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- PDB-9qgm: Cryo-EM structure of the PlPVC1 central spike, 3-fold symmetrized... -

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Basic information

Entry
Database: PDB / ID: 9qgm
TitleCryo-EM structure of the PlPVC1 central spike, 3-fold symmetrized (C3), in extended state
Components(Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17) x 2
KeywordsVIRUS LIKE PARTICLE / Contractile injection system
Function / homologyProtein of unknown function DUF5908 / Family of unknown function (DUF5908) / Phage tail baseplate hub (GPD) / Gp5/Type VI secretion system Vgr protein, OB-fold domain / Type VI secretion system/phage-baseplate injector OB domain / Vgr protein, OB-fold domain superfamily / Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17 / Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17
Function and homology information
Biological speciesPhotorhabdus luminescens (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.82 Å
AuthorsMarin-Arraiza, L. / Taylor, N.M.I.
Funding support Denmark, Spain, 5items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF14CC0001 Denmark
Novo Nordisk FoundationNNF17OC0031006 Denmark
Novo Nordisk FoundationNNF23OC0081528 Denmark
LundbeckfondenR434-2023-289 Denmark
La Caixa FoundationLCF/BQ/EU21/11890147 Spain
CitationJournal: Nat Commun / Year: 2025
Title: Structural characterization of an extracellular contractile injection system from Photorhabdus luminescens in extended and contracted states
Authors: Marin-Arraiza, L. / Roa-Eguiara, A. / Pape, T. / Sofos, N. / Hendriks, I.A. / Lund Nielsen, M. / Steiner-Rebrova, E.M. / Taylor, N.M.I.
History
DepositionMar 14, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
8A: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17
8B: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17
8C: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17
6A: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17
6B: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17
6C: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17


Theoretical massNumber of molelcules
Total (without water)196,6276
Polymers196,6276
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 Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17


Mass: 58964.836 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Pvc8 - central spike protein / Source: (gene. exp.) Photorhabdus luminescens (bacteria) / Gene: plu1723 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7N647
#2: Protein Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17


Mass: 6577.516 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Pvc6 - plug protein / Source: (gene. exp.) Photorhabdus luminescens (bacteria) / Gene: plu1725 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7N645
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: PlPVC spike needle (C3) in extended state / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Photorhabdus luminescens (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 41 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21_5207: / Category: model refinement
CTF correctionDetails: Patch CTF Estimation in cryoSPARC, fit local CTF to micrograph, including tilted, bent, deformed samples
Type: NONE
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 2.82 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 47836 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00313188
ELECTRON MICROSCOPYf_angle_d0.517883
ELECTRON MICROSCOPYf_dihedral_angle_d4.4541725
ELECTRON MICROSCOPYf_chiral_restr0.0452073
ELECTRON MICROSCOPYf_plane_restr0.0032331

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