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- EMDB-15831: CryoEM structure of the pointy tip (proteins pIII/pVI/pVIII) from... -

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Basic information

Entry
Database: EMDB / ID: EMD-15831
TitleCryoEM structure of the pointy tip (proteins pIII/pVI/pVIII) from the f1 filamentous bacteriophage
Map data
Sample
  • Virus: Enterobacteria phage f1 (virus)
    • Protein or peptide: Capsid protein G8P
    • Protein or peptide: Head virion protein G6P
    • Protein or peptide: Attachment protein G3P
KeywordsViral proteins / Infection / VIRUS
Function / homology
Function and homology information


viral extrusion / virion attachment to host cell pilus / adhesion receptor-mediated virion attachment to host cell / helical viral capsid / host cell membrane / virion component / viral capsid / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / membrane
Similarity search - Function
Protein of unknown function DUF5455 / Family of unknown function (DUF5455) / Bacteriophage, G3P, N2-domain superfamily / Attachment protein G3P, N-terminal / Attachment protein G3P, N-terminal domain superfamily / Phage Coat Protein A / Phage major coat protein, Gp8 / Bacteriophage M13, G8P, capsid domain superfamily / Capsid protein G8P
Similarity search - Domain/homology
Attachment protein G3P / Head virion protein G6P / Capsid protein G8P
Similarity search - Component
Biological speciesEnterobacteria phage f1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.97 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-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15831.png

Downloads & links

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Map

FileDownload / File: emd_15831.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: 0.222
Minimum - Maximum-0.22791488 - 0.8886775
Average (Standard dev.)-0.000029006906 (±0.020483384)
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_15831_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_15831_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: Capsid protein G8P
    • Protein or peptide: Head virion protein G6P
    • Protein or peptide: Attachment protein G3P

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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: Capsid protein G8P

MacromoleculeName: Capsid protein G8P / type: protein_or_peptide / ID: 1 / Number of copies: 35 / 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

UniProtKB: Capsid protein G8P

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Macromolecule #2: Head virion protein G6P

MacromoleculeName: Head virion protein G6P / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage f1 (virus)
Molecular weightTheoretical: 12.357984 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPVLLGIPLL LRFLGFLLVT LFGYLLTFLK KGFGKIAIAI SLFLALIIGL NSILVGYLSD ISAQLPSDFV QGVQLILPSN ALPCFYVIL SVKAAIFIFD VKQKIVSYLD WDK

UniProtKB: Head virion protein G6P

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Macromolecule #3: Attachment protein G3P

MacromoleculeName: Attachment protein G3P / type: protein_or_peptide / ID: 3 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage f1 (virus)
Molecular weightTheoretical: 42.573766 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: AETVESCLAK PHTENSFTNV WKDDKTLDRY ANYEGCLWNA TGVVVCTGDE TQCYGTWVPI GLAIPENEGG GSEGGGSEGG GSEGGGTKP PEYGDTPIPG YTYINPLDGT YPPGTEQNPA NPNPSLEESQ PLNTFMFQNN RFRNRQGALT VYTGTVTQGT D PVKTYYQY ...String:
AETVESCLAK PHTENSFTNV WKDDKTLDRY ANYEGCLWNA TGVVVCTGDE TQCYGTWVPI GLAIPENEGG GSEGGGSEGG GSEGGGTKP PEYGDTPIPG YTYINPLDGT YPPGTEQNPA NPNPSLEESQ PLNTFMFQNN RFRNRQGALT VYTGTVTQGT D PVKTYYQY TPVSSKAMYD AYWNGKFRDC AFHSGFNEDP FVCEYQGQSS DLPQPPVNAG GGSGGGSGGG SEGGGSEGGG SE GGGSEGG GSGGGSGSGD FDYEKMANAN KGAMTENADE NALQSDAKGK LDSVATDYGA AIDGFIGDVS GLANGNGATG DFA GSNSQM AQVGDGDNSP LMNNFRQYLP SLPQSVECRP FVFGAGKPYE FSIDCDKINL FRGVFAFLLY VATFMYVFST FANI LRNKE S

UniProtKB: Attachment protein G3P

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

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 86242
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: OTHER
Output model

PDB-8b3o:
CryoEM structure of the pointy tip (proteins pIII/pVI/pVIII) from the f1 filamentous bacteriophage

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