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- PDB-9bgm: Pseudomonas phage DEV neck and tail (portal, head-to-tail and tai... -

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Basic information

Entry
Database: PDB / ID: 9bgm
TitlePseudomonas phage DEV neck and tail (portal, head-to-tail and tail tube proteins)
Components
  • gp75 tail tube
  • gp80 portal protein
  • gp83 head-to-tail
KeywordsVIRAL PROTEIN / portal / tail hub / tail tube / complex / STRUCTURAL PROTEIN / gp75 / gp83 / gp80
Function / homologyTail protein / N4 gp54-like protein / Portal protein
Function and homology information
Biological speciesPseudomonas phage vB_PaeP_DEV (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsIglesias, S.M. / Hou, C.-F.D. / Li, F. / Cingolani, G.
Funding support United States, 2items
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, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
a: gp75 tail tube
b: gp83 head-to-tail
c: gp80 portal protein
A: gp75 tail tube
B: gp83 head-to-tail
C: gp80 portal protein
D: gp75 tail tube
E: gp83 head-to-tail
F: gp80 portal protein
G: gp75 tail tube
H: gp83 head-to-tail
I: gp80 portal protein
J: gp75 tail tube
K: gp83 head-to-tail
L: gp80 portal protein
M: gp75 tail tube
N: gp83 head-to-tail
O: gp80 portal protein
P: gp75 tail tube
Q: gp83 head-to-tail
R: gp80 portal protein
S: gp75 tail tube
T: gp83 head-to-tail
V: gp80 portal protein
W: gp75 tail tube
X: gp83 head-to-tail
Y: gp80 portal protein
Z: gp75 tail tube
d: gp83 head-to-tail
e: gp80 portal protein
f: gp75 tail tube
g: gp83 head-to-tail
h: gp80 portal protein
i: gp75 tail tube
j: gp83 head-to-tail
k: gp80 portal protein


Theoretical massNumber of molelcules
Total (without water)1,738,50736
Polymers1,738,50736
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
gp75 tail tube


Mass: 35267.215 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage vB_PaeP_DEV (virus) / References: UniProt: A0A2K8I3N9
#2: Protein
gp83 head-to-tail


Mass: 27868.934 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage vB_PaeP_DEV (virus) / References: UniProt: A0A2K8I0C0
#3: Protein
gp80 portal protein


Mass: 81739.453 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage vB_PaeP_DEV (virus) / References: UniProt: A0A2K8IC08
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Portal to tail complex of Pseudomonas phage DEV / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Pseudomonas phage vB_PaeP_DEV (virus)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C12 (12 fold cyclic)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3228 / Symmetry type: POINT

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