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- PDB-9nzs: Cryo-EM structure of OsCas12f-gRNA-DNA ternary complex. State III -

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Basic information

Entry
Database: PDB / ID: 9nzs
TitleCryo-EM structure of OsCas12f-gRNA-DNA ternary complex. State III
Components
  • Cas12f
  • DNA target poly C
  • Non-target strand DNA
  • Targer strand DNA
  • guide RNA
KeywordsRNA BINDING PROTEIN/DNA/RNA / RNA-guided endonuclease / RNA BINDING PROTEIN / RNA BINDING PROTEIN-DNA-RNA complex
Function / homologyDNA / DNA (> 10) / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesOscillibacter sp. (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.68 Å
AuthorsGuan, K. / Taylor, D.W.
Funding support United States, 1items
OrganizationGrant numberCountry
Welch FoundationF-1938 United States
CitationJournal: To Be Published
Title: Cryo-EM structure of CRISPR-Cas12f nucleases
Authors: Guan, K. / Ocampo, R.F. / Taylor, D.W.
History
DepositionApr 1, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cas12f
B: Cas12f
C: Targer strand DNA
D: Non-target strand DNA
E: guide RNA
G: DNA target poly C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,5417
Polymers176,4766
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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DNA chain , 3 types, 3 molecules CDG

#2: DNA chain Targer strand DNA


Mass: 13835.940 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Oscillibacter sp. (bacteria)
#3: DNA chain Non-target strand DNA


Mass: 13878.857 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Oscillibacter sp. (bacteria)
#5: DNA chain DNA target poly C


Mass: 1111.770 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Oscillibacter sp. (bacteria)

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Protein / RNA chain / Non-polymers , 3 types, 4 molecules ABE

#1: Protein Cas12f


Mass: 49389.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oscillibacter sp. (bacteria) / Production host: Escherichia coli (E. coli)
#4: RNA chain guide RNA


Mass: 48870.070 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Oscillibacter sp. (bacteria)
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Ternary complex of OsCas12f-gRNA-DNA complex. State III
Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Source (natural)Organism: Oscillibacter sp. (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 49 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.68 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42153 / Symmetry type: POINT
RefinementHighest resolution: 3.68 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0079988
ELECTRON MICROSCOPYf_angle_d1.24914264
ELECTRON MICROSCOPYf_dihedral_angle_d25.1783168
ELECTRON MICROSCOPYf_chiral_restr0.0791669
ELECTRON MICROSCOPYf_plane_restr0.0111196

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