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- EMDB-35588: Cryo-EM structure of Cas12o1-crRNA-DNA complex at 3.1 Angstroms r... -

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Basic information

Entry
Database: EMDB / ID: EMD-35588
TitleCryo-EM structure of Cas12o1-crRNA-DNA complex at 3.1 Angstroms resolution, Conformation 1
Map data
Sample
  • Complex: Ternary complex of Cas12o1 with crRNA and target DNA, Conformation 1
KeywordsCRISPR-CasJ19 / RNA BINDING PROTEIN/RNA/DNA / RNA BINDING PROTEIN-RNA-DNA complex
Biological speciesunidentified (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsZhang X / Duan Z / Zhu J
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Cell Res / Year: 2025
Title: Structure and genome editing activity of the novel CRISPR-Cas12o1 effector.
Authors: Zhiqiang Duan / Xi Zhang / Jun-Tao Zhang / Xingkun Ji / Ruiheng Liu / Ying Chen / Shanshan Li / Nannan Jia / Huizhi Gao / Yu Xin / Ning Jia / Jian-Kang Zhu /
History
DepositionMar 8, 2023-
Header (metadata) releaseMar 13, 2024-
Map releaseMar 13, 2024-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_35588.png

Downloads & links

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Map

FileDownload / File: emd_35588.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 192 pix.
= 253.44 Å		1.32 Å/pix.
x 192 pix.
= 253.44 Å		1.32 Å/pix.
x 192 pix.
= 253.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-1.7260325 - 2.62582
Average (Standard dev.)0.0005537584 (±0.050361242)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 253.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_35588_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_35588_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_35588_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 : Ternary complex of Cas12o1 with crRNA and target DNA, Conformation 1

EntireName: Ternary complex of Cas12o1 with crRNA and target DNA, Conformation 1
Components
  • Complex: Ternary complex of Cas12o1 with crRNA and target DNA, Conformation 1

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Supramolecule #1: Ternary complex of Cas12o1 with crRNA and target DNA, Conformation 1

SupramoleculeName: Ternary complex of Cas12o1 with crRNA and target DNA, Conformation 1
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: unidentified (others)

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 242907
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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