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- EMDB-49959: Cryo-EM structure of OsCas12f-gRNA-DNA ternary complex State I -

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Basic information

Entry
Database: EMDB / ID: EMD-49959
TitleCryo-EM structure of OsCas12f-gRNA-DNA ternary complex State I
Map datastructure of OsCas12f-gRNA-DNA ternary complex
Sample
  • Complex: Cryo-EM structure of the OsCas12f-sgRNA-target DNA ternary complex
    • Protein or peptide: Cas12f
    • DNA: Target strand DNA
    • DNA: Non-target strand DNA
    • RNA: guide RNA
  • Ligand: ZINC ION
KeywordsRNA-guided DNA endonuclease / RNA BINDING PROTEIN / RNA BINDING PROTEIN-DNA-RNA complex
Biological speciesOscillibacter sp. (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsGuan K / Ocampo RF / Taylor DW
Funding support United States, 1 items
OrganizationGrant numberCountry
Welch FoundationF-1938 United States
CitationJournal: To Be Published
Title: Cryo-EM structure of OsCas12f-gRNA-DNA ternary complex
Authors: Guan K / Taylor DW
History
DepositionApr 1, 2025-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49959.png

Downloads & links

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Map

FileDownload / File: emd_49959.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of OsCas12f-gRNA-DNA ternary complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 320 pix.
= 300.8 Å		0.94 Å/pix.
x 320 pix.
= 300.8 Å		0.94 Å/pix.
x 320 pix.
= 300.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.94 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.22479315 - 0.540456
Average (Standard dev.)0.00041830013 (±0.012521399)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 300.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map B

Fileemd_49959_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_49959_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of the OsCas12f-sgRNA-target DNA ternary complex

EntireName: Cryo-EM structure of the OsCas12f-sgRNA-target DNA ternary complex
Components
  • Complex: Cryo-EM structure of the OsCas12f-sgRNA-target DNA ternary complex
    • Protein or peptide: Cas12f
    • DNA: Target strand DNA
    • DNA: Non-target strand DNA
    • RNA: guide RNA
  • Ligand: ZINC ION

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Supramolecule #1: Cryo-EM structure of the OsCas12f-sgRNA-target DNA ternary complex

SupramoleculeName: Cryo-EM structure of the OsCas12f-sgRNA-target DNA ternary complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Oscillibacter sp. (bacteria)

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Macromolecule #1: Cas12f

MacromoleculeName: Cas12f / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Oscillibacter sp. (bacteria)
Molecular weightTheoretical: 49.389547 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGKGVLAKVM KYELRYLDGC GDFSNMQEQV WALQRQTREI LNRSIQIAFQ WDCANSEHHR KTGEYLDLKT ETGYKRLDGH IYNCLKGQY EDMATSNLNA TIQKAWKKYN SSKKEILRGS MSIPSYKMNQ PLTLDKNTVK LSEGERNPIV TLTLFSDKFK R AQGVSNVK ...String:
MGKGVLAKVM KYELRYLDGC GDFSNMQEQV WALQRQTREI LNRSIQIAFQ WDCANSEHHR KTGEYLDLKT ETGYKRLDGH IYNCLKGQY EDMATSNLNA TIQKAWKKYN SSKKEILRGS MSIPSYKMNQ PLTLDKNTVK LSEGERNPIV TLTLFSDKFK R AQGVSNVK FSMPLHDGTQ RAIFANLMNG TYQLGECQLV YKRPKWFLFV TYKFPPVEHP LDPDKILGVD MGEACALYAS TF GEHGYLK IDGGEITKYA KKMEARIRSM QKQAAHCGEG RIGHGTKTRV SVVYQAKDKV ARFRDTINHR YSKALIDYAL KNQ CGTIQM EDLTGIKEDT GFPKFLRHWT YYDLQSKIEA KAAEHGIQVV KINPRHTSQR CSRCGHIDKA NRTSQADFCC TKCG FSANA DFNASQNISI RNIDKIIAKA IGANRKQT

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Macromolecule #2: Target strand DNA

MacromoleculeName: Target strand DNA / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Oscillibacter sp. (bacteria)
Molecular weightTheoretical: 13.83594 KDa
SequenceString:
(DA)(DG)(DC)(DA)(DA)(DG)(DG)(DC)(DA)(DA) (DC)(DG)(DC)(DT)(DC)(DC)(DA)(DA)(DT)(DG) (DC)(DA)(DC)(DC)(DC)(DA)(DA)(DG)(DA) (DC)(DA)(DG)(DC)(DA)(DG)(DA)(DA)(DA)(DT) (DT) (DA)(DC)(DG)(DT)(DA)

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Macromolecule #3: Non-target strand DNA

MacromoleculeName: Non-target strand DNA / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Oscillibacter sp. (bacteria)
Molecular weightTheoretical: 13.878857 KDa
SequenceString:
(DT)(DA)(DC)(DG)(DT)(DA)(DA)(DT)(DT)(DT) (DC)(DT)(DG)(DC)(DT)(DG)(DT)(DC)(DT)(DT) (DG)(DG)(DG)(DT)(DG)(DC)(DA)(DT)(DT) (DG)(DG)(DA)(DG)(DC)(DG)(DT)(DT)(DG)(DC) (DC) (DT)(DT)(DG)(DC)(DT)

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Macromolecule #4: guide RNA

MacromoleculeName: guide RNA / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: Oscillibacter sp. (bacteria)
Molecular weightTheoretical: 48.87007 KDa
SequenceString:
AGGGCCGACU UCCCGGCCCA AAAUCGAGAC AGUAGCCGUA AAACGUUGAG UUUCAGCGUG GGCGACACAC UCGAAAAGGU UAAGAUAUG CACAUAGUAA UCCGUGCAUG AGCCGCGAAA GCGGCUUGAA GGUGCUGUCU UGGGUGCAUU GG

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 132962
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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