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- PDB-9cod: C15 symmetrized DEV collar -

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Basic information

Entry
Database: PDB / ID: 9cod
TitleC15 symmetrized DEV collar
ComponentsSGNH hydrolase-type esterase domain-containing protein
KeywordsSTRUCTURAL PROTEIN / complex / 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 aeruginosa (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.7 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
DepositionJul 16, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release
Revision 1.0Oct 16, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 16, 2024Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Oct 16, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 16, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 16, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 16, 2024Data content type: Mask / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Oct 16, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1May 21, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 21, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SGNH hydrolase-type esterase domain-containing protein
B: SGNH hydrolase-type esterase domain-containing protein
C: SGNH hydrolase-type esterase domain-containing protein
D: SGNH hydrolase-type esterase domain-containing protein
E: SGNH hydrolase-type esterase domain-containing protein
F: SGNH hydrolase-type esterase domain-containing protein
G: SGNH hydrolase-type esterase domain-containing protein
H: SGNH hydrolase-type esterase domain-containing protein
I: SGNH hydrolase-type esterase domain-containing protein
J: SGNH hydrolase-type esterase domain-containing protein
K: SGNH hydrolase-type esterase domain-containing protein
L: SGNH hydrolase-type esterase domain-containing protein
M: SGNH hydrolase-type esterase domain-containing protein
N: SGNH hydrolase-type esterase domain-containing protein
O: SGNH hydrolase-type esterase domain-containing protein


Theoretical massNumber of molelcules
Total (without water)1,771,63815
Polymers1,771,63815
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
SGNH hydrolase-type esterase domain-containing protein


Mass: 118109.180 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A2K8I2V0
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: Scaffolding protein of Pseudomonas phage DEV / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Pseudomonas phage vB_PaeP_DEV (virus)
Source (recombinant)Organism: Pseudomonas aeruginosa (bacteria)
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

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3200 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00412705
ELECTRON MICROSCOPYf_angle_d1.02317340
ELECTRON MICROSCOPYf_dihedral_angle_d6.2791695
ELECTRON MICROSCOPYf_chiral_restr0.0441950
ELECTRON MICROSCOPYf_plane_restr0.0042295

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