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- EMDB-53140: Cryo-EM structure of the PlPVC1 fiber in extended state -

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Basic information

Entry
Database: EMDB / ID: EMD-53140
TitleCryo-EM structure of the PlPVC1 fiber in extended state
Map dataCryo-EM structure of the PlPVC fiber in extended state
Sample
  • Complex: Cryo-EM structure of PlPVC fiber and interaction between PlPVC baseplate and PlPVC fiber in extended state
    • Protein or peptide: Tail fiber protein
    • Protein or peptide: Baseplate protein J-like domain-containing protein
Keywordscontractile injection system / VIRUS LIKE PARTICLE
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.0 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_53140.png

Downloads & links

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Map

FileDownload / File: emd_53140.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of the PlPVC fiber in extended state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.5 Å/pix.
x 560 pix.
= 840. Å		1.5 Å/pix.
x 560 pix.
= 840. Å		1.5 Å/pix.
x 560 pix.
= 840. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.5 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.1634562 - 2.1153908
Average (Standard dev.)-0.00040091126 (±0.043742847)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 840.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53140_msk_1.map
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 fiber in extended state

Fileemd_53140_half_map_1.map
AnnotationCryo-EM structure of the PlPVC fiber 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 fiber in extended state

Fileemd_53140_half_map_2.map
AnnotationCryo-EM structure of the PlPVC fiber 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 : Cryo-EM structure of PlPVC fiber and interaction between PlPVC ba...

EntireName: Cryo-EM structure of PlPVC fiber and interaction between PlPVC baseplate and PlPVC fiber in extended state
Components
  • Complex: Cryo-EM structure of PlPVC fiber and interaction between PlPVC baseplate and PlPVC fiber in extended state
    • Protein or peptide: Tail fiber protein
    • Protein or peptide: Baseplate protein J-like domain-containing protein

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Supramolecule #1: Cryo-EM structure of PlPVC fiber and interaction between PlPVC ba...

SupramoleculeName: Cryo-EM structure of PlPVC fiber and interaction between PlPVC baseplate and PlPVC fiber in extended state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Photorhabdus luminescens (bacteria)

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Macromolecule #1: Tail fiber protein

MacromoleculeName: Tail fiber protein / type: protein_or_peptide / ID: 1 / Details: Pvc13 - tail fiber protein / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus luminescens (bacteria)
Molecular weightTheoretical: 45.745395 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEKEHNPYNS ETNLETNLEN TNIKSTGPSA DDLKSRFKEG SIPLQTDYAD LIDIADIGRR AVGKAPDQTN NPNSALELDD NSGLKIKIN STGGLKADQD GLSVKLKDKS LLADPNGLAV NAGRGVKINN DQLEVDGYHG IEIVNEGVKV KASNGINVNS D GVSVKAGN ...String:
MEKEHNPYNS ETNLETNLEN TNIKSTGPSA DDLKSRFKEG SIPLQTDYAD LIDIADIGRR AVGKAPDQTN NPNSALELDD NSGLKIKIN STGGLKADQD GLSVKLKDKS LLADPNGLAV NAGRGVKINN DQLEVDGYHG IEIVNEGVKV KASNGINVNS D GVSVKAGN GISVSGKGVE VKAKDKGSIS VDSDGIAVKY WDGGGIVATD NSGLYLKLEG GNTNNGWSGV SGLSLSKNGV KV KAGNGIT VDSSGVSIDP KTVLPKGMIV MFSGSSAPTG WAFCDGNHGT PDLRSRFVMC SETISETGKS SNKASGSGNG KNY SRNTTS TTVSVSVTVK NTTLTESQIP YHYHIGGMGY WTNKGMKYGT EYYSEYASYI RNDLDSVMQS ANGARYAYTS PSGG GQGHN HPATASSPSH DHSVNVIPPY YLLAFIMKL

UniProtKB: Tail fiber protein

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Macromolecule #2: Baseplate protein J-like domain-containing protein

MacromoleculeName: Baseplate protein J-like domain-containing protein / type: protein_or_peptide / ID: 2 / Details: Pvc12 - baseplate protein / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus luminescens (bacteria)
Molecular weightTheoretical: 110.905555 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNNQDALFPI VKDDIAFETL LTQAKTVIEQ QSGQLWSNTE ENDPGITLLE ACCYGASDLA YRHSLPLRDL LTPEKQEQTL GDGIFPQEF GPQQMLTCGP ITAEDYRRAL LDLHSSDTDN ETSEDYFFFN DVRLICEPES ERYKYWYNKE SREYSFIQEQ E QEQEQLQL ...String:
MNNQDALFPI VKDDIAFETL LTQAKTVIEQ QSGQLWSNTE ENDPGITLLE ACCYGASDLA YRHSLPLRDL LTPEKQEQTL GDGIFPQEF GPQQMLTCGP ITAEDYRRAL LDLHSSDTDN ETSEDYFFFN DVRLICEPES ERYKYWYNKE SREYSFIQEQ E QEQEQLQL TLRGNYWLYL LPNRETEDDK TLTQKRLNDF LKDNRNLGES VSKIIWLQPV DFLLQLDIEL DDDVSDLADI FA QVYMTTE QMVLTSPLRY STQAMIEQGY SNEEIFEGPY LHHGWIPELS AAKDYTKPTE LKLSHLANRL LAIPGVQNIT RLA LGKHDE NISPLADDSW SWTIAQGYYP RLWGNDPLDL ISSSASPLTI TAKGGVKITV SKQDIENKII AEPLIETQPE LLNW GKHRK VLDYYPVSNK LPACYGLQTY AETQQQVHLH QFMLPFEQML ANGCAELALL PKLLAFKQRG NTVYGTQWPF KANTV GQQV HQEIMPDLIK QLNNDSQINS DDGIHSQNYT KELSILNYLL EYFGTHRAAR PLTLDSLDFL STQRGYLAQQ PELTYQ RNN IRIDKVSALQ KRIAARLGLG GKCFEETSKL DELPFYLIEH RQLLPVKPDT KFDKEQKPDK LKIKSVPNSK NQQLIIT QN GTTGQLLYGQ VINLIIKEKE NQDIRVKFIL RGQMITDITG ESFILDTRNS TALARSLIDV QNAYNDGNLY WCNSPVWM E DMDYQLVYAS EIYQTGTENE RWITSSPQSP FPAMIEENDE ITLKYVITPS GPKKSDHELK ANVIKFDRIQ GKILIKLTQ DSQDNFPLAA DAWRYRWYFS SEKYALADRF SFVVSMVINS QLVKNDDVDP YKLESWAKTE ILAEFPAHLS MIIHWLSPED FKDFVSTYQ RWQNNGAPLG DEAYHVLETL TLGRLPSAAT GIGNMRIATA QQRIGVVGES GKEWNTEVII SNQLVYVPYT G ENLNKR

UniProtKB: Baseplate protein J-like domain-containing protein

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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: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.0 Å / Resolution method: FSC 0.143 CUT-OFF
Details: 71148 particles from a symmetry expanded set Resolution range 4-6 angstrom
Number images used: 71148
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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