauskas, D.Venclovas, C.Montoya, G.Karvelis, T.Siksnys, V.

(2023) Nature 616: 384-389

  • DOI: https://doi.org/10.1038/s41586-023-05826-x
  • Primary Citation of Related Structures:  
    8BF8, 8EX9, 8EXA

  • PubMed Abstract: 

    The widespread TnpB proteins of IS200/IS605 transposon family have recently emerged as the smallest RNA-guided nucleases capable of targeted genome editing in eukaryotic cells 1,2 . Bioinformatic analysis identified TnpB proteins as the likely predecessors of Cas12 nucleases 3-5 , which along with Cas9 are widely used for targeted genome manipulation. Whereas Cas12 family nucleases are well characterized both biochemically and structurally 6 , the molecular mechanism of TnpB remains unknown. Here we present the cryogenic-electron microscopy structures of the Deinococcus radiodurans TnpB-reRNA (right-end transposon element-derived RNA) complex in DNA-bound and -free forms. The structures reveal the basic architecture of TnpB nuclease and the molecular mechanism for DNA target recognition and cleavage that is supported by biochemical experiments. Collectively, these results demonstrate that TnpB represents the minimal structural and functional core of the Cas12 protein family and provide a framework for developing TnpB-based genome editing tools.


  • Organizational Affiliation

    Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania. gsasnaus@ibt.lt.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-guided DNA endonuclease TnpB408Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
Gene Names: tnpBorf2tnpCDR_0666DR_0978DR_1381DR_1593DR_1651DR_1933DR_2324
EC: 3.1.21
UniProt
Find proteins for Q7DF80 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
Explore Q7DF80 
Go to UniProtKB:  Q7DF80
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7DF80
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (150-MER)150Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (43-MER)43synthetic construct
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (43-MER)43synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.96 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.4.0

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Novo Nordisk FoundationDenmarkNNF14CC0001
Novo Nordisk FoundationDenmarkNNF0024386
Novo Nordisk FoundationDenmarkNNF17SA0030214
Novo Nordisk FoundationDenmarkNNF18OC0055061

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-05
    Type: Initial release
  • Version 1.1: 2023-04-19
    Changes: Database references
  • Version 1.2: 2023-04-26
    Changes: Database references
  • Version 1.3: 2024-06-19
    Changes: Data collection