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- EMDB-49955: Cryo-EM structure of RhCas12f-gRNA-DNA ternary complex -

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Basic information

Entry
Database: EMDB / ID: EMD-49955
TitleCryo-EM structure of RhCas12f-gRNA-DNA ternary complex
Map datastructure of RhCas12f-gRNA-DNA ternary complex
Sample
  • Complex: RhCas12f-gRNA-DNA ternary complex
    • Protein or peptide: IS200/IS605 family element transposase accessory protein TnpB
    • DNA: Target strand DNA
    • DNA: Non-target strand DNA
    • RNA: guide RNA
KeywordsRNA-guided DNA endonuclease / RNA BINDING PROTEIN / RNA BINDING PROTEIN-DNA-RNA complex
Function / homology: / Transposase IS605, OrfB, C-terminal / Cas12f1-like, TNB domain / DNA binding / IS200/IS605 family element transposase accessory protein TnpB
Function and homology information
Biological speciesRuminiclostridium herbifermentans (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.07 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 CRISPR-Cas12f nucleases
Authors: Guan K / Ocampo RF / 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_49955.png

Downloads & links

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Map

FileDownload / File: emd_49955.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of RhCas12f-gRNA-DNA ternary complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.19151548 - 0.39287424
Average (Standard dev.)0.0003062046 (±0.009489809)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 265.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map B

Fileemd_49955_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_49955_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 : RhCas12f-gRNA-DNA ternary complex

EntireName: RhCas12f-gRNA-DNA ternary complex
Components
  • Complex: RhCas12f-gRNA-DNA ternary complex
    • Protein or peptide: IS200/IS605 family element transposase accessory protein TnpB
    • DNA: Target strand DNA
    • DNA: Non-target strand DNA
    • RNA: guide RNA

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Supramolecule #1: RhCas12f-gRNA-DNA ternary complex

SupramoleculeName: RhCas12f-gRNA-DNA ternary complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Ruminiclostridium herbifermentans (bacteria)

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Macromolecule #1: IS200/IS605 family element transposase accessory protein TnpB

MacromoleculeName: IS200/IS605 family element transposase accessory protein TnpB
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Ruminiclostridium herbifermentans (bacteria)
Molecular weightTheoretical: 48.051246 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MITVRKLKIL IDGESRNESY KFIRDSMYAQ YLALNKAMSY LGTAYLSRDK EIFKEAIKSL NNSNPIFDNI NFGKGIDTKS SVNQTVKKH IQADIKNGLA KGERSIRNYK RDYPLMTRGR DLKFFYCDTN STKVKVKWVN GIIFDVMLGK EYNKNDLELR S FLNRVINK ...String:
MITVRKLKIL IDGESRNESY KFIRDSMYAQ YLALNKAMSY LGTAYLSRDK EIFKEAIKSL NNSNPIFDNI NFGKGIDTKS SVNQTVKKH IQADIKNGLA KGERSIRNYK RDYPLMTRGR DLKFFYCDTN STKVKVKWVN GIIFDVMLGK EYNKNDLELR S FLNRVINK EYKISQSSIC FDKHNRLILN LSVNITDNIP NEVVKGRIVG VDLGMKIPAY VTLNDSEYIG KPIGDINDFL KV RKQFKER KERLQKQLAI NKGGRGITNK MQLMDAFTNK EKNFANTYNH GVSKAIINFA KKYKAEQINV EFLALAGSEK EIL SSTIRY WSYYQLQQMI EYKANREGIA VKYVDPYLTS QTCCKCGNYE VGQRINQELF ECKLCGNKMN ADRNASFNIA RSTK YISSK EESDFYKQLK

UniProtKB: IS200/IS605 family element transposase accessory protein TnpB

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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: Ruminiclostridium herbifermentans (bacteria)
Molecular weightTheoretical: 13.830896 KDa
SequenceString:
(DA)(DA)(DT)(DT)(DC)(DC)(DA)(DC)(DT)(DG) (DA)(DG)(DG)(DA)(DC)(DT)(DC)(DC)(DA)(DA) (DC)(DA)(DT)(DC)(DA)(DC)(DC)(DA)(DT) (DG)(DC)(DA)(DG)(DG)(DT)(DG)(DG)(DG)(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: Ruminiclostridium herbifermentans (bacteria)
Molecular weightTheoretical: 13.883903 KDa
SequenceString:
(DT)(DA)(DC)(DG)(DT)(DA)(DA)(DC)(DC)(DC) (DA)(DC)(DC)(DT)(DG)(DC)(DA)(DT)(DG)(DG) (DT)(DG)(DA)(DT)(DG)(DT)(DT)(DG)(DG) (DA)(DG)(DT)(DC)(DC)(DT)(DC)(DA)(DG)(DT) (DG) (DG)(DA)(DA)(DT)(DT)

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Macromolecule #4: guide RNA

MacromoleculeName: guide RNA / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: Ruminiclostridium herbifermentans (bacteria)
Molecular weightTheoretical: 51.642645 KDa
SequenceString:
ACGGCUGAUU UAGCAGCCGA AGUCUGAGGG CAUGUAGAAA AAAGUAUAGG UAUAUACCAA CAUACUUGCA UUGCCACUCG GAAAGGGUU AACCUUGGUC AUUGUGUUAC CGACCAAGCA UUCCAGAAAU GGAAUGUAAA UCCUGCAUGG UGAUGUUGGA G

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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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 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: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 316144
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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