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- PDB-23vv: Cryo-EM structure of the UnCas12m4a-crRNA-tgDNA ternary complex i... -

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Basic information

Entry
Database: PDB / ID: 23vv
TitleCryo-EM structure of the UnCas12m4a-crRNA-tgDNA ternary complex in the NTS-cleaving state
Components
  • (DNA (39-MER)) x 2
  • RNA (56-MER)
  • UnCas12m4a
KeywordsDNA BINDING PROTEIN / nuclease
Function / homologyTHYMIDINE-5'-THIOPHOSPHATE / DNA / DNA (> 10) / RNA / RNA (> 10)
Function and homology information
Biological speciesbacterium (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsMorinaga, H. / Omura, S.N. / Nureki, O.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED) Japan
CitationJournal: To Be Published
Title: Intact RuvC catalytic site and bipartite ssDNA kinking are required for Cas12m nuclease activation
Authors: 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.
History
DepositionFeb 21, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 2, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: DNA (39-MER)
C: DNA (39-MER)
A: UnCas12m4a
B: RNA (56-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,76014
Polymers113,2784
Non-polymers2,48210
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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DNA chain , 2 types, 2 molecules DC

#1: DNA chain DNA (39-MER)


Mass: 11976.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) bacterium (bacteria)
#2: DNA chain DNA (39-MER)


Mass: 12215.320 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) bacterium (bacteria)

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Protein / RNA chain , 2 types, 2 molecules AB

#3: Protein UnCas12m4a


Mass: 71029.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) bacterium (bacteria) / Production host: Escherichia coli (E. coli)
#4: RNA chain RNA (56-MER)


Mass: 18057.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) bacterium (bacteria) / Production host: Escherichia coli (E. coli)

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Non-polymers , 3 types, 10 molecules

#5: Chemical
ChemComp-PST / THYMIDINE-5'-THIOPHOSPHATE


Type: DNA linking / Mass: 338.274 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C10H15N2O7PS
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1UnCas12m4a-crRNA-target DNA (NTS-cleaving state)COMPLEX#1-#40MULTIPLE SOURCES
2crRNA-target DNACOMPLEX#1-#31MULTIPLE SOURCES
3UnCas12m4aCOMPLEX#31RECOMBINANT
4crRNACOMPLEX#42RECOMBINANT
5target DNACOMPLEX#1-#22RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Lachnospiraceae bacterium ND2006 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 286808 / Symmetry type: POINT

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