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- EMDB-44517: Pseudomonas phage DEV neck and tail (portal, head-to-tail and tai... -

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Basic information

Entry
Database: EMDB / ID: EMD-44517
TitlePseudomonas phage DEV neck and tail (portal, head-to-tail and tail tube proteins)
Map data
Sample
  • Complex: Portal to tail complex of Pseudomonas phage DEV
    • Protein or peptide: gp75 tail tube
    • Protein or peptide: gp83 head-to-tail
    • Protein or peptide: gp80 portal protein
Keywordsportal / tail hub / tail tube / complex / STRUCTURAL PROTEIN / gp75 / gp83 / gp80 / VIRAL PROTEIN
Function / homologyTail protein / N4 gp54-like protein / Portal protein
Function and homology information
Biological speciesPseudomonas phage vB_PaeP_DEV (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 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_44517.png

Downloads & links

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Map

FileDownload / File: emd_44517.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.12 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: 0.02
Minimum - Maximum-0.01572903 - 0.052771408
Average (Standard dev.)-0.00027810902 (±0.0027997014)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
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_44517_msk_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_44517_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_44517_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Portal to tail complex of Pseudomonas phage DEV

EntireName: Portal to tail complex of Pseudomonas phage DEV
Components
  • Complex: Portal to tail complex of Pseudomonas phage DEV
    • Protein or peptide: gp75 tail tube
    • Protein or peptide: gp83 head-to-tail
    • Protein or peptide: gp80 portal protein

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Supramolecule #1: Portal to tail complex of Pseudomonas phage DEV

SupramoleculeName: Portal to tail complex 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: gp75 tail tube

MacromoleculeName: gp75 tail tube / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage vB_PaeP_DEV (virus)
Molecular weightTheoretical: 35.267215 KDa
SequenceString: MAVEPITIAD LTEVKLDGKG ALDQLLQVTR LHLAKEHDAG RLKGQEYAAV LTGGITAVLQ NAVMFLLQKD EAANKAALVE AQIKLTEKQ GELLDKQIAQ ADKDAELIAA KVKLTLEQAK LPDSQIRSAG FQDLLVQEQT KVQTAQTRRI DQEILSAGFQ D LLVKEQTA ...String:
MAVEPITIAD LTEVKLDGKG ALDQLLQVTR LHLAKEHDAG RLKGQEYAAV LTGGITAVLQ NAVMFLLQKD EAANKAALVE AQIKLTEKQ GELLDKQIAQ ADKDAELIAA KVKLTLEQAK LPDSQIRSAG FQDLLVQEQT KVQTAQTRRI DQEILSAGFQ D LLVKEQTA KTKQDVLTAV QQTKVMEQQV LESTQKVLNM KQELLNLVAQ ECLLKAQFDL TKDQGLNTQE QTILVRQKVA SE RAQTIGA GVDADSVIGR QKELYKAQAD GFKRDAEQKA AKILIDTWNV RRTTDTGTQA NTTNRLDDAN VGRVVNMLMT GVG A

UniProtKB: N4 gp54-like protein

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Macromolecule #2: gp83 head-to-tail

MacromoleculeName: gp83 head-to-tail / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage vB_PaeP_DEV (virus)
Molecular weightTheoretical: 27.868934 KDa
SequenceString: MTIQLKQVID LLAEGELSNI KYVNIDTGAL VLERVPSLIR AINLGVLDLH KRFLLKEGML KIQLEEGRRL YPLRPAYQVG QKPKPGVPQ FITEGNKLGR QSILKIEKII GDNGVEYYLN DTWQPLNITT PEFDVLEISD EFYCHSSSKT LEVRYRRAPT P MKICVDNL ...String:
MTIQLKQVID LLAEGELSNI KYVNIDTGAL VLERVPSLIR AINLGVLDLH KRFLLKEGML KIQLEEGRRL YPLRPAYQVG QKPKPGVPQ FITEGNKLGR QSILKIEKII GDNGVEYYLN DTWQPLNITT PEFDVLEISD EFYCHSSSKT LEVRYRRAPT P MKICVDNL DSWGCIDIDL PYTHLQALLY FVASRCQTPI GFMENTAQEG FNFSQKYEAE CANLDAQNLR IDPVGNQDRF TR GGWV

UniProtKB: Tail protein

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Macromolecule #3: gp80 portal protein

MacromoleculeName: gp80 portal protein / type: protein_or_peptide / ID: 3 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage vB_PaeP_DEV (virus)
Molecular weightTheoretical: 81.739453 KDa
SequenceString: MADVDEDYLT LPNEDGDPSK RLQPEWSNAP SLAQLKQDYQ EAKQVTDEKI TQINRWLDYM HVRGEGKPKT EKGKSAVQPP TIRKQAEWR YSSLSEPFLS SPNIFEVNPV TWEDAESARQ NGLVLNQQFN TKLNKQRFID EYVRAGVDEG TIIVKVGWNY Q SRTVKEQV ...String:
MADVDEDYLT LPNEDGDPSK RLQPEWSNAP SLAQLKQDYQ EAKQVTDEKI TQINRWLDYM HVRGEGKPKT EKGKSAVQPP TIRKQAEWR YSSLSEPFLS SPNIFEVNPV TWEDAESARQ NGLVLNQQFN TKLNKQRFID EYVRAGVDEG TIIVKVGWNY Q SRTVKEQV VTYEMMPDSS EELAQIYQTA AQIREESPSE YPEIPEDVRL GLEETEANGI QVRAVPVGSE EEEREETVEN HP TVQVCDY NNIVIDPSCG SDFSKAKFLI ETFESSYAEL KADGRYKNLD KIQVEGQNLL SEPDYTGPSE GVRNFDFQDK SRK RLVVHE YWGYYDIHGD GVLHPIVATW VGAVMIRMEE NPFPDKKIPY VVVSYIPRKR DLYGESDGAL LIDNQRIIGA VTRG MIDTM ARSANGQVGV MKGALDVTNR RRFDRGENYE FNPGADPRAA VHMHTFPEIP QSAQYMINLQ QAEAESMTGV KAFNA GISG AALGDTATAV RGALDAASKR ELGILRRLSA GIIEIGRKII AMNAEFLDDV EVVRITNEHF VDIRRDDLAG NFDLKL DIS TAEEDNAKVN DLTFMLQTMG PNMDPMMAQQ IMGQIMELKK MPDFAKRIRE FQPQPDPIAQ QKAQLELMLL QAQIEAE RA RAAHYMSGAG LQDSKVGTEQ AKARALASQA DMTDLNFLEQ ESGVQQARKR ELQQAQSEAQ GKLAMLNSQL KRLDEATS A RTSQK

UniProtKB: Portal 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: C12 (12 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 3228
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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