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- EMDB-69299: Cryo-EM structure of the TfCas12m3-crRNA-tgDNA ternary complex -

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Basic information

Entry
Database: EMDB / ID: EMD-69299
TitleCryo-EM structure of the TfCas12m3-crRNA-tgDNA ternary complex
Map dataSharpening map with Gaussian filter
Sample
  • Complex: TfCas12m3-crRNA-target DNA
    • Complex: crRNA-target DNA
      • Complex: TfCas12m3
        • Protein or peptide: CRISPR-associated DNA-binding protein Cas12m
      • Complex: target DNA
        • DNA: DNA (35-MER)
        • DNA: DNA (39-MER)
    • Complex: RNA
      • RNA: RNA (59-MER)
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: water
KeywordsDNA binding protein
Function / homologyTransposase IS605, OrfB, C-terminal / Cas12f1-like, TNB domain / defense response to virus / DNA binding / DNA-templated transcription / RNA binding / metal ion binding / CRISPR-associated DNA-binding protein Cas12m
Function and homology information
Biological speciesLachnospiraceae bacterium ND2006 (bacteria) / Thermanaerosceptrum fracticalcis (bacteria) / DNA molecule (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.39 Å
AuthorsMorinaga H / Omura SN / Nureki O
Funding support Japan, 1 items
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 SN / Alfonse L / Ornstein A / Kobayashi TA / Onishi K / Makarova KS / Shmakov SA / Munoz G / Garrity AJ / DiTommaso T / Koonin EV / Maben Z / Nureki O
History
DepositionFeb 21, 2026-
Header (metadata) releaseSep 2, 2026-
Map releaseSep 2, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_69299.png

Downloads & links

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Map

FileDownload / File: emd_69299.map.gz / Format: CCP4 / Size: 18.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpening map with Gaussian filter
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 170 pix.
= 141.1 Å		0.83 Å/pix.
x 170 pix.
= 141.1 Å		0.83 Å/pix.
x 170 pix.
= 141.1 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.7455153 - 1.3310062
Average (Standard dev.)0.0022510318 (±0.032809827)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin959595
Dimensions170170170
Spacing170170170
CellA=B=C: 141.09999 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_69299_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_69299_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_69299_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : TfCas12m3-crRNA-target DNA

EntireName: TfCas12m3-crRNA-target DNA
Components
  • Complex: TfCas12m3-crRNA-target DNA
    • Complex: crRNA-target DNA
      • Complex: TfCas12m3
        • Protein or peptide: CRISPR-associated DNA-binding protein Cas12m
      • Complex: target DNA
        • DNA: DNA (35-MER)
        • DNA: DNA (39-MER)
    • Complex: RNA
      • RNA: RNA (59-MER)
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: water

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Supramolecule #1: TfCas12m3-crRNA-target DNA

SupramoleculeName: TfCas12m3-crRNA-target DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Lachnospiraceae bacterium ND2006 (bacteria)

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Supramolecule #2: crRNA-target DNA

SupramoleculeName: crRNA-target DNA / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3

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Supramolecule #3: RNA

SupramoleculeName: RNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4

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Supramolecule #4: TfCas12m3

SupramoleculeName: TfCas12m3 / type: complex / ID: 4 / Parent: 2 / Macromolecule list: #1

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Supramolecule #5: target DNA

SupramoleculeName: target DNA / type: complex / ID: 5 / Parent: 2 / Macromolecule list: #2-#3

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Macromolecule #1: CRISPR-associated DNA-binding protein Cas12m

MacromoleculeName: CRISPR-associated DNA-binding protein Cas12m / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermanaerosceptrum fracticalcis (bacteria)
Molecular weightTheoretical: 67.784781 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGHHHHHHGG METAATKNYL ALSFGCLSPT RGEEYLLDQI KKKHDLWNKL VEKDREHREK VRQVMVFESE TTKKIKELEE ELNSLREEI KNQRKTKRTG KVDLTDQKAR IEEIKPQLKQ LKEKFKEERS FIFEARKQEL AQLEKERWAV VKELGKGSGL Y WCNLEDVV ...String:
MGHHHHHHGG METAATKNYL ALSFGCLSPT RGEEYLLDQI KKKHDLWNKL VEKDREHREK VRQVMVFESE TTKKIKELEE ELNSLREEI KNQRKTKRTG KVDLTDQKAR IEEIKPQLKQ LKEKFKEERS FIFEARKQEL AQLEKERWAV VKELGKGSGL Y WCNLEDVV NSYDIGRKKA KAAGGEMRFH RWDGTGKVTV RFQKGLPVNE MFSCTNNLLQ IDPVDKDAWY NPVRAIRRKK SR TRVRLRA CSENKKPLFI ELPVVLHREI PEDALIRTAS VIREKVGMRY RYKLNLVLEI LGENTNRILP ALEGTAAIDL GWR TVKDGL RVACLVDDKG HSEELILDND VLHEFNKIKD LQSIRDNLFN ETKAKLMELL KTLELPDEAK ERTSHMANWR SQQK MLRLH QYWRENRLPG DDEVWEVLEY WRKREIHLYE WQENLRDQVL RRRKEIYRIF AAKITRKYKT IVLEEFTLNK TVQKP NPEE GPAGTLPANR NRFIAAISEF RNELANACRK NHVEFTYVPA ENTTITCHKC GHKEKFDAAA QIIHTCSTCG ELWDQD YNA AKNLLAFSQK GGVK

UniProtKB: CRISPR-associated DNA-binding protein Cas12m

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Macromolecule #2: DNA (35-MER)

MacromoleculeName: DNA (35-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: DNA molecule (others)
Molecular weightTheoretical: 11.905615 KDa
SequenceString:
(DG)(DC)(DA)(DC)(DT)(DT)(DG)(DC)(DC)(DG) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DA)(DC)(DG)(DT)(DA)(DT)(DG)(DC)(DG)

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Macromolecule #3: DNA (39-MER)

MacromoleculeName: DNA (39-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: DNA molecule (others)
Molecular weightTheoretical: 12.033734 KDa
SequenceString:
(DC)(DG)(DC)(DA)(DT)(DA)(DC)(DG)(DT)(DG) (DT)(DG)(DA)(DA)(DG)(DC)(DG)(DC)(DA)(DG) (DC)(DT)(DA)(DA)(DT)(DT)(DT)(DA)(DC) (DC)(DG)(DG)(DC)(DA)(DA)(DG)(DT)(DG)(DC)

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Macromolecule #4: RNA (59-MER)

MacromoleculeName: RNA (59-MER) / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: Thermanaerosceptrum fracticalcis (bacteria)
Molecular weightTheoretical: 19.000295 KDa
SequenceString:
GGGUUGCAAU GCCUAGCUCA GAGGUUUAAA GACUGAGACG UAAAUUAGCU GCGCUUCAC

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 5 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 18 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.39 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 449315
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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