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- EMDB-49165: Cryo-EM structure of the dCas12f-gRNA complex -

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Basic information

Entry
Database: EMDB / ID: EMD-49165
TitleCryo-EM structure of the dCas12f-gRNA complex
Map data
Sample
  • Complex: dCas12f-gRNA complex
    • Protein or peptide: Nuclease-deactivated Cas12f
    • RNA: gRNA (88-MER)
  • Ligand: MAGNESIUM ION
KeywordsdCas12f / binary complex / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Biological speciesFlagellimonas taeanensis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsChang L / Sternberg SH / Xiao R / Hoffmann FT / Wiegand T / Xie D
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM138675 United States
National Science Foundation (NSF, United States)2339799 United States
CitationJournal: To Be Published
Title: Structural basis of RNA-guided transcription via Cas12f-Sigma factor association
Authors: Renjian X / Leifu C
History
DepositionFeb 10, 2025-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49165.png

Downloads & links

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Map

FileDownload / File: emd_49165.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 256 pix.
= 210.432 Å		0.82 Å/pix.
x 256 pix.
= 210.432 Å		0.82 Å/pix.
x 256 pix.
= 210.432 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.822 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.0016945603 - 2.1796563
Average (Standard dev.)0.0015831382 (±0.02888567)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 210.432 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_49165_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_49165_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 : dCas12f-gRNA complex

EntireName: dCas12f-gRNA complex
Components
  • Complex: dCas12f-gRNA complex
    • Protein or peptide: Nuclease-deactivated Cas12f
    • RNA: gRNA (88-MER)
  • Ligand: MAGNESIUM ION

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Supramolecule #1: dCas12f-gRNA complex

SupramoleculeName: dCas12f-gRNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Flagellimonas taeanensis (bacteria)

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Macromolecule #1: Nuclease-deactivated Cas12f

MacromoleculeName: Nuclease-deactivated Cas12f / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Flagellimonas taeanensis (bacteria)
Molecular weightTheoretical: 42.913262 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGKSTLKHTR KIQILIDLPT KDEKKEVMDM MYQWRDRCFR AANIIVTHLY VQEMIKDFFY LSEGIKYKLA DEKKDEKGIL QRSRMNTTY RVVSDRFKGE MPTNILSTLN HGLISSFNKN RVQYWKGERS LPNFKKDMAF PFGLQGISRL VYDEEKKAFC F RLYRVPFK ...String:
MGKSTLKHTR KIQILIDLPT KDEKKEVMDM MYQWRDRCFR AANIIVTHLY VQEMIKDFFY LSEGIKYKLA DEKKDEKGIL QRSRMNTTY RVVSDRFKGE MPTNILSTLN HGLISSFNKN RVQYWKGERS LPNFKKDMAF PFGLQGISRL VYDEEKKAFC F RLYRVPFK TYLGKDFTDK RMLLERLVKG DVKLCASNIQ LNGGKIFWLA VFEIEKEKHS LKPEVIAEAS LSLEYPIVVK TG KNRLTIG TKEEFLYRRL AIQAARRRTQ VGATYSRSGK GKKRKLKAVD KYHKTESNYV AHRIHVYSRK LIDFCIKHQA GTL ILMNQE DKVGIAKEEE FVLRNWSYYE LMTKIKYKAE KAGIELIIG

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Macromolecule #2: gRNA (88-MER)

MacromoleculeName: gRNA (88-MER) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Flagellimonas taeanensis (bacteria)
Molecular weightTheoretical: 29.92277 KDa
SequenceString:
AUUUUGAGGG UGCUUGUACA CCCAUAGGGU GAGGUUAAGA AUUACACUCA CUAAGUGUGA ACAACACAUA CAACUUGUGG GAUAUACGC UAAC

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 59.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 116049
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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