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- EMDB-27397: Gokushovirus EC6098 -

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Basic information

Entry
Database: EMDB / ID: EMD-27397
TitleGokushovirus EC6098
Map dataCryo-EM reconstruction of the gokushovirus EC6098
Sample
  • Virus: Escherichia phage EC6098 (virus)
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Putative DNA binding proteinDNA-binding protein
Function / homologyMicroviridae F protein / Microviridae F protein superfamily / Capsid protein (F protein) / Capsid/spike protein, ssDNA virus / structural molecule activity / Major capsid protein / Putative DNA binding protein
Function and homology information
Biological speciesEscherichia phage EC6098 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsLee H / Fane BA / Hafenstein SL
Funding support1 items
OrganizationGrant numberCountry
Other private
CitationJournal: J Virol / Year: 2022
Title: Cryo-EM Structure of Gokushovirus ΦEC6098 Reveals a Novel Capsid Architecture for a Single-Scaffolding Protein, Microvirus Assembly System.
Authors: Hyunwook Lee / Alexis J Baxter / Carol M Bator / Bentley A Fane / Susan L Hafenstein /
Abstract: Ubiquitous and abundant in ecosystems and microbiomes, gokushoviruses constitute a subfamily, distantly related to bacteriophages ΦX174, α3, and G4. A high-resolution cryo-EM structure of ...Ubiquitous and abundant in ecosystems and microbiomes, gokushoviruses constitute a subfamily, distantly related to bacteriophages ΦX174, α3, and G4. A high-resolution cryo-EM structure of gokushovirus ΦEC6098 was determined, and the atomic model was built . Although gokushoviruses lack external scaffolding and spike proteins, which extensively interact with the ΦX174 capsid protein, the core of the ΦEC6098 coat protein (VP1) displayed a similar structure. There are, however, key differences. At each ΦEC6098 icosahedral 3-fold axis, a long insertion loop formed mushroom-like protrusions, which have been noted in lower-resolution gokushovirus structures. Hydrophobic interfaces at the bottom of these protrusions may confer stability to the capsid shell. In ΦX174, the N-terminus of the capsid protein resides directly atop the 3-fold axes of symmetry; however, the ΦEC6098 N-terminus stretched across the inner surface of the capsid shell, reaching nearly to the 5-fold axis of the neighboring pentamer. Thus, this extended N-terminus interconnected pentamers on the inside of the capsid shell, presumably promoting capsid assembly, a function performed by the ΦX174 external scaffolding protein. There were also key differences between the ΦX174-like DNA-binding J proteins and its ΦEC6098 homologue VP8. As seen with the J proteins, C-terminal VP8 residues were bound into a pocket within the major capsid protein; however, its N-terminal residues were disordered, likely due to flexibility. We show that the combined location and interaction of VP8's C-terminus and a portion of VP1's N-terminus are reminiscent of those seen with the ΦX174 and α3 J proteins. There is a dramatic structural and morphogenetic divide within the . The well-studied ΦX174-like viruses have prominent spikes at their icosahedral vertices, which are absent in gokushoviruses. Instead, gokushovirus major coat proteins form extensive mushroom-like protrusions at the 3-fold axes of symmetry. In addition, gokushoviruses lack an external scaffolding protein, the more critical of the two ΦX174 assembly proteins, but retain an internal scaffolding protein. The ΦEC6098 virion suggests that key external scaffolding functions are likely performed by coat protein domains unique to gokushoviruses. Thus, within one family, different assembly paths have been taken, demonstrating how a two-scaffolding protein system can evolve into a one-scaffolding protein system, or vice versa.
History
DepositionJun 21, 2022-
Header (metadata) releaseOct 12, 2022-
Map releaseOct 12, 2022-
UpdateNov 23, 2022-
Current statusNov 23, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27397.png

Downloads & links

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Map

FileDownload / File: emd_27397.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM reconstruction of the gokushovirus EC6098
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 4.0
Minimum - Maximum-3.5077171 - 14.297173
Average (Standard dev.)1.5206478e-09 (±1.0000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-250-250-250
Dimensions500500500
Spacing500500500
CellA=B=C: 550.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: The sharpened map of the gokushovirus EC6098

Fileemd_27397_additional_1.map
AnnotationThe sharpened map of the gokushovirus EC6098
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: The first half map of the gokushovirus EC6098

Fileemd_27397_half_map_1.map
AnnotationThe first half map of the gokushovirus EC6098
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: The second half map of the gokushovirus EC6098

Fileemd_27397_half_map_2.map
AnnotationThe second half map of the gokushovirus EC6098
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Escherichia phage EC6098

EntireName: Escherichia phage EC6098 (virus)
Components
  • Virus: Escherichia phage EC6098 (virus)
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Putative DNA binding proteinDNA-binding protein

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Supramolecule #1: Escherichia phage EC6098

SupramoleculeName: Escherichia phage EC6098 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2720215 / Sci species name: Escherichia phage EC6098 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host systemOrganism: Escherichia coli (E. coli)

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Macromolecule #1: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage EC6098 (virus)
Molecular weightTheoretical: 63.367758 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSKFGRKVPS NAKSQHNFSV IPSANIQRSV FNRSSGYKTT FDAGYLIPVF LDEALPGDTF HLKTSVLARL STPVVPFMDN LRLDIQYFS VPYRLVWDNW QKFNGEQKNP GDSTDYLIPQ IKAPAGGFPV GSLADYFGVP TGVENISVSA LPFRAYNLIY N EWYRDENL ...String:
MSKFGRKVPS NAKSQHNFSV IPSANIQRSV FNRSSGYKTT FDAGYLIPVF LDEALPGDTF HLKTSVLARL STPVVPFMDN LRLDIQYFS VPYRLVWDNW QKFNGEQKNP GDSTDYLIPQ IKAPAGGFPV GSLADYFGVP TGVENISVSA LPFRAYNLIY N EWYRDENL INSAPLPLGD EEETGLANFP LRKRAKRHDY FTSALPWPQK GEGVEIGLGV PPSYTLEYPY YKEGMGFISS NY GASGNIG RTFPTYIARS SVGDDSSSNI GNAAYFSEGL ENGINFPNAP ARGRYDVLGG FDPNTPPVTL KKEGGEVVDN LTI NSLRQA FQLQRLLERD ARGGTRYIEI IRSHFGVISP DARVQRPEYL GSGSFDININ PVLQNSATTD ASPQGNLAAY GVSG GVNRG FSHSFVEHCF VIGLVSVRAD LTYQQGIPRM FSRQTRFDFY WPALAHLGEQ AILNKEIYAQ GNAKDDEVFG YQERY AEYR YRPSQITGKL RSTDPQSLDV WHLAQRFDSL PALNQEFIEE NPPMKRVLAV QDEPQFIMDA FFDLKCVRPM PVYSVP GLI DHF

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Macromolecule #2: Putative DNA binding protein

MacromoleculeName: Putative DNA binding protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage EC6098 (virus)
Molecular weightTheoretical: 4.83082 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARSRRRMSK RSSRRSFRKY AKTHKRNFKA RSMRGGIRL

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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: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN 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: 3.3000000000000003 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 32308

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