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- PDB-23vw: Cryo-EM structure of the TfCas12m3-crRNA-tgDNA ternary complex -

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Basic information

Entry
Database: PDB / ID: 23vw
TitleCryo-EM structure of the TfCas12m3-crRNA-tgDNA ternary complex
Components
  • CRISPR-associated DNA-binding protein Cas12m
  • DNA (35-MER)
  • DNA (39-MER)
  • RNA (59-MER)
KeywordsDNA BINDING PROTEIN
Function / homology
Function and homology information


defense response to virus / DNA binding / DNA-templated transcription / RNA binding / metal ion binding
Similarity search - Function
Transposase IS605, OrfB, C-terminal / Cas12f1-like, TNB domain
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / RNA (> 10) / CRISPR-associated DNA-binding protein Cas12m
Similarity search - Component
Biological speciesThermanaerosceptrum fracticalcis (bacteria)
DNA molecule (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.39 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
A: CRISPR-associated DNA-binding protein Cas12m
D: DNA (35-MER)
C: DNA (39-MER)
B: RNA (59-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,91110
Polymers110,7244
Non-polymers1876
Water32418
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

#2: DNA chain DNA (35-MER)


Mass: 11905.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others)
#3: DNA chain DNA (39-MER)


Mass: 12033.734 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others)

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Protein / RNA chain , 2 types, 2 molecules AB

#1: Protein CRISPR-associated DNA-binding protein Cas12m / TfCas12m3


Mass: 67784.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermanaerosceptrum fracticalcis (bacteria)
Gene: cas12m, BR63_03280 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7G6E019
#4: RNA chain RNA (59-MER)


Mass: 19000.295 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Thermanaerosceptrum fracticalcis (bacteria)

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Non-polymers , 3 types, 24 molecules

#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

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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
1TfCas12m3-crRNA-target DNACOMPLEX#1-#40MULTIPLE SOURCES
2crRNA-target DNACOMPLEX#1-#31MULTIPLE SOURCES
3RNACOMPLEX#41RECOMBINANT
4TfCas12m3COMPLEX#12RECOMBINANT
5target DNACOMPLEX#2-#32SYNTHETIC
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: 2.39 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 449315 / Symmetry type: POINT

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