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- EMDB-45776: C15 symmetrized DEV collar -

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Basic information

Entry
Database: EMDB / ID: EMD-45776
TitleC15 symmetrized DEV collar
Map dataC15 symmetrized DEV collar
Sample
  • Complex: Scaffolding protein of Pseudomonas phage DEV
    • Protein or peptide: SGNH hydrolase-type esterase domain-containing protein
Keywordscomplex / STRUCTURAL PROTEIN / gp53
Function / homology: / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / phosphatidylcholine lysophospholipase activity / SGNH hydrolase-type esterase domain-containing protein
Function and homology information
Biological speciesPseudomonas phage vB_PaeP_DEV (virus) / Pseudomonas aeruginosa (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.7 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
DepositionJul 16, 2024-
Header (metadata) releaseOct 16, 2024-
Map releaseOct 16, 2024-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45776.png

Downloads & links

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Map

FileDownload / File: emd_45776.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationC15 symmetrized DEV collar
Projections & slices

Image control

Size
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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)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.12 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0018
Minimum - Maximum-0.017438434 - 0.03480356
Average (Standard dev.)0.00002187145 (±0.00056112587)
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_45776_msk_1.map
Projections & Slices
AxesZYX

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Half map: Half Map A

Fileemd_45776_half_map_1.map
AnnotationHalf Map A
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_45776_half_map_2.map
AnnotationHalf Map B
Projections & Slices
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Sample components

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Entire : Scaffolding protein of Pseudomonas phage DEV

EntireName: Scaffolding protein of Pseudomonas phage DEV
Components
  • Complex: Scaffolding protein of Pseudomonas phage DEV
    • Protein or peptide: SGNH hydrolase-type esterase domain-containing protein

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Supramolecule #1: Scaffolding protein of Pseudomonas phage DEV

SupramoleculeName: Scaffolding 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: SGNH hydrolase-type esterase domain-containing protein

MacromoleculeName: SGNH hydrolase-type esterase domain-containing protein
type: protein_or_peptide / ID: 1 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 118.10918 KDa
SequenceString: MTTKVIFTFH NPDGSPQANE KFTVRLTRPG MSDAEHCVVI PETYEMVTDA KGEFTMDLES STSAYRVTAI GDDDEYEDDP CSQYTFTFY VPDSADPVYV QELILMPPPT NLPWDEEAMN KITQAVVDAR EARDEAEAQA DRAEVQVDLA KAEVVKAQDE V VKAKAEVT ...String:
MTTKVIFTFH NPDGSPQANE KFTVRLTRPG MSDAEHCVVI PETYEMVTDA KGEFTMDLES STSAYRVTAI GDDDEYEDDP CSQYTFTFY VPDSADPVYV QELILMPPPT NLPWDEEAMN KITQAVVDAR EARDEAEAQA DRAEVQVDLA KAEVVKAQDE V VKAKAEVT KAQAEVTKAA QQVELAKVEV GKAEASAAAA KVSETNAANA AAGSAASATA ATNQANRAKT EADRSKSEAD RA RDLADAM AEKVEGGSLP PLVGMNETFT YEGTDPYRWT VSGPATAVSD GSVMRLTKTD GSGSRAFVRQ AVSFPDSHWI VYM RVKTQT GTAAQNRSAQ IRFIAADKKD CVVYFNINAN GLVEPNTIHM QGTEGGTRNA ATMFTGLSTE TWLDLAVKYD AVNR HIELF RRLDTGVWQK GGGRLMVDAI KPAFIEVSSM PVAPQNWWLD LDFISVCKPN LICYGDSIAA GQNEYGVTRG SNSYN NNRN WAGTWFGKVP LYATNRNNLV LVQGVEGRRT WQYLSQLSEI SNSGVKVVFM HASTNDVNDA SMTMEKRTSD TQAIID QLH AVGAQVVLFN SMQGTKAYND ASSTTVKLRD YTDQWWNTEL PKVNGLAQTL DIARLIAKDG YMDPALGASD GLHLTNA SA QKIADKLGQF FSNSSDTNGF ASLDSPAFTG IPTVPTQTPF LPFGKTIANT EYVVTFIQDW TQRYGYGDLT MYSRTGAQ L SGGGVRSGYY HVPAGAGNPL PSGLNTSLAF VDHKSYDTNK GWQLWNPAYT GRLFIRTTNS AGTWQTPVEL ATFTWLDDN NVTKPRTLKF MELPLFNPPG SPSLSGFVPI QDSADGGWRN LSATPTGVAL LSASSAGGAL SYLGGMPIAN HTLPSNSIDN AALNGFYSV PSGTAGLPLG MDTTNGHAGI TSVFDNVTKY QLLFPRTGGA GSYATSVFYR ARSNNGWESW VRLLASNQLE G SVTTEPLT TAIFQNNGNN NQNVGRSVRF ADGTQIVYAT IRLTYSAVDV LQYTYTYPMG FVAPPTITVQ PILGARADIN DM PYFAVTS PFTYNVGNGN ALVQIYRVAG YTAHSFASTS FINCAVVAVG RWK

UniProtKB: SGNH hydrolase-type esterase domain-containing 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 3200
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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