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- EMDB-43682: PbAbiF dimer bound to ncRNA -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-43682
TitlePbAbiF dimer bound to ncRNA
Map dataSharpened map of PbAbiF (C2 symmetry)
Sample
  • Complex: AbiF RNP
    • Protein or peptide: Abi family protein
    • RNA: AbiF ncRNA
Keywordstoxin-antitoxin / RNP / RNA-binding protein / HEPN / TOXIN / TOXIN-RNA complex
Biological speciesuncultured Prevotellaceae bacterium (environmental samples)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.56 Å
AuthorsWilkinson ME / Zilberzwige-Tal S / Altae-Tran H / Zhang F
Funding support United States, 2 items
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 ME / Vo SC / Shmakov S / Yao CJ / Strebinger D / Edmonds KK / Mears KS / Makarova KS / Macrae RK / Koonin EV / Zhang F
History
DepositionFeb 10, 2024-
Header (metadata) releaseFeb 12, 2025-
Map releaseFeb 12, 2025-
UpdateFeb 12, 2025-
Current statusFeb 12, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43682.png

Downloads & links

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Map

FileDownload / File: emd_43682.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of PbAbiF (C2 symmetry)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.99 Å/pix.
x 240 pix.
= 238.68 Å		0.99 Å/pix.
x 240 pix.
= 238.68 Å		0.99 Å/pix.
x 240 pix.
= 238.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9945 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.050837386 - 0.09070917
Average (Standard dev.)0.000029140598 (±0.0036831172)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 238.68 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_43682_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: PbAbiF refinement, half-map 1

Fileemd_43682_half_map_1.map
AnnotationPbAbiF refinement, half-map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: PbAbiF refinement, half-map 2

Fileemd_43682_half_map_2.map
AnnotationPbAbiF refinement, half-map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : AbiF RNP

EntireName: AbiF RNP
Components
  • Complex: AbiF RNP
    • Protein or peptide: Abi family protein
    • RNA: AbiF ncRNA

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Supramolecule #1: AbiF RNP

SupramoleculeName: AbiF RNP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: uncultured Prevotellaceae bacterium (environmental samples)
Molecular weightTheoretical: 100 KDa

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Macromolecule #1: Abi family protein

MacromoleculeName: Abi family protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: uncultured Prevotellaceae bacterium (environmental samples)
Molecular weightTheoretical: 35.008711 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSNRIPFPKP YTSAHDLVSL LQSRGLTIAD TAKTERYLEF IGYYRLSAYM YPLLQMPKEQ HRYKPNTTFD QVMMLYRFDK KLRLLIFNE IEKIEVAVRS AIVNIGSDMI GSPFWMTDGS NFIDPRKFRH TMDLIDAELG RSREDFIVHF KQTYSDAYPP A WILAEVLP ...String:
MSNRIPFPKP YTSAHDLVSL LQSRGLTIAD TAKTERYLEF IGYYRLSAYM YPLLQMPKEQ HRYKPNTTFD QVMMLYRFDK KLRLLIFNE IEKIEVAVRS AIVNIGSDMI GSPFWMTDGS NFIDPRKFRH TMDLIDAELG RSREDFIVHF KQTYSDAYPP A WILAEVLP FGVITNIFSN IKTARIKKSI ARKFGLQVAP FESWLTIVAL TRNSCCHHAR VWNKQNTIRP MIPNRMTGRW II LPTDALR IYFNLCIIKY FLDIISPQND MKAKIDALLS SYSSIDINAM GFPRGWESEP LWQ

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Macromolecule #2: AbiF ncRNA

MacromoleculeName: AbiF ncRNA / type: rna / ID: 2 / Number of copies: 2
Source (natural)Organism: uncultured Prevotellaceae bacterium (environmental samples)
Molecular weightTheoretical: 15.954489 KDa
SequenceString:
ACUAGAACCC GCCAAGCCUC UCAACGAUGC UCAAAUGUGC GGGUCGUUUU

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2 mg/mL
BufferpH: 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
GridModel: Quantifoil / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 285 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 4272 / Average exposure time: 0.69 sec. / Average electron dose: 42.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.2 µm / Nominal defocus min: 1.4000000000000001 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1142600
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 12790
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final 3D classificationNumber classes: 4 / Avg.num./class: 36000 / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8vz6:
PbAbiF dimer bound to ncRNA

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