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- EMDB-29675: A Vibrio cholerae viral satellite enables efficient horizontal tr... -

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Basic information

Entry
Database: EMDB / ID: EMD-29675
TitleA Vibrio cholerae viral satellite enables efficient horizontal transfer by using an external scaffold to assemble hijacked coat proteins into small capsids
Map data
Sample
  • Complex: PLE Procapsid
    • Protein or peptide: major head protein
    • Protein or peptide: Serine protease
KeywordsPLE / Procapsid / VIRUS LIKE PARTICLE
Function / homologyMajor capsid protein GpE / Phage major capsid protein E / host cell cytoplasm / Putative major head protein / Phage protein
Function and homology information
Biological speciesVibrio cholerae (bacteria) / Vibrio phage ICP1_2011_A (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsSubramanian S / Boyd CM / Seed KD / Parent KN
Funding support United States, 6 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM110185 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM116789 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM140803 United States
National Science Foundation (NSF, United States)1750125 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI127652 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI127652 United States
CitationJournal: Elife / Year: 2024
Title: A viral satellite maximizes its spread and inhibits phage by remodeling hijacked phage coat proteins into small capsids.
Authors: Caroline M Boyd / Sundharraman Subramanian / Drew T Dunham / Kristin N Parent / Kimberley D Seed /
Abstract: Phage satellites commonly remodel capsids they hijack from the phages they parasitize, but only a few mechanisms regulating the change in capsid size have been reported. Here, we investigated how a ...Phage satellites commonly remodel capsids they hijack from the phages they parasitize, but only a few mechanisms regulating the change in capsid size have been reported. Here, we investigated how a satellite from , phage-inducible chromosomal island-like element (PLE), remodels the capsid it has been predicted to steal from the phage ICP1 (Netter et al., 2021). We identified that a PLE-encoded protein, TcaP, is both necessary and sufficient to form small capsids during ICP1 infection. Interestingly, we found that PLE is dependent on small capsids for efficient transduction of its genome, making it the first satellite to have this requirement. ICP1 isolates that escaped TcaP-mediated remodeling acquired substitutions in the coat protein, suggesting an interaction between these two proteins. With a procapsid-like particle (PLP) assembly platform in , we demonstrated that TcaP is a bona fide scaffold that regulates the assembly of small capsids. Further, we studied the structure of PLE PLPs using cryogenic electron microscopy and found that TcaP is an external scaffold that is functionally and somewhat structurally similar to the external scaffold, Sid, encoded by the unrelated satellite P4 (Kizziah et al., 2020). Finally, we showed that TcaP is largely conserved across PLEs. Together, these data support a model in which TcaP directs the assembly of small capsids comprised of ICP1 coat proteins, which inhibits the complete packaging of the ICP1 genome and permits more efficient packaging of replicated PLE genomes.
History
DepositionFeb 2, 2023-
Header (metadata) releaseJan 17, 2024-
Map releaseJan 17, 2024-
UpdateJan 24, 2024-
Current statusJan 24, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

Downloads & links

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Map

FileDownload / File: emd_29675.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.328 Å
Density
Contour LevelBy AUTHOR: 0.28
Minimum - Maximum-1.0406 - 2.2134502
Average (Standard dev.)0.0015282676 (±0.07740508)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-299-299-299
Dimensions600600600
Spacing600600600
CellA=B=C: 796.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_29675_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #2

Fileemd_29675_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #1

Fileemd_29675_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire : PLE Procapsid

EntireName: PLE Procapsid
Components
  • Complex: PLE Procapsid
    • Protein or peptide: major head protein
    • Protein or peptide: Serine protease

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Supramolecule #1: PLE Procapsid

SupramoleculeName: PLE Procapsid / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Vibrio cholerae (bacteria) / Strain: El Tor

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Macromolecule #1: major head protein

MacromoleculeName: major head protein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Vibrio phage ICP1_2011_A (virus)
Molecular weightTheoretical: 38.428023 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MARMGDFGVV DYTSLMALAP RSKNFLELLG VFSESNTRYI DSRYAEFERE EKGVTKMNAM ARGGSRKYIG SEKARKEIIE VPFAPLDGV TVASEVEAFR QYGTESQTAS VEALVQRKIE HIQRSHGIYI RDCQYTALLK DKILAEDEDG NEITALAKNF S TLWGVSRK ...String:
MARMGDFGVV DYTSLMALAP RSKNFLELLG VFSESNTRYI DSRYAEFERE EKGVTKMNAM ARGGSRKYIG SEKARKEIIE VPFAPLDGV TVASEVEAFR QYGTESQTAS VEALVQRKIE HIQRSHGIYI RDCQYTALLK DKILAEDEDG NEITALAKNF S TLWGVSRK TGAINTTTAV NPFSVLATKR QEIIDSMGEN NGFTSMVVLC TTRDFNAIVD HPDVRAAYEG RDGGAEYLTR RL GDAVDFQ VFTHKGVTLV EDTSGKLTDG SAYMFPLGVQ DMFQAVYAPA DSTDHVNTIS QGSYLFLNAG ENWRRDVIES EVS YACMVT RSELICDLTI TVAHHHHHH

UniProtKB: Putative major head protein

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Macromolecule #2: Serine protease

MacromoleculeName: Serine protease / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae (bacteria) / Strain: El Tor
Molecular weightTheoretical: 33.231152 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MTTITTTTNN TFDLANVIAE YKAGFEQYKA DNKQYNADAY RRKIESINSD AALTNGAFNQ FAYGSQMFEG KTLQEIAESL KTMQVKDSS REDENGLIFP HVTLQLVSPT TPAQYYGLIA EAVKLGFEVC PDWRLHVGTG RNFPACRLVR QAEWYKPHNE K LMAERIAE ...String:
MTTITTTTNN TFDLANVIAE YKAGFEQYKA DNKQYNADAY RRKIESINSD AALTNGAFNQ FAYGSQMFEG KTLQEIAESL KTMQVKDSS REDENGLIFP HVTLQLVSPT TPAQYYGLIA EAVKLGFEVC PDWRLHVGTG RNFPACRLVR QAEWYKPHNE K LMAERIAE AEKQEAERLK AEYFNEHRVQ AYVEQAQRKF MATQAQQAAI SLSAAISREL YASSGLSDDD LAVVAQSDVW AF NTLAPQL QEKDPNVISA ALTGAGFVKG KHKLSDGKQA TLWVKDGADV TALTLESKYI Q

UniProtKB: Phage protein

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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: 7.5
Component:
ConcentrationFormulaName
50.0 mMC4H11NO3-HCltris(hydroxymethyl)aminomethane hydrochloride
100.0 mMNaClsodium chloride
10.0 mMMgSO4magnesium sulfate
1.0 mMCaCl2calcium chloride

Details: 50 mM Tris-HCl, pH 7.4, 100 mM NaCl, 10 mM MgSO4, 1 mM CaCl2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 36.41 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 379643
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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