Evidence map›Paper›PMID 37460897›Full record

ArticleNature structural & molecular biology2023

Mechanistic and evolutionary insights into a type V-M CRISPR-Cas effector enzyme.

Satoshi N Omura, Ryoya Nakagawa, Christian Südfeld, Ricardo Villegas Warren, Wen Y Wu, Hisato Hirano, Charlie Laffeber, Tsukasa Kusakizako, Yoshiaki Kise, Joyce H G Lebbink and 3 more

Open access · hybridAbstract read
In one paragraph

Article in Nature structural & molecular biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.

0numbers the graph read from it
0cells of the map it votes in
19citing papers in PubMed
4.2field-weighted citation impact, top 5% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

19 citing papers in PubMed, 27 citations in OpenAlex.

  1. Article
  2. Review
  3. Article
  4. Article
  5. Article
  6. Structural visualization of the molecular evolution of CRISPR-Cas9.Nature structural & molecular biology · 2026
    Article
  7. Article
  8. Article
  9. Article
  10. Efforts to Downsize Base Editors for Clinical Applications.International journal of molecular sciences · 2025
    Review
  11. Emerging tools in plant genome editing.Frontiers in genome editing · 2025
    Review
  12. Review
  13. Article
  14. Article
  15. Article
  16. Review
  17. Article
  18. Recent application of CRISPR-Cas12 and OMEGA system for genome editing.Molecular therapy : the journal of the American Society of Gene Therapy · 2024
    Review
  19. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

13 authors at 3 institutions in 2 countries.

Satoshi N OmuraDepartment of Biological Sciences, Graduate School of Science, the University of Tokyo, Tokyo, Japan.
Ryoya NakagawaDepartment of Biological Sciences, Graduate School of Science, the University of Tokyo, Tokyo, Japan.
Christian SüdfeldLaboratory of Microbiology, Wageningen University and Research, Wageningen, the Netherlands.
Ricardo Villegas WarrenLaboratory of Microbiology, Wageningen University and Research, Wageningen, the Netherlands.ORCID http://orcid.org/0009-0000-4399-818X
Wen Y WuLaboratory of Microbiology, Wageningen University and Research, Wageningen, the Netherlands.
Hisato HiranoDepartment of Biological Sciences, Graduate School of Science, the University of Tokyo, Tokyo, Japan.
Charlie LaffeberDepartment of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands.
Tsukasa KusakizakoDepartment of Biological Sciences, Graduate School of Science, the University of Tokyo, Tokyo, Japan.ORCID http://orcid.org/0000-0002-6186-6647
Yoshiaki KiseDepartment of Biological Sciences, Graduate School of Science, the University of Tokyo, Tokyo, Japan.
Joyce H G LebbinkDepartment of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands.ORCID http://orcid.org/0000-0002-6240-2895
Yuzuru ItohDepartment of Biological Sciences, Graduate School of Science, the University of Tokyo, Tokyo, Japan.
John van der OostLaboratory of Microbiology, Wageningen University and Research, Wageningen, the Netherlands. john.vanderoost@wur.nl.ORCID http://orcid.org/0000-0001-5024-1871
Osamu NurekiDepartment of Biological Sciences, Graduate School of Science, the University of Tokyo, Tokyo, Japan. nureki@bs.s.u-tokyo.ac.jp.ORCID http://orcid.org/0000-0003-1813-7008
The University of Tokyo · JPWageningen University & Research · NLErasmus MC · NL

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

RNA-guided type V CRISPR-Cas12 effectors provide adaptive immunity against mobile genetic elements (MGEs) in bacteria and archaea. Among diverse Cas12 enzymes, the recently identified Cas12m2 (CRISPR-Cas type V-M) is highly compact and has a unique RuvC active site. Although the non-canonical RuvC triad does not permit dsDNA cleavage, Cas12m2 still protects against invading MGEs through transcriptional silencing by strong DNA binding. However, the molecular mechanism of RNA-guided genome inactivation by Cas12m2 remains unknown. Here we report cryo-electron microscopy structures of two states of Cas12m2-CRISPR RNA (crRNA)-target DNA ternary complexes and the Cas12m2-crRNA binary complex, revealing structural dynamics during crRNA-target DNA heteroduplex formation. The structures indicate that the non-target DNA strand is tightly bound to a unique arginine-rich cluster in the recognition (REC) domains and the non-canonical active site in the RuvC domain, ensuring strong DNA-binding affinity of Cas12m2. Furthermore, a structural comparison of Cas12m2 with TnpB, a putative ancestor of Cas12 enzymes, suggests that the interaction of the characteristic coiled-coil REC2 insertion with the protospacer-adjacent motif-distal region of the heteroduplex is crucial for Cas12m2 to engage in adaptive immunity. Collectively, our findings improve mechanistic understanding of diverse type V CRISPR-Cas effectors and provide insights into the evolution of TnpB to Cas12 enzymes.

Indexed as

CRISPR-Associated ProteinsCRISPR-Cas SystemsBacteriaCryoelectron MicroscopyDNARNACRISPR-Associated ProteinsDNARNA

Identifiers

PMID37460897
PMCPMC10442227
OpenAlexW4384561706

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.