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- EMDB-15832: CryoEM structure of the round tip (proteins pVII/pVIII/pIX) from ... -

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Basic information

Entry
Database: EMDB / ID: EMD-15832
TitleCryoEM structure of the round tip (proteins pVII/pVIII/pIX) from the f1 filamentous bacteriophage
Map data
Sample
  • Virus: Enterobacteria phage f1 (virus)
    • Protein or peptide: Tail virion protein G7P
    • Protein or peptide: Tail virion protein G9P
    • Protein or peptide: Capsid protein G8P
Function / homology
Function and homology information


helical viral capsid / host cell membrane / virion component / membrane
Similarity search - Function
Tail virion protein G7P / Tail virion protein G7P / Phage major coat protein, Gp8 / Bacteriophage M13, G8P, capsid domain superfamily / Capsid protein G8P
Similarity search - Domain/homology
Tail virion protein G7P / Tail virion protein G9P / Capsid protein G8P
Similarity search - Component
Biological speciesEnterobacteria phage f1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.81 Å
AuthorsConners R / McLaren M / Gold VAM
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust210363/Z/18/Z United Kingdom
CitationJournal: Nat Commun / Year: 2023
Title: Cryo-electron microscopy of the f1 filamentous phage reveals insights into viral infection and assembly.
Authors: Rebecca Conners / Rayén Ignacia León-Quezada / Mathew McLaren / Nicholas J Bennett / Bertram Daum / Jasna Rakonjac / Vicki A M Gold /
Abstract: Phages are viruses that infect bacteria and dominate every ecosystem on our planet. As well as impacting microbial ecology, physiology and evolution, phages are exploited as tools in molecular ...Phages are viruses that infect bacteria and dominate every ecosystem on our planet. As well as impacting microbial ecology, physiology and evolution, phages are exploited as tools in molecular biology and biotechnology. This is particularly true for the Ff (f1, fd or M13) phages, which represent a widely distributed group of filamentous viruses. Over nearly five decades, Ffs have seen an extraordinary range of applications, yet the complete structure of the phage capsid and consequently the mechanisms of infection and assembly remain largely mysterious. In this work, we use cryo-electron microscopy and a highly efficient system for production of short Ff-derived nanorods to determine a structure of a filamentous virus including the tips. We show that structure combined with mutagenesis can identify phage domains that are important in bacterial attack and for release of new progeny, allowing new models to be proposed for the phage lifecycle.
History
DepositionSep 16, 2022-
Header (metadata) releaseMay 24, 2023-
Map releaseMay 24, 2023-
UpdateMay 24, 2023-
Current statusMay 24, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15832.png

Downloads & links

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Map

FileDownload / File: emd_15832.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 384 pix.
= 422.861 Å		1.1 Å/pix.
x 384 pix.
= 422.861 Å		1.1 Å/pix.
x 384 pix.
= 422.861 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1012 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.23579149 - 0.8382511
Average (Standard dev.)-0.00010193119 (±0.020769611)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 422.86078 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_15832_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_15832_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Enterobacteria phage f1

EntireName: Enterobacteria phage f1 (virus)
Components
  • Virus: Enterobacteria phage f1 (virus)
    • Protein or peptide: Tail virion protein G7P
    • Protein or peptide: Tail virion protein G9P
    • Protein or peptide: Capsid protein G8P

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Supramolecule #1: Enterobacteria phage f1

SupramoleculeName: Enterobacteria phage f1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10863 / Sci species name: Enterobacteria phage f1 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Escherichia coli (E. coli) / Strain: F+ strains

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Macromolecule #1: Tail virion protein G7P

MacromoleculeName: Tail virion protein G7P / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage f1 (virus)
Molecular weightTheoretical: 3.603215 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MEQVADFDTI YQAMIQISVV LCFALGIIAG GQR

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Macromolecule #2: Tail virion protein G9P

MacromoleculeName: Tail virion protein G9P / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage f1 (virus)
Molecular weightTheoretical: 3.65527 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSVLVYSFAS FVLGWCLRSG ITYFTRLMET SS

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Macromolecule #3: Capsid protein G8P

MacromoleculeName: Capsid protein G8P / type: protein_or_peptide / ID: 3 / Number of copies: 45 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage f1 (virus)
Molecular weightTheoretical: 5.212021 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AEGDDPAKAA FDSLQASATE MIGYAWAMVV VIVGATIGIK LFKKFTSKAS

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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

BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: Wait time 5 sec., drain time 0 sec., blot force 0, blot time 4 sec..

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.3 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.81 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 255372
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: OTHER
Output model

PDB-8b3p:
CryoEM structure of the round tip (proteins pVII/pVIII/pIX) from the f1 filamentous bacteriophage

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