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- EMDB-53138: Cryo-EM structure of the PlPVC1 central spike, 3-fold symmetrized... -

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Basic information

Entry
Database: EMDB / ID: EMD-53138
TitleCryo-EM structure of the PlPVC1 central spike, 3-fold symmetrized (C3), in extended state
Map dataCryo-EM structure of the PlPVC spike needle, 3-fold symmetrized (C3), in extended state
Sample
  • Complex: PlPVC spike needle (C3) in extended state
    • Protein or peptide: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17
    • Protein or peptide: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17
KeywordsContractile injection system / VIRUS LIKE PARTICLE
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.82 Å
AuthorsMarin-Arraiza L / Taylor NMI
Funding support Denmark, Spain, 5 items
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 IA / Lund Nielsen M / Steiner-Rebrova EM / Taylor NMI
History
DepositionMar 14, 2025-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53138.png

Downloads & links

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Map

FileDownload / File: emd_53138.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of the PlPVC spike needle, 3-fold symmetrized (C3), in extended state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 360 pix.
= 432. Å		1.2 Å/pix.
x 360 pix.
= 432. Å		1.2 Å/pix.
x 360 pix.
= 432. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.175
Minimum - Maximum-0.7204229 - 1.4789579
Average (Standard dev.)0.002771763 (±0.05920488)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 432.00003 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Cryo-EM structure of the PlPVC spike needle, 3-fold...

Fileemd_53138_half_map_1.map
AnnotationCryo-EM structure of the PlPVC spike needle, 3-fold symmetrized (C3), in extended state
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM structure of the PlPVC spike needle, 3-fold...

Fileemd_53138_half_map_2.map
AnnotationCryo-EM structure of the PlPVC spike needle, 3-fold symmetrized (C3), in extended state
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : PlPVC spike needle (C3) in extended state

EntireName: PlPVC spike needle (C3) in extended state
Components
  • Complex: PlPVC spike needle (C3) in extended state
    • Protein or peptide: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17
    • Protein or peptide: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17

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Supramolecule #1: PlPVC spike needle (C3) in extended state

SupramoleculeName: PlPVC spike needle (C3) in extended state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Photorhabdus luminescens (bacteria)

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Macromolecule #1: Photorhabdus luminescens subsp. laumondii TTO1 complete genome se...

MacromoleculeName: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17
type: protein_or_peptide / ID: 1 / Details: Pvc8 - central spike protein / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus luminescens (bacteria)
Molecular weightTheoretical: 58.964836 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKIPEITIKI SGKTLNQFTA INLTVNHYIN GIPSVNITLG IAGDANYIFD AKAQAELANC RPNNELIVQI QKTILFKGII VRQALKFKG QDSLMTLTAK HPLQKLTDGL HSQLFSKQSD EAIIKKLFSQ AGIQTTIKQA PQLKTVHEQM VQFRCNDWTF L KSRLIATN ...String:
MKIPEITIKI SGKTLNQFTA INLTVNHYIN GIPSVNITLG IAGDANYIFD AKAQAELANC RPNNELIVQI QKTILFKGII VRQALKFKG QDSLMTLTAK HPLQKLTDGL HSQLFSKQSD EAIIKKLFSQ AGIQTTIKQA PQLKTVHEQM VQFRCNDWTF L KSRLIATN TWLLPGNEVV TLITPKALNQ STVHTIHQST NDQDIVLFEA NLQWDNQRSP KTVSVQSWDI TQQKLSQTIQ VK NSGLGSN KLAVDSITTL TNQDWQWVFN YPLDNEQAKY LAQGIMDNLR SDNVSGSFEV EGDSCYQPGD VLALNGFGQG MDG QGIITG VSQIINQRQG WRTRLTLGMP PDAEQAVPPV KELHVGIVEK YQPDSQSLGR IPVKIPALNL TNSVLFARLG KPYA SHESG FCFYPEPGDE VIIGFFECDP RFPVILGSMH NPKNKAPVEP SEKNPMKTLV IKQGDHQQAL VFNNQDKTVA LNSGK NTLS LQQDKDITLN SANNLITNAQ EIKIQAEKSL SASGKSGVDI KGAKINLTQ

UniProtKB: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17

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Macromolecule #2: Photorhabdus luminescens subsp. laumondii TTO1 complete genome se...

MacromoleculeName: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17
type: protein_or_peptide / ID: 2 / Details: Pvc6 - plug protein / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus luminescens (bacteria)
Molecular weightTheoretical: 6.577516 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MTVEIKELII QAKVTDSASD LLSPRTLAQE ALDNARLIEM VKQEVLDALR EAGGRYELN

UniProtKB: Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 6/17

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 41.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Patch CTF Estimation in cryoSPARC, fit local CTF to micrograph, including tilted, bent, deformed samples
Type: NONE
Startup modelType of model: INSILICO MODEL / In silico model: Ab-initio model was generated in cryoSPARC
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.82 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 47836
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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