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- EMDB-49957: Structure of Al3Cas12f State II -

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Basic information

Entry
Database: EMDB / ID: EMD-49957
TitleStructure of Al3Cas12f State II
Map dataStructure of Al3Cas12f State II
Sample
  • Complex: Cas12f:sgRNA:dsDNA
    • DNA: Target Strand DNA
    • DNA: Non-Target Strand DNA
    • Protein or peptide: Cas12f Nuclease
    • RNA: sgRNA
KeywordsCas12f CRISPR Endonuclease Dimeric / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA-RNA complex
Biological speciesDeltaproteobacteria (d-proteobacteria) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsFregoso Ocampo R / Guan K
Funding support United States, 1 items
OrganizationGrant numberCountry
Welch FoundationF-1938 United States
CitationJournal: To Be Published
Title: Structure of MetagenCas12f State II
Authors: Fregoso Ocampo R / Guan K
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_49957.png

Downloads & links

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Map

FileDownload / File: emd_49957.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of Al3Cas12f State II
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-0.9710089 - 1.4631336
Average (Standard dev.)-0.00000438391 (±0.027630499)
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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Half map: Half Map A

Fileemd_49957_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_49957_half_map_2.map
AnnotationHalf Map B
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:sgRNA:dsDNA

EntireName: Cas12f:sgRNA:dsDNA
Components
  • Complex: Cas12f:sgRNA:dsDNA
    • DNA: Target Strand DNA
    • DNA: Non-Target Strand DNA
    • Protein or peptide: Cas12f Nuclease
    • RNA: sgRNA

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Supramolecule #1: Cas12f:sgRNA:dsDNA

SupramoleculeName: Cas12f:sgRNA:dsDNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: RNP bound to its sgRNA forming a 20bp R-loop with its target dsDNA
Source (natural)Organism: Deltaproteobacteria (d-proteobacteria)
Molecular weightTheoretical: 125.676 KDa

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Macromolecule #1: Target Strand DNA

MacromoleculeName: Target Strand DNA / type: dna / ID: 1 / 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 #2: Non-Target Strand DNA

MacromoleculeName: Non-Target Strand DNA / type: dna / ID: 2 / 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 #3: Cas12f Nuclease

MacromoleculeName: Cas12f Nuclease / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 58.75759 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSMATEYTCI TRKIEVHLHR HGEYEEAKQR LIDDYRVWDT INDNLYKAAN RIVSHCFFND AYEYRLKIHS PRFQEIEKLL KYPKRNKLT DEDIKQLKAE RKQLFADFKK QRHTFLRGGV AEGANPEQNS TYKVISNEFL EVIPSEILTN LNQNISSTYK N YSLDVERG ...String:
GSMATEYTCI TRKIEVHLHR HGEYEEAKQR LIDDYRVWDT INDNLYKAAN RIVSHCFFND AYEYRLKIHS PRFQEIEKLL KYPKRNKLT DEDIKQLKAE RKQLFADFKK QRHTFLRGGV AEGANPEQNS TYKVISNEFL EVIPSEILTN LNQNISSTYK N YSLDVERG IRTIPNYKRG IPVPFSIKQR GELMLKSRDD GSIYVRFPLG LEWDLSFGRD RSNNREIVER VLSGQYDVGN SS IQESKNR KRFLLLVVKI PKENHNLNPD RIVGVDLGIN IPLYAALNDN DYGGMGIGSR EQFLNMRMRM DAKKRELQRN LRQ STNGGH GRKQKLQALE RFEGKERNWV HLQNHIFSKS IIEYAVKNNA GAIQMERLTG FGRDKNDEVD SNFKFILRYW SFFE LQTMI EYKANAAGIE VRYVDPYHTS QTCSFCGHYE KGQRLNQSTF VCKNPDCEKG KGKKLSDGTY QGINADWNAA RNIAL SDKI VDRKKKGGSG GSGGSGPPKK KRKV

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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
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

Particle selectionNumber selected: 3070006
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 69185
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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