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- EMDB-37798: Cryo-EM structure of Cas12-1-N2/crRNA/Target DNA complex -

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Basic information

Entry
Database: EMDB / ID: EMD-37798
TitleCryo-EM structure of Cas12-1-N2/crRNA/Target DNA complex
Map data
Sample
  • Complex: The ternary complex of Cas12-1-N2 with crRNA and Target DNA
    • Protein or peptide: Cas12-1-N2
    • DNA: TS
    • RNA: crRNA
    • DNA: NTS
KeywordsCrispr-Cas / RNA BINDING PROTEIN-RNA-DNA complex
Biological speciesunclassified sequences (unknown)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.29 Å
AuthorsKuo Z / Xi Z
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32188102 China
CitationJournal: To Be Published
Title: Cryo-EM structure of Cas12-1-N2/crRNA/Target DNA complex
Authors: Kuo Z / Xi Z
History
DepositionOct 16, 2023-
Header (metadata) releaseApr 16, 2025-
Map releaseApr 16, 2025-
UpdateApr 16, 2025-
Current statusApr 16, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37798.png

Downloads & links

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Map

FileDownload / File: emd_37798.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 384 pix.
= 253.44 Å		0.66 Å/pix.
x 384 pix.
= 253.44 Å		0.66 Å/pix.
x 384 pix.
= 253.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.037353784 - 2.2616246
Average (Standard dev.)0.0005502655 (±0.014451895)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 253.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_37798_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_37798_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 : The ternary complex of Cas12-1-N2 with crRNA and Target DNA

EntireName: The ternary complex of Cas12-1-N2 with crRNA and Target DNA
Components
  • Complex: The ternary complex of Cas12-1-N2 with crRNA and Target DNA
    • Protein or peptide: Cas12-1-N2
    • DNA: TS
    • RNA: crRNA
    • DNA: NTS

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Supramolecule #1: The ternary complex of Cas12-1-N2 with crRNA and Target DNA

SupramoleculeName: The ternary complex of Cas12-1-N2 with crRNA and Target DNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: unclassified sequences (unknown)

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Macromolecule #1: Cas12-1-N2

MacromoleculeName: Cas12-1-N2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: unclassified sequences (unknown)
Molecular weightTheoretical: 33.550656 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: FCPPAKVNIL AQSRPLSEWP INLVSKGVQE YVYGLTAAER EANGDFGTSR KSLDRWFART GVPTHGYTTV QGLNLILRHT FNRYDGVIK KVETRNEKRR SKATRINVSR EADGLPPIEA EPEETAFGPD GKLKERPGIN PSIYCYQQVS PVPYNPAKHP A LPFSGVDP ...String:
FCPPAKVNIL AQSRPLSEWP INLVSKGVQE YVYGLTAAER EANGDFGTSR KSLDRWFART GVPTHGYTTV QGLNLILRHT FNRYDGVIK KVETRNEKRR SKATRINVSR EADGLPPIEA EPEETAFGPD GKLKERPGIN PSIYCYQQVS PVPYNPAKHP A LPFSGVDP GAPLPLGTPN RLSIPKGQPG YVPEWQRPHL STKNKRIRKW YARANWRRKP GRKSVLDEAK LKEAALKEAI PI IVTIGKD WIVMDARGLL RAVYWRGIAK PGLSLKELLG FFSGDPVLDP KRGIATFTFK LGA

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Macromolecule #2: TS

MacromoleculeName: TS / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: unclassified sequences (unknown)
Molecular weightTheoretical: 12.941301 KDa
SequenceString:
(DC)(DT)(DG)(DC)(DC)(DC)(DT)(DT)(DG)(DC) (DA)(DA)(DC)(DT)(DT)(DC)(DA)(DG)(DC)(DA) (DG)(DC)(DA)(DC)(DG)(DT)(DA)(DG)(DG) (DG)(DG)(DA)(DG)(DA)(DA)(DT)(DT)(DG)(DG) (DC) (DC)(DA)

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Macromolecule #4: NTS

MacromoleculeName: NTS / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: unclassified sequences (unknown)
Molecular weightTheoretical: 12.923272 KDa
SequenceString:
(DT)(DG)(DG)(DC)(DC)(DA)(DA)(DT)(DT)(DC) (DT)(DC)(DC)(DC)(DC)(DT)(DA)(DC)(DG)(DT) (DG)(DC)(DT)(DG)(DC)(DT)(DG)(DA)(DA) (DG)(DT)(DT)(DG)(DC)(DA)(DA)(DG)(DG)(DG) (DC) (DA)(DG)

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Macromolecule #3: crRNA

MacromoleculeName: crRNA / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: unclassified sequences (unknown)
Molecular weightTheoretical: 14.652684 KDa
SequenceString:
UCAACGCUUG CUCGGUUCGC CGAGACUCCC CUACGUGCUG CUGAAG

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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

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 113093
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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