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- PDB-8vz6: PbAbiF dimer bound to ncRNA -

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Basic information

Entry
Database: PDB / ID: 8vz6
TitlePbAbiF dimer bound to ncRNA
Components
  • Abi family protein
  • AbiF ncRNA
KeywordsTOXIN/RNA / toxin-antitoxin / RNP / RNA-binding protein / HEPN / TOXIN / TOXIN-RNA complex
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesuncultured Prevotellaceae bacterium (environmental samples)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.56 Å
AuthorsWilkinson, M.E. / Zilberzwige-Tal, S. / Altae-Tran, H. / Zhang, F.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01HG009761 United States
CitationJournal: To Be Published
Title: Emergence of a CRISPR RNA-guiding mechanism from a type III toxin-antitoxin system
Authors: Zilberzwige-Tal, S. / Altae-Tran, H. / Kannan, S. / Wilkinson, M.E. / Vo, S.C. / Shmakov, S. / Yao, C.J. / Strebinger, D. / Edmonds, K.K. / Mears, K.S. / Makarova, K.S. / Macrae, R.K. / Koonin, E.V. / Zhang, F.
History
DepositionFeb 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Abi family protein
R: AbiF ncRNA
B: Abi family protein
S: AbiF ncRNA


Theoretical massNumber of molelcules
Total (without water)101,9264
Polymers101,9264
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 Abi family protein


Mass: 35008.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: NCBI GCA_900316285.1 contig: ONCG01000034.1 start 16721 end 17623 strand +
Source: (gene. exp.) uncultured Prevotellaceae bacterium (environmental samples)
Production host: Escherichia coli (E. coli)
#2: RNA chain AbiF ncRNA


Mass: 15954.489 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: NCBI GCA_900316285.1 contig: ONCG01000034.1 start 16721 end 17623 strand +
Source: (gene. exp.) uncultured Prevotellaceae bacterium (environmental samples)
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: AbiF RNP / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.1 MDa / Experimental value: NO
Source (natural)Organism: uncultured Prevotellaceae bacterium (environmental samples)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.9
Details: 10 mM HEPES-KOH pH 7.9, 250 mM potassium acetate, 2.5 mM magnesium acetate, 5 mM beta-mercaptoethanol, 5 mM desthiobiotin
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 285 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 3200 nm / Nominal defocus min: 1400 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 0.69 sec. / Electron dose: 42.2 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4272
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1Topazparticle selection
2EPUimage acquisition
4CTFFIND4.1CTF correction
7ISOLDEmodel fitting
8Cootmodel fitting
11RELION4final Euler assignment
12RELION4classification
13RELION43D reconstruction
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1142600
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12790 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0067326
ELECTRON MICROSCOPYf_angle_d1.14210390
ELECTRON MICROSCOPYf_dihedral_angle_d16.611830
ELECTRON MICROSCOPYf_chiral_restr0.061230
ELECTRON MICROSCOPYf_plane_restr0.008954

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