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- PDB-9qgn: Cryo-EM structure of the PlPVC1 cap, 6-fold symmetrized (C6), in ... -

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Basic information

Entry
Database: PDB / ID: 9qgn
TitleCryo-EM structure of the PlPVC1 cap, 6-fold symmetrized (C6), in extended state
Components
  • DUF4255 domain-containing protein
  • Phage tail protein
  • Phage tail sheath family protein
KeywordsVIRUS LIKE PARTICLE / Contractile injection system
Function / homology
Function and homology information


structural molecule activity
Similarity search - Function
Pvc16, N-terminal / Pvc16 N-terminal domain / Conserved hypothetical protein CHP02241 / Bacteriophage T4, Gp19, tail tube / T4-like virus tail tube protein gp19 / : / Tail sheath protein, C-terminal domain / Phage tail sheath C-terminal domain
Similarity search - Domain/homology
Phage tail sheath family protein / Phage tail protein / DUF4255 domain-containing protein
Similarity search - Component
Biological speciesPhotorhabdus luminescens (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.46 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
A: DUF4255 domain-containing protein
B: DUF4255 domain-containing protein
C: DUF4255 domain-containing protein
D: DUF4255 domain-containing protein
E: DUF4255 domain-containing protein
F: DUF4255 domain-containing protein
1A: Phage tail protein
1B: Phage tail protein
1C: Phage tail protein
1D: Phage tail protein
1E: Phage tail protein
1F: Phage tail protein
1G: Phage tail protein
1H: Phage tail protein
1I: Phage tail protein
1J: Phage tail protein
1K: Phage tail protein
1L: Phage tail protein
2A: 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


Theoretical massNumber of molelcules
Total (without water)632,75124
Polymers632,75124
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
DUF4255 domain-containing protein


Mass: 33299.473 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Pvc16 - cap protein / Source: (gene. exp.) Photorhabdus luminescens (bacteria) / Gene: GPY51_18165 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6L9JUZ8
#2: Protein
Phage tail protein


Mass: 16574.574 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Details: Pvc1 - tube protein / Source: (gene. exp.) Photorhabdus luminescens (bacteria) / Gene: GPY51_18090 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6L9JSR5
#3: Protein
Phage tail sheath family protein


Mass: 39009.828 Da / Num. of mol.: 6
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
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 cap (C6) 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: C6 (6 fold cyclic)
3D reconstructionResolution: 2.46 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 57353 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00244358
ELECTRON MICROSCOPYf_angle_d0.41960552
ELECTRON MICROSCOPYf_dihedral_angle_d3.6695932
ELECTRON MICROSCOPYf_chiral_restr0.0447044
ELECTRON MICROSCOPYf_plane_restr0.0037854

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