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- EMDB-49954: Structure of Cas12f-MG119-28 State I -

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Basic information

Entry
Database: EMDB / ID: EMD-49954
TitleStructure of Cas12f-MG119-28 State I
Map dataStructure of Al3Cas12f State I
Sample
  • Complex: Cas12f Cleavage Intermediate in State I
    • Protein or peptide: Cas12f Effector
    • DNA: Target Strand DNA
    • DNA: Non-target Strand DNA
    • RNA: sgRNA
KeywordsCRISPR-Cas12 / Endonuclease / Dimeric / Effector / sgRNA / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA-RNA complex
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsFregoso Ocampo R / Guan K / Taylor DW
Funding support United States, 1 items
OrganizationGrant numberCountry
Welch FoundationF-1938 United States
CitationJournal: To Be Published
Title: MetagenCas12f Intermediate Structure
Authors: Fregoso Ocampo R / 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_49954.png

Downloads & links

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Map

FileDownload / File: emd_49954.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of Al3Cas12f State I
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 320 pix.
= 298.56 Å		0.93 Å/pix.
x 320 pix.
= 298.56 Å		0.93 Å/pix.
x 320 pix.
= 298.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.933 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-1.2765944 - 1.7158943
Average (Standard dev.)-0.00011502825 (±0.028626328)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 298.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Additional Map

Fileemd_49954_additional_1.map
AnnotationAdditional Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_49954_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_49954_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 : Cas12f Cleavage Intermediate in State I

EntireName: Cas12f Cleavage Intermediate in State I
Components
  • Complex: Cas12f Cleavage Intermediate in State I
    • Protein or peptide: Cas12f Effector
    • DNA: Target Strand DNA
    • DNA: Non-target Strand DNA
    • RNA: sgRNA

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Supramolecule #1: Cas12f Cleavage Intermediate in State I

SupramoleculeName: Cas12f Cleavage Intermediate in State I / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 125.67672 KDa

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Macromolecule #1: Cas12f Effector

MacromoleculeName: Cas12f Effector / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 58.613465 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MATEYTCITR KIEVHLHRHG EYEEAKQRLI DDYRVWDTIN DNLYKAANRI VSHCFFNDAY EYRLKIHSPR FQEIEKLLKY PKRNKLTDE DIKQLKAERK QLFADFKKQR HTFLRGGVAE GANPEQNSTY KVISNEFLEV IPSEILTNLN QNISSTYKNY S LDVERGIR ...String:
MATEYTCITR KIEVHLHRHG EYEEAKQRLI DDYRVWDTIN DNLYKAANRI VSHCFFNDAY EYRLKIHSPR FQEIEKLLKY PKRNKLTDE DIKQLKAERK QLFADFKKQR HTFLRGGVAE GANPEQNSTY KVISNEFLEV IPSEILTNLN QNISSTYKNY S LDVERGIR TIPNYKRGIP VPFSIKQRGE LMLKSRDDGS IYVRFPLGLE WDLSFGRDRS NNREIVERVL SGQYDVGNSS IQ ESKNRKR FLLLVVKIPK ENHNLNPDRI VGVDLGINIP LYAALNDNDY GGMGIGSREQ FLNMRMRMDA KKRELQRNLR QST NGGHGR KQKLQALERF EGKERNWVHL QNHIFSKSII EYAVKNNAGA IQMERLTGFG RDKNDEVDSN FKFILRYWSF FELQ TMIEY KANAAGIEVR YVDPYHTSQT CSFCGHYEKG QRLNQSTFVC KNPDCEKGKG KKLSDGTYQG INADWNAARN IALSD KIVD RKKKGGSGGS GGSGPPKKKR KV

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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: Escherichia coli (E. coli)
Molecular weightTheoretical: 15.353835 KDa
SequenceString:
(DC)(DT)(DG)(DA)(DT)(DC)(DC)(DT)(DG)(DG) (DT)(DG)(DC)(DT)(DG)(DC)(DA)(DG)(DC)(DT) (DT)(DC)(DC)(DT)(DT)(DA)(DC)(DA)(DC) (DT)(DT)(DC)(DC)(DC)(DA)(DA)(DG)(DA)(DG) (DG) (DA)(DG)(DA)(DA)(DG)(DC)(DA)(DG) (DT)(DT)

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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: Escherichia coli (E. coli)
Molecular weightTheoretical: 15.451913 KDa
SequenceString:
(DA)(DA)(DC)(DT)(DG)(DC)(DT)(DT)(DC)(DT) (DC)(DC)(DT)(DC)(DT)(DT)(DG)(DG)(DG)(DA) (DA)(DG)(DT)(DG)(DT)(DA)(DA)(DG)(DG) (DA)(DA)(DG)(DC)(DT)(DG)(DC)(DA)(DG)(DC) (DA) (DC)(DC)(DA)(DG)(DG)(DA)(DT)(DC) (DA)(DG)

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Macromolecule #4: sgRNA

MacromoleculeName: sgRNA / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 49.819699 KDa
SequenceString:
CAAACCCCUU CGGGGGAGGG CGCGUUGGAG CGCCUUAGUU UGAGGUGCAG AAUCAAAAAA ACUGCGACGA UGGAGGUCGU UUCAGUCUC UGUACACUCA AAAAAUUCAC UUGAGAAAUC AAGUGAAUAU CCAACGGAAG UGUAAGGAAG CUGCA

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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: 7.5
VitrificationCryogen name: ETHANE

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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: OTHER / 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: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 141537
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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