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- PDB-9nzr: Structure of Al3Cas12f State II -

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Basic information

Entry
Database: PDB / ID: 9nzr
TitleStructure of Al3Cas12f State II
Components
  • Cas12f Nuclease
  • Non-Target Strand DNA
  • Target Strand DNA
  • sgRNA
KeywordsDNA BINDING PROTEIN/DNA/RNA / Cas12f CRISPR Endonuclease Dimeric / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA-RNA complex
Function / homologyDNA / DNA (> 10) / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsFregoso Ocampo, R. / Guan, K.
Funding support United States, 1items
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, 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: FSC / Data content type: FSC / 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
D: Target Strand DNA
E: Non-Target Strand DNA
A: Cas12f Nuclease
B: Cas12f Nuclease
C: sgRNA


Theoretical massNumber of molelcules
Total (without water)198,1415
Polymers198,1415
Non-polymers00
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

#1: DNA chain Target Strand DNA


Mass: 15353.835 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#2: DNA chain Non-Target Strand DNA


Mass: 15451.913 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#3: Protein Cas12f Nuclease


Mass: 58757.590 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#4: RNA chain sgRNA


Mass: 49819.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
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: Cas12f:sgRNA:dsDNA / Type: COMPLEX
Details: RNP bound to its sgRNA forming a 20bp R-loop with its target dsDNA
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.125676 MDa / Experimental value: NO
Source (natural)Organism: Deltaproteobacteria (d-proteobacteria)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21 DE3
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
8PHENIXmodel refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3070006
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 69185 / Symmetry type: POINT
RefinementHighest resolution: 3.26 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00411670
ELECTRON MICROSCOPYf_angle_d0.83816617
ELECTRON MICROSCOPYf_dihedral_angle_d22.4823457
ELECTRON MICROSCOPYf_chiral_restr0.0461913
ELECTRON MICROSCOPYf_plane_restr0.0071474

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