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- EMDB-44518: Pseudomonas phage DEV 5-fold vertex (major coat protein) -

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Basic information

Entry
Database: EMDB / ID: EMD-44518
TitlePseudomonas phage DEV 5-fold vertex (major coat protein)
Map data
Sample
  • Complex: Major coat protein of Pseudomonas phage DEV
    • Protein or peptide: gp77 major coat protein
Keywordsvirion coat / complex / STRUCTURAL PROTEIN / gp77
Function / homologyMajor coat protein
Function and homology information
Biological speciesPseudomonas phage vB_PaeP_DEV (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsIglesias SM / Hou CFD / Li F / Cingolani G
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM100888 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM140733 United States
CitationJournal: Nat Commun / Year: 2024
Title: Integrative structural analysis of Pseudomonas phage DEV reveals a genome ejection motor.
Authors: Ravi K Lokareddy / Chun-Feng David Hou / Francesca Forti / Stephano M Iglesias / Fenglin Li / Mikhail Pavlenok / David S Horner / Michael Niederweis / Federica Briani / Gino Cingolani /
Abstract: DEV is an obligatory lytic Pseudomonas phage of the N4-like genus, recently reclassified as Schitoviridae. The DEV genome encodes 91 ORFs, including a 3398 amino acid virion-associated RNA polymerase ...DEV is an obligatory lytic Pseudomonas phage of the N4-like genus, recently reclassified as Schitoviridae. The DEV genome encodes 91 ORFs, including a 3398 amino acid virion-associated RNA polymerase (vRNAP). Here, we describe the complete architecture of DEV, determined using a combination of cryo-electron microscopy localized reconstruction, biochemical methods, and genetic knockouts. We built de novo structures of all capsid factors and tail components involved in host attachment. We demonstrate that DEV long tail fibers are essential for infection of Pseudomonas aeruginosa but dispensable for infecting mutants with a truncated lipopolysaccharide devoid of the O-antigen. We determine that DEV vRNAP is part of a three-gene operon conserved in 191 Schitoviridae genomes. We propose these three proteins are ejected into the host to form a genome ejection motor spanning the cell envelope. We posit that the design principles of the DEV ejection apparatus are conserved in all Schitoviridae.
History
DepositionApr 19, 2024-
Header (metadata) releaseSep 4, 2024-
Map releaseSep 4, 2024-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44518.png

Downloads & links

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Map

FileDownload / File: emd_44518.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesX (Sec.)Y (Row.)Z (Col.)
1.12 Å/pix.
x 512 pix.
= 573.44 Å		1.12 Å/pix.
x 512 pix.
= 573.44 Å		1.12 Å/pix.
x 512 pix.
= 573.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.12 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.5
Minimum - Maximum-10.656238 - 19.395845000000001
Average (Standard dev.)0.000000000001161 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 573.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_44518_msk_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_44518_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_44518_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Sample components

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Entire : Major coat protein of Pseudomonas phage DEV

EntireName: Major coat protein of Pseudomonas phage DEV
Components
  • Complex: Major coat protein of Pseudomonas phage DEV
    • Protein or peptide: gp77 major coat protein

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Supramolecule #1: Major coat protein of Pseudomonas phage DEV

SupramoleculeName: Major coat protein of Pseudomonas phage DEV / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pseudomonas phage vB_PaeP_DEV (virus)

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Macromolecule #1: gp77 major coat protein

MacromoleculeName: gp77 major coat protein / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage vB_PaeP_DEV (virus)
Molecular weightTheoretical: 44.114113 KDa
Recombinant expressionOrganism: Pseudomonas (RNA similarity group I)
SequenceString: MAGPVDNIKP MKYNDPANGV ESSIGPQIHT RYWYKRALID AAKEAYFGQL ADTFSMPKHY GKEIVRLHYI PLLDDRNVND QGIDASGAT IANGNLYGSS RDVGNITAKM PTLTEIGGRV NRVGFKRVEI KGKLEKYGFF REYTQEQLDF DSDPAMEGHV T TEMVKGAN ...String:
MAGPVDNIKP MKYNDPANGV ESSIGPQIHT RYWYKRALID AAKEAYFGQL ADTFSMPKHY GKEIVRLHYI PLLDDRNVND QGIDASGAT IANGNLYGSS RDVGNITAKM PTLTEIGGRV NRVGFKRVEI KGKLEKYGFF REYTQEQLDF DSDPAMEGHV T TEMVKGAN EITEDLLQID LLNSAGTVRY PGAATSDAEV DASTEVTYDS LMRLRLDLDN ARAPTKIKMI TGTRMIDTRT VG NARALYV GSDLVPTIEA MKDNHGNPAF IPIEKYAAGG ATMHGEVGQL GRFRVIVNPQ MMHWAGVGKA VDPNDQVPMH ESG GKYSVF PMLCVASEAF TTVGFATDGK NVKFKIITKR PGEATADRSD PYGEMGFMSI KWYYGFMVFR PEWIALLKTV ARL

UniProtKB: Major coat 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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 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: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 18913
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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