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- PDB-9qgp: Cryo-EM structure of the PlPVC1 sheath, 6-fold symmetrized (C6), ... -

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Basic information

Entry
Database: PDB / ID: 9qgp
TitleCryo-EM structure of the PlPVC1 sheath, 6-fold symmetrized (C6), in contracted state
Components(Phage tail sheath family protein) x 3
KeywordsVIRUS LIKE PARTICLE / contractile injection system
Function / homology: / Tail sheath protein, subtilisin-like domain / Phage tail sheath protein subtilisin-like domain / Tail sheath protein, C-terminal domain / Phage tail sheath C-terminal domain / Phage tail sheath family protein / Phage tail sheath family protein / Phage tail sheath family protein
Function and homology information
Biological speciesPhotorhabdus luminescens (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 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

Downloads & links

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Assembly

Deposited unit
2A: Phage tail sheath family protein
3A: Phage tail sheath family protein
4A: Phage tail sheath family protein
4B: Phage tail sheath family protein
4C: Phage tail sheath family protein
4D: Phage tail sheath family protein
4E: Phage tail sheath family protein
4F: Phage tail sheath family protein
2B: Phage tail sheath family protein
2C: Phage tail sheath family protein
2D: Phage tail sheath family protein
2E: Phage tail sheath family protein
2F: Phage tail sheath family protein
3B: Phage tail sheath family protein
3C: Phage tail sheath family protein
3D: Phage tail sheath family protein
3E: Phage tail sheath family protein
3F: Phage tail sheath family protein
2G: Phage tail sheath family protein
2H: Phage tail sheath family protein
2I: Phage tail sheath family protein
2J: Phage tail sheath family protein
2K: Phage tail sheath family protein
2L: Phage tail sheath family protein


Theoretical massNumber of molelcules
Total (without water)1,040,56024
Polymers1,040,56024
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
Phage tail sheath family protein


Mass: 39009.828 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Details: Pvc2 - sheath protein / Source: (gene. exp.) Photorhabdus luminescens (bacteria) / Gene: GPY51_18095 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6L9JN00
#2: Protein
Phage tail sheath family protein


Mass: 51330.875 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Pvc3 - sheath protein / Source: (gene. exp.) Photorhabdus luminescens (bacteria) / Gene: GPY51_18100 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6L9JMV2
#3: Protein
Phage tail sheath family protein


Mass: 44076.059 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Pvc4 - sheath initiator protein / Source: (gene. exp.) Photorhabdus luminescens (bacteria) / Gene: GPY51_18105 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6L9JN29
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 sheath (C6) in contracted 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: 7.5
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: 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: 40 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: C6 (6 fold cyclic)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30862 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00269144
ELECTRON MICROSCOPYf_angle_d0.4694308
ELECTRON MICROSCOPYf_dihedral_angle_d4.0519326
ELECTRON MICROSCOPYf_chiral_restr0.04210638
ELECTRON MICROSCOPYf_plane_restr0.00312186

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