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- PDB-9qgo: Interaction between PlPVC1 baseplate and fiber in extended state -

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Basic information

Entry
Database: PDB / ID: 9qgo
TitleInteraction between PlPVC1 baseplate and fiber in extended state
Components
  • Baseplate protein J-like domain-containing protein
  • Tail fiber protein
KeywordsVIRUS LIKE PARTICLE / contractile injection system
Function / homologyPhage tail collar domain / Phage Tail Collar Domain / Attachment protein shaft domain superfamily / virion attachment to host cell / Tail fiber protein / Baseplate protein J-like domain-containing protein
Function and homology information
Biological speciesPhotorhabdus luminescens (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6 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: Tail fiber protein
B: Tail fiber protein
C: Tail fiber protein
a: Baseplate protein J-like domain-containing protein
b: Baseplate protein J-like domain-containing protein
c: Baseplate protein J-like domain-containing protein


Theoretical massNumber of molelcules
Total (without water)469,9536
Polymers469,9536
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 Tail fiber protein


Mass: 45745.395 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Pvc13 - tail fiber protein / Source: (gene. exp.) Photorhabdus luminescens (bacteria) / Gene: GPY51_18150 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6L9JMW1
#2: Protein Baseplate protein J-like domain-containing protein


Mass: 110905.555 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Pvc12 - baseplate protein / Source: (gene. exp.) Photorhabdus luminescens (bacteria) / Gene: GPY51_18145 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6L9JN06
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: Cryo-EM structure of PlPVC fiber and interaction between PlPVC baseplate and PlPVC fiber 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: 1.21rc1_5109: / Category: model refinement
CTF correctionDetails: Patch CTF Estimation in cryoSPARC, fit local CTF to micrograph, including tilted, bent, deformed samples
Type: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 71148
Details: 71148 particles from a symmetry expanded set Resolution range 4-6 angstrom
Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0041520
ELECTRON MICROSCOPYf_angle_d0.8522054
ELECTRON MICROSCOPYf_dihedral_angle_d4.573202
ELECTRON MICROSCOPYf_chiral_restr0.044244
ELECTRON MICROSCOPYf_plane_restr0.005264

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