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- PDB-9sjm: Type I-F_HNH variant Cascade target-free RNP, HNH domain in inwar... -

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Basic information

Entry
Database: PDB / ID: 9sjm
TitleType I-F_HNH variant Cascade target-free RNP, HNH domain in inwards position
Components
  • Cas5f
  • Cas6f
  • Cas7f
  • Cas8f fusion with HNH
  • crRNA
KeywordsRNA BINDING PROTEIN / CRISPR-Cas Type I-F HNH nuclease
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / endonuclease activity / nucleic acid binding / zinc ion binding
Similarity search - Function
CRISPR-associated protein Csy1 / CRISPR-associated protein (Cas_Csy1) / HNH endonuclease / HNH endonuclease / CRISPR-associated endoribonuclease Cas6/Csy4, subtype I-F/YPEST / CRISPR-associated endoribonuclease Cas6/Csy4, subtype I-F/YPEST superfamily / CRISPR-associated protein (Cas_Csy4) / CRISPR-associated protein Csy2 / CRISPR-associated protein (Cas_Csy2) / HNH nucleases ...CRISPR-associated protein Csy1 / CRISPR-associated protein (Cas_Csy1) / HNH endonuclease / HNH endonuclease / CRISPR-associated endoribonuclease Cas6/Csy4, subtype I-F/YPEST / CRISPR-associated endoribonuclease Cas6/Csy4, subtype I-F/YPEST superfamily / CRISPR-associated protein (Cas_Csy4) / CRISPR-associated protein Csy2 / CRISPR-associated protein (Cas_Csy2) / HNH nucleases / CRISPR-associated protein Csy3 / CRISPR-associated protein (Cas_Csy3) / HNH nuclease
Similarity search - Domain/homology
RNA / RNA (> 10) / Cas5f / Cas6f / Cas7f / Cas8f fusion with HNH
Similarity search - Component
Biological speciesSelenomonas sp. (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.13 Å
AuthorsFuglsang, A. / Montoya, G.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF14CC0001 Denmark
CitationJournal: To Be Published
Title: Conformational Dynamics of CRISPR-Cas Type I-F-HNH informs Nickase Engineering in a Cascade Scaffold
Authors: Fuglsang, A. / Montoya, G.
History
DepositionAug 31, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 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

Downloads & links

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Assembly

Deposited unit
A: Cas8f fusion with HNH
B: Cas5f
I: Cas6f
D: Cas7f
E: Cas7f
F: Cas7f
C: Cas7f
G: Cas7f
H: Cas7f
J: crRNA


Theoretical massNumber of molelcules
Total (without water)344,78710
Polymers344,78710
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: Protein Cas8f fusion with HNH


Mass: 43706.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Selenomonas sp. (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0AAX7FM29
#2: Protein Cas5f


Mass: 28703.135 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Selenomonas sp. (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0AAX7FM22
#3: Protein Cas6f


Mass: 20735.873 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Selenomonas sp. (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0AAX7FM27
#4: Protein
Cas7f


Mass: 38700.172 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Selenomonas sp. (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0AAX7FM28
#5: RNA chain crRNA


Mass: 19440.611 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Selenomonas sp. (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
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: Type I-F_HNH effector complex bound to dsDNA / Type: COMPLEX / Entity ID: #3, #1 / Source: RECOMBINANT
Molecular weightValue: 0.35 MDa / Experimental value: NO
Source (natural)Organism: Selenomonas sp. (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17308 / Symmetry type: POINT
RefinementCross valid method: NONE

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