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- EMDB-9760: Cryo-EM Structure of an Extracellular Contractile Injection Syste... -

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Basic information

Entry
Database: EMDB / ID: EMD-9760
TitleCryo-EM Structure of an Extracellular Contractile Injection System, PVC sheath-tube complex in extended state
Map data
Sample
  • Complex: sheath and tube in extended state
    • Protein or peptide: Pvc2
    • Protein or peptide: Pvc1
Keywordsassembly / Photorhabdus asymbiotica / PVC / contractile injection system / bacteriophage-like / PROTEIN TRANSPORT
Function / homology
Function and homology information


structural molecule activity
Similarity search - Function
Conserved hypothetical protein CHP02241 / Bacteriophage T4, Gp19, tail tube / T4-like virus tail tube protein gp19 / 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
Similarity search - Domain/homology
Phage tail sheath protein / Conserved hypothetical phage tail region protein
Similarity search - Component
Biological speciesPhotorhabdus asymbiotica (bacteria) / Photorhabdus asymbiotica subsp. asymbiotica (strain ATCC 43949 / 3105-77) (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsJiang F / Li N
CitationJournal: Cell / Year: 2019
Title: Cryo-EM Structure and Assembly of an Extracellular Contractile Injection System.
Authors: Feng Jiang / Ningning Li / Xia Wang / Jiaxuan Cheng / Yaoguang Huang / Yun Yang / Jianguo Yang / Bin Cai / Yi-Ping Wang / Qi Jin / Ning Gao /
Abstract: Contractile injection systems (CISs) are cell-puncturing nanodevices that share ancestry with contractile tail bacteriophages. Photorhabdus virulence cassette (PVC) represents one group of ...Contractile injection systems (CISs) are cell-puncturing nanodevices that share ancestry with contractile tail bacteriophages. Photorhabdus virulence cassette (PVC) represents one group of extracellular CISs that are present in both bacteria and archaea. Here, we report the cryo-EM structure of an intact PVC from P. asymbiotica. This over 10-MDa device resembles a simplified T4 phage tail, containing a hexagonal baseplate complex with six fibers and a capped 117-nanometer sheath-tube trunk. One distinct feature of the PVC is the presence of three variants for both tube and sheath proteins, indicating a functional specialization of them during evolution. The terminal hexameric cap docks onto the topmost layer of the inner tube and locks the outer sheath in pre-contraction state with six stretching arms. Our results on the PVC provide a framework for understanding the general mechanism of widespread CISs and pave the way for using them as delivery tools in biological or therapeutic applications.
History
DepositionDec 23, 2018-
Header (metadata) releaseApr 10, 2019-
Map releaseApr 10, 2019-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.13
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.13
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6j0b
  • Surface level: 0.13
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6j0b
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9760.png

Downloads & links

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Map

FileDownload / File: emd_9760.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 256 pix.
= 286.976 Å		1.12 Å/pix.
x 256 pix.
= 286.976 Å		1.12 Å/pix.
x 256 pix.
= 286.976 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.121 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13 / Movie #1: 0.13
Minimum - Maximum-0.61936927 - 1.1287512
Average (Standard dev.)0.0034258547 (±0.053775564)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 286.976 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1211.1211.121
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z286.976286.976286.976
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.6191.1290.003

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Supplemental data

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Sample components

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Entire : sheath and tube in extended state

EntireName: sheath and tube in extended state
Components
  • Complex: sheath and tube in extended state
    • Protein or peptide: Pvc2
    • Protein or peptide: Pvc1

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Supramolecule #1: sheath and tube in extended state

SupramoleculeName: sheath and tube in extended state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Photorhabdus asymbiotica (bacteria)

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Macromolecule #1: Pvc2

MacromoleculeName: Pvc2 / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus asymbiotica subsp. asymbiotica (strain ATCC 43949 / 3105-77) (bacteria)
Strain: ATCC 43949 / 3105-77
Molecular weightTheoretical: 39.374281 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTTVTSYPGV YIEELNSLAL SVSNSATAVP VFAVDEQNQY ISEDNAIRIN SWMDYLNLIG NFNNEDKLDV SVRAYFANGG GYCYLVKTT SLEKIIPTLD DVTLLVAAGE DIKTTVDVLC QPGKGLFAVF DGPETELTIN GAEEAKQAYT ATPFAAVYYP W LKADWANI ...String:
MTTVTSYPGV YIEELNSLAL SVSNSATAVP VFAVDEQNQY ISEDNAIRIN SWMDYLNLIG NFNNEDKLDV SVRAYFANGG GYCYLVKTT SLEKIIPTLD DVTLLVAAGE DIKTTVDVLC QPGKGLFAVF DGPETELTIN GAEEAKQAYT ATPFAAVYYP W LKADWANI DIPPSAVMAG VYASVDLSRG VWKAPANVAL KGGLEPKFLV TDELQGEYNT GRAINMIRNF SNTGTTVWGA RT LEDKDNW RYVPVRRLFN SVERDIKRAM SFAMFEPNNQ PTWERVRAAI SNYLYSLWQQ GGLAGSKEED AYFVQIGKGI TMT QEQIDA GQMIVKVGLA AVRPAEFIIL QFTQDVEQR

UniProtKB: Phage tail sheath protein

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Macromolecule #2: Pvc1

MacromoleculeName: Pvc1 / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus asymbiotica subsp. asymbiotica (strain ATCC 43949 / 3105-77) (bacteria)
Strain: ATCC 43949 / 3105-77
Molecular weightTheoretical: 16.532557 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSTSTSQIAV EYPIPVYRFI VSVGDEKIPF NSVSGLDISY DTIEYRDGVG NWFKMPGQSQ STNITLRKGV FPGKTELFDW INSIQLNQV EKKDITISLT NDAGTELLMT WNVSNAFPTS LTSPSFDATS NDIAVQEITL MADRVIMQAV

UniProtKB: Conserved hypothetical phage tail region protein

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R2/2 / Material: COPPER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 46.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 39.3 Å
Applied symmetry - Helical parameters - Δ&Phi: 19.9 °
Applied symmetry - Helical parameters - Axial symmetry: C6 (6 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 551000
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE

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