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- PDB-9shx: Type I-F_HNH variant Cascade bound to dsDNA, HNH domain in middle... -

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Basic information

Entry
Database: PDB / ID: 9shx
TitleType I-F_HNH variant Cascade bound to dsDNA, HNH domain in middle position
Components
  • Cas5f
  • Cas6f
  • Cas7f
  • Cas8f fusion with HNH
  • Non-target strand
  • Target strand
  • 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
DNA / DNA (> 10) / 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: 2.4 Å
AuthorsFuglsang, A. / Montoya, G.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF14CC0001 Denmark
Citation
Journal: 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.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionAug 28, 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
D: Cas7f
E: Cas7f
F: Cas7f
C: Cas7f
G: Cas7f
B: Cas5f
H: Cas7f
A: Cas8f fusion with HNH
I: Cas6f
L: Non-target strand
K: Target strand
J: crRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)373,16813
Polymers373,14412
Non-polymers241
Water181
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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Protein , 4 types, 9 molecules DEFCGHBAI

#1: 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
#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 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
#4: 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

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DNA chain , 2 types, 2 molecules LK

#5: DNA chain Non-target strand


Mass: 14233.219 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Selenomonas sp. (bacteria)
#6: DNA chain Target strand


Mass: 14062.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Selenomonas sp. (bacteria)

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RNA chain , 1 types, 1 molecules J

#7: RNA chain crRNA


Mass: 19502.576 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)

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Non-polymers , 2 types, 2 molecules

#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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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: 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: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 174646 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 51.98 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002924768
ELECTRON MICROSCOPYf_angle_d0.564433962
ELECTRON MICROSCOPYf_chiral_restr0.03973765
ELECTRON MICROSCOPYf_plane_restr0.00423947
ELECTRON MICROSCOPYf_dihedral_angle_d17.32634405

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