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- EMDB-53139: Cryo-EM structure of the PlPVC1 cap, 6-fold symmetrized (C6), in ... -

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Basic information

Entry
Database: EMDB / ID: EMD-53139
TitleCryo-EM structure of the PlPVC1 cap, 6-fold symmetrized (C6), in extended state
Map dataCryo-EM structure of the PlPVC cap in extended state
Sample
  • Complex: PlPVC cap (C6) in extended state
    • Protein or peptide: DUF4255 domain-containing protein
    • Protein or peptide: Phage tail protein
    • Protein or peptide: Phage tail sheath family protein
KeywordsContractile injection system / VIRUS LIKE PARTICLE
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.46 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_53139.png

Downloads & links

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Map

FileDownload / File: emd_53139.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of the PlPVC cap in extended state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 560 pix.
= 672. Å		1.2 Å/pix.
x 560 pix.
= 672. Å		1.2 Å/pix.
x 560 pix.
= 672. 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: 0.35
Minimum - Maximum-0.57271016 - 1.4613732
Average (Standard dev.)-0.000006120524 (±0.045746196)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 672.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Cryo-EM structure of the PlPVC cap in extended state

Fileemd_53139_half_map_1.map
AnnotationCryo-EM structure of the PlPVC cap 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 cap in extended state

Fileemd_53139_half_map_2.map
AnnotationCryo-EM structure of the PlPVC cap 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 cap (C6) in extended state

EntireName: PlPVC cap (C6) in extended state
Components
  • Complex: PlPVC cap (C6) in extended state
    • Protein or peptide: DUF4255 domain-containing protein
    • Protein or peptide: Phage tail protein
    • Protein or peptide: Phage tail sheath family protein

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Supramolecule #1: PlPVC cap (C6) in extended state

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

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Macromolecule #1: DUF4255 domain-containing protein

MacromoleculeName: DUF4255 domain-containing protein / type: protein_or_peptide / ID: 1 / Details: Pvc16 - cap protein / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus luminescens (bacteria)
Molecular weightTheoretical: 33.299473 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTIIIASDNA IIEINQALNT ILSQYLNITG QNIDIRFDLP EINSIQSEPT VSVFLYEIHE DLQLRSAESR RYNPSTNTLL PGWVNINCN YLITYWDASK PSSDSSSPDS QPNNQAAQVM TRILNALINN RQLTGLPGAY TRIIPQQENL NSLGNFWQAL G NRPRLSLL ...String:
MTIIIASDNA IIEINQALNT ILSQYLNITG QNIDIRFDLP EINSIQSEPT VSVFLYEIHE DLQLRSAESR RYNPSTNTLL PGWVNINCN YLITYWDASK PSSDSSSPDS QPNNQAAQVM TRILNALINN RQLTGLPGAY TRIIPQQENL NSLGNFWQAL G NRPRLSLL YSITVPMKLK NIEDNVIPVS KISASVDQKP NLDNSQINQA LIDKLCVELG GTEDVRLALA KVNLTTKPDT EN NQNQENE SVIVEVSGIT SVTYLPQIKD TLTKWKSSQE AIVKINGVSI VVSKENADKL IGI

UniProtKB: DUF4255 domain-containing protein

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Macromolecule #2: Phage tail protein

MacromoleculeName: Phage tail protein / type: protein_or_peptide / ID: 2 / Details: Pvc1 - tube protein / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus luminescens (bacteria)
Molecular weightTheoretical: 16.574574 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAITPEQIAV EYPIPTYRFV VSVGDEQIPF NNVSGLDVHY DVIEYKDGIG NYYKMPGQRQ SINITLRKGV FPGDTKLFDW INSIQLNQV EKKDIAISLT NEAGTEILMT WNVANAFPTS FTSPSFDATS NEIAVQEIAL TADRVTIQAA

UniProtKB: Phage tail 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: Pvc2 - sheath protein / Number of copies: 6 / 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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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: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.46 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 57353
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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