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- EMDB-53141: Cryo-EM structure of the PlPVC1 sheath, 6-fold symmetrized (C6), ... -

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Basic information

Entry
Database: EMDB / ID: EMD-53141
TitleCryo-EM structure of the PlPVC1 sheath, 6-fold symmetrized (C6), in contracted state
Map dataCryo-EM structure of the PlPVC sheath, 6-fold symmetrized, in contracted state
Sample
  • Complex: PlPVC sheath (C6) in contracted state
    • Protein or peptide: Phage tail sheath family protein
    • Protein or peptide: Phage tail sheath family protein
    • Protein or peptide: Phage tail sheath family protein
Keywordscontractile injection system / VIRUS LIKE PARTICLE
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 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_53141.png

Downloads & links

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Map

FileDownload / File: emd_53141.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of the PlPVC sheath, 6-fold symmetrized, in contracted state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 700 pix.
= 840. Å		1.2 Å/pix.
x 700 pix.
= 840. Å		1.2 Å/pix.
x 700 pix.
= 840. 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: 0.3
Minimum - Maximum-0.6941862 - 1.6247001
Average (Standard dev.)-0.00036443063 (±0.04129703)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions700700700
Spacing700700700
CellA=B=C: 840.00006 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53141_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 sheath, 6-fold symmetrized,...

Fileemd_53141_half_map_1.map
AnnotationCryo-EM structure of the PlPVC sheath, 6-fold symmetrized, in contracted 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 sheath, 6-fold symmetrized,...

Fileemd_53141_half_map_2.map
AnnotationCryo-EM structure of the PlPVC sheath, 6-fold symmetrized, in contracted 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 sheath (C6) in contracted state

EntireName: PlPVC sheath (C6) in contracted state
Components
  • Complex: PlPVC sheath (C6) in contracted state
    • Protein or peptide: Phage tail sheath family protein
    • Protein or peptide: Phage tail sheath family protein
    • Protein or peptide: Phage tail sheath family protein

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Supramolecule #1: PlPVC sheath (C6) in contracted state

SupramoleculeName: PlPVC sheath (C6) in contracted state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Photorhabdus luminescens (bacteria)

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Macromolecule #1: Phage tail sheath family protein

MacromoleculeName: Phage tail sheath family protein / type: protein_or_peptide / ID: 1 / Details: Pvc2 - sheath protein / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus luminescens (bacteria)
Molecular weightTheoretical: 39.009828 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTTITTYPGV YIEEDASLSL SVSSSATAVP VFAVAGDNPL ISGKPYIRIS NWLEYLTLKN EQFDPANTLD ISLRAYFING GGYCYLVQT TDLEKQVPKL DDVTLLVAAG ENITTAVSTL CKPGKGLFAI FDGPTTELKS DGTSNSDYDP NPFAAVYYPW L TADWTTTI ...String:
MTTITTYPGV YIEEDASLSL SVSSSATAVP VFAVAGDNPL ISGKPYIRIS NWLEYLTLKN EQFDPANTLD ISLRAYFING GGYCYLVQT TDLEKQVPKL DDVTLLVAAG ENITTAVSTL CKPGKGLFAI FDGPTTELKS DGTSNSDYDP NPFAAVYYPW L TADWTTTI DIPPSAAIAG VYCSVDSTRG VWKAPANVPI QGGLQPKYPV TDDLQAQYNQ GKALNMIRTF PKSGTLVWGA RT LEDNDNW RYIPVRRLFN SAERDIKNAM SFAVFEPNSQ PTWERVRSAV NNYLYSLWQQ GGLAGNKPDD AYFVQIGKDI TMT DDDIKQ GKMIIKIGMA AVRPAEFIIL QFTQNTAQ

UniProtKB: Phage tail sheath family protein

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Macromolecule #2: Phage tail sheath family protein

MacromoleculeName: Phage tail sheath family protein / type: protein_or_peptide / ID: 2 / Details: Pvc3 - sheath protein / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus luminescens (bacteria)
Molecular weightTheoretical: 51.330875 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPTIPTYPGV YIEEDASLNL SVNQGNTAIP VFIGLFSPKN TNLKSQVTRV NSWLDFTNLF NAGCIAPITI KSTKRASMPA PTLLENVKG DTAVVATPGI SVDADNKDPT YTYKVIVNYT TSSDALKLYF QNGGGPCYIL PQLDRLTQGF LDSIPELIKQ A LEITLIVC ...String:
MPTIPTYPGV YIEEDASLNL SVNQGNTAIP VFIGLFSPKN TNLKSQVTRV NSWLDFTNLF NAGCIAPITI KSTKRASMPA PTLLENVKG DTAVVATPGI SVDADNKDPT YTYKVIVNYT TSSDALKLYF QNGGGPCYIL PQLDRLTQGF LDSIPELIKQ A LEITLIVC PEWDSGYQSK IYNSLTSSLL NAGYFLIADN QDKNTALITE VASQTATYYP AVKVSQLIQA EDSQIAVSGY ED AKTKSDE VKNLAQLKEK NPTVYQQAVQ KIQAIQDEIA ANGNIIPVSA VMAGIYCATD ASRGVWKAPA NIVLSGISDV AER LTDDEQ GEMNSKGINA IRYFSHKGFV VWGARTLQND DNWRYIPVRR LFNAAERDIK QAMQSVVFEP NSQPTWERVK SAID NYLYS LWQQGALAGN KPQEAYFVQI GKDVTMSDDD IKQGKMIVKV GMAAVRPAEF IILQFSQQVA Q

UniProtKB: Phage tail sheath family protein

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Macromolecule #3: Phage tail sheath family protein

MacromoleculeName: Phage tail sheath family protein / type: protein_or_peptide / ID: 3 / Details: Pvc4 - sheath initiator protein / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus luminescens (bacteria)
Molecular weightTheoretical: 44.076059 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEITQPSVTI TENLIFPKQN DSFIGIPVFI GYTSSPVDKT AIKLHSLADF ARSFPESGLM YYSVRHFFEN GGQQAYVLSL GTEQQLSDF SSLITALQQA WLAQTIAAEN DITLIITPDV IRFDQTEISD TQRDLWLQLW QSVLNLCKSR RGIMGLLDAP D DPTLAAKC ...String:
MEITQPSVTI TENLIFPKQN DSFIGIPVFI GYTSSPVDKT AIKLHSLADF ARSFPESGLM YYSVRHFFEN GGQQAYVLSL GTEQQLSDF SSLITALQQA WLAQTIAAEN DITLIITPDV IRFDQTEISD TQRDLWLQLW QSVLNLCKSR RGIMGLLDAP D DPTLAAKC LQQFSSADRQ WGVVYWPLLK SAYQDNTQNP IVLSPTAAVA AVIQRNDNQQ GVWTAPANIA LSKVISPVRA YI EANALFN PDGTSLNLVR SFPGKGIRIW GCRTLENTHD SPWSYIQTRR LVSYIEAYMT QLGRAFVFEP NNAITWMKFK GQA HNWLRQ LWLKGGLRGT QEDQAFEVLL GVDESMREAD LRAGKMIIKI RLAVLIPAEF IELNLTFDTR TGTIPS

UniProtKB: Phage tail sheath family 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: 7.5
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: 40.0 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: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 30862
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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