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- PDB-9n6t: FnCas9 scaRNA gRNA 1101 DNA non-productive state -

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Basic information

Entry
Database: PDB / ID: 9n6t
TitleFnCas9 scaRNA gRNA 1101 DNA non-productive state
Components
  • 1101 NTS
  • 1101 TS
  • CRISPR-associated endonuclease Cas9
  • scaRNA gRNA
KeywordsHydrolase/DNA/RNA / CRISPR / Cas9 / IMMUNE SYSTEM / Hydrolase-DNA-RNA complex
Function / homology
Function and homology information


endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / DNA binding / RNA binding / metal ion binding
Similarity search - Function
CRISPR system subtype II-B RNA-guided endonuclease Cas9/Csx12 / : / : / CRISPR-associated endonuclease Cas9 alpha-helical lobe / CRISPR-associated endonuclease Cas9, C-terminal domain / Cas9-type HNH domain / Cas9-type HNH domain profile.
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / RNA (> 10) / CRISPR-associated endonuclease Cas9
Similarity search - Component
Biological speciesFrancisella tularensis subsp. novicida (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.77 Å
AuthorsHibshman, G.N. / Taylor, D.W.
Funding support United States, 2items
OrganizationGrant numberCountry
Welch FoundationF-1938 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM138348 United States
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: Structural basis of a dual-function type II-B CRISPR-Cas9
Authors: Hibshman, G.N. / Taylor, D.W.
History
DepositionFeb 5, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 1101 TS
C: 1101 NTS
D: scaRNA gRNA
A: CRISPR-associated endonuclease Cas9


Theoretical massNumber of molelcules
Total (without water)230,1434
Polymers230,1434
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 1101 TS


Mass: 7912.127 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Francisella tularensis subsp. novicida (bacteria)
#2: DNA chain 1101 NTS


Mass: 3719.468 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Francisella tularensis subsp. novicida (bacteria)
#3: RNA chain scaRNA gRNA


Mass: 27886.447 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Francisella tularensis subsp. novicida (bacteria)
#4: Protein CRISPR-associated endonuclease Cas9


Mass: 190625.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. novicida (bacteria)
Gene: cas9, FTN_0757 / Production host: Escherichia coli (E. coli)
References: UniProt: A0Q5Y3, Hydrolases; Acting on ester bonds
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 FnCas9 with scaRNA gRNA and 1101 DNA
Type: COMPLEX / Entity ID: #4, #1-#3 / Source: RECOMBINANT
Molecular weightValue: 0.190329 MDa / Experimental value: YES
Source (natural)Organism: Francisella tularensis subsp. novicida (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
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: 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: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 283943 / Symmetry type: POINT
RefinementHighest resolution: 2.77 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00512501
ELECTRON MICROSCOPYf_angle_d0.96117425
ELECTRON MICROSCOPYf_dihedral_angle_d17.7552896
ELECTRON MICROSCOPYf_chiral_restr0.0581977
ELECTRON MICROSCOPYf_plane_restr0.0091779

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