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- PDB-8fuk: V. cholerae TniQ-Cascade complex with Type III-B crRNA -

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Basic information

Entry
Database: PDB / ID: 8fuk
TitleV. cholerae TniQ-Cascade complex with Type III-B crRNA
Components
  • CRISPR-associated protein Cas8
  • Cas6
  • Cas7
  • TniQ
  • Type III-B crRNA
KeywordsANTIVIRAL PROTEIN/RNA / Type I-F CAST / DNA Transposition / CRISPR Transposon / ANTIVIRAL PROTEIN-RNA complex
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / endonuclease activity
Similarity search - Function
TniQ / TniQ / 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) / CRISPR-associated protein Csy3 / CRISPR-associated protein (Cas_Csy3)
Similarity search - Domain/homology
RNA / RNA (> 10) / Cas6 / Cas8 / Cas7 / TniQ
Similarity search - Component
Biological speciesmetagenome (others)
Vibrio cholerae (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.36 Å
AuthorsChou, C.W. / Finkelstein, I.J. / Hu, K.
Funding support United States, 2items
OrganizationGrant numberCountry
Welch Foundation2674221058 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)2616141758 United States
CitationJournal: To be Published
Title: V. cholerae TniQ-Cascade complex with Type III-B crRNA
Authors: Chou, C.W. / Finkelstein, I.J. / Hu, K.
History
DepositionJan 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: Type III-B crRNA
A: Cas7
B: Cas7
C: Cas7
D: Cas7
E: Cas7
F: Cas7
G: CRISPR-associated protein Cas8
H: Cas6
I: TniQ
J: TniQ


Theoretical massNumber of molelcules
Total (without water)445,27111
Polymers445,27111
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: RNA chain Type III-B crRNA


Mass: 19333.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Protein
Cas7


Mass: 39886.031 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: csy3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6I8WFX5
#3: Protein CRISPR-associated protein Cas8


Mass: 72294.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: FXE93_08750 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6I8WFX4
#4: Protein Cas6


Mass: 23130.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: cas6f / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6I8WFX3
#5: Protein TniQ


Mass: 45597.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: FXE93_08745 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6I8WFX7

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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 TniQ-Cascade with Type III-B crRNA / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightValue: 0.45 MDa / Experimental value: NO
Source (natural)Organism: Vibrio cholerae (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: BL21 (DE3)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 39.2 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: 2200 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1235

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.20.1_4487refinement
PHENIX1.20.1_4487refinement
EM software
IDNameCategory
2SerialEMimage acquisition
7Cootmodel fitting
9PHENIXmodel refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 67000 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 65.01 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003124325
ELECTRON MICROSCOPYf_angle_d0.561833295
ELECTRON MICROSCOPYf_chiral_restr0.04133705
ELECTRON MICROSCOPYf_plane_restr0.00594033
ELECTRON MICROSCOPYf_dihedral_angle_d9.86113709

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