23VV | pdb_000023vv

Cryo-EM structure of the UnCas12m4a-crRNA-tgDNA ternary complex in the NTS-cleaving state

PDB DOI: https://doi.org/10.2210/pdb23VV/pdb
EM Map EMD-69298: EMDB EMDataResource

Classification: DNA BINDING PROTEIN
Organism(s): bacterium
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2026-02-21 Released: 2026-09-02
Deposition Author(s): Morinaga, H., Omura, S.N., Nureki, O.
Funding Organization(s): Japan Agency for Medical Research and Development (AMED)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.84 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Intact RuvC catalytic site and bipartite ssDNA kinking are required for Cas12m nuclease activation

Morinaga, H., Omura, S.N., Alfonse, L., Ornstein, A., Kobayashi, T.A., Onishi, K., Makarova, K.S., Shmakov, S.A., Munoz, G., Garrity, A.J., DiTommaso, T., Koonin, E.V., Maben, Z., Nureki, O.

To be published.

Macromolecule Content

Total Structure Weight: 115.76 kDa
Atom Count: 7,073
Modeled Residue Count: 694
Deposited Residue Count: 748
Unique protein chains: 1
Unique nucleic acid chains: 3

Macromolecules

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
UnCas12m4a	C [auth A]	614	bacterium	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 1
DNA (39-MER)	A [auth D]	39	bacterium
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 2
DNA (39-MER)	B [auth C]	39	bacterium
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 4
RNA (56-MER)	D [auth B]	56	bacterium
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Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PST Query on PST Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain F [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	THYMIDINE-5'-THIOPHOSPHATE C₁₀ H₁₅ N₂ O₇ P S OJRKJKYGUAALCJ-XLPZGREQSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain N [auth A] MOL2 format, chain N [auth A] mmCIF format, chain N [auth A]	N [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Interactions & Density Focus chain N [auth A]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A]	L [auth A], M [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain L [auth A] Focus chain M [auth A]