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- EMDB-9765: Cryo-EM Structure of an Extracellular Contractile Injection Syste... -

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Basic information

Entry
Database: EMDB / ID: EMD-9765
TitleCryo-EM Structure of an Extracellular Contractile Injection System, baseplate in extended state, refined in C6 symmetry
Map data
Samplebaseplate in extended stateTripod (photography):
Pvc9 / Pvc11 / Pvc12 / Pvc4 / Pvc7 / Pvc2 / Pvc5 / Pvc1 / Pvc3
Function / homology
Function and homology information


virus tail / structural molecule activity
IraD/Gp25-like / Bacteriophage T4, Gp19, tail tube / Conserved hypothetical protein CHP02241 / Tail sheath protein, C-terminal domain / Tail sheath protein, subtilisin-like domain / in:ipr040471:
Phage_sheath_1C domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Phage baseplate assembly protein / Uncharacterized protein / Conserved hypothetical phage tail region protein
Biological speciesPhotorhabdus asymbiotica (bacteria) / Photorhabdus asymbiotica subsp. asymbiotica (strain ATCC 43949 / 3105-77) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsJiang F / Li N / Wang X / Cheng J / Huang Y / Yang Y / Yang J / Cai B / Wang Y / Jin Q / Gao 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.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionDec 25, 2018-
Header (metadata) releaseApr 10, 2019-
Map releaseApr 10, 2019-
UpdateApr 17, 2019-
Current statusApr 17, 2019Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.12
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.12
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6j0n
  • Surface level: 0.12
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6j0n
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_9765.map.gz / Format: CCP4 / Size: 178 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 360 pix.
= 403.56 Å
1.12 Å/pix.
x 360 pix.
= 403.56 Å
1.12 Å/pix.
x 360 pix.
= 403.56 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
Contour LevelBy AUTHOR: 0.12 / Movie #1: 0.12
Minimum - Maximum-0.51128185 - 0.80977404
Average (Standard dev.)0.0033832553 (±0.032561515)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 403.56003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1211.1211.121
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z403.560403.560403.560
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.5110.8100.003

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Supplemental data

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Sample components

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Entire baseplate in extended state

EntireName: baseplate in extended stateTripod (photography) / Number of components: 10

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Component #1: protein, baseplate in extended state

ProteinName: baseplate in extended stateTripod (photography) / Recombinant expression: No
SourceSpecies: Photorhabdus asymbiotica (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: protein, Pvc9

ProteinName: Pvc9 / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 15.990021 kDa
SourceSpecies: Photorhabdus asymbiotica subsp. asymbiotica (strain ATCC 43949 / 3105-77) (bacteria)
Strain: ATCC 43949 / 3105-77
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: protein, Pvc11

ProteinName: Pvc11 / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 82.807523 kDa
SourceSpecies: Photorhabdus asymbiotica subsp. asymbiotica (strain ATCC 43949 / 3105-77) (bacteria)
Strain: ATCC 43949 / 3105-77
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #4: protein, Pvc12

ProteinName: Pvc12 / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 107.761789 kDa
SourceSpecies: Photorhabdus asymbiotica subsp. asymbiotica (strain ATCC 43949 / 3105-77) (bacteria)
Strain: ATCC 43949 / 3105-77
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #5: protein, Pvc4

ProteinName: Pvc4 / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 45.866652 kDa
SourceSpecies: Photorhabdus asymbiotica subsp. asymbiotica (strain ATCC 43949 / 3105-77) (bacteria)
Strain: ATCC 43949 / 3105-77
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #6: protein, Pvc7

ProteinName: Pvc7 / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 25.336664 kDa
SourceSpecies: Photorhabdus asymbiotica subsp. asymbiotica (strain ATCC 43949 / 3105-77) (bacteria)
Strain: ATCC 43949 / 3105-77
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #7: protein, Pvc2

ProteinName: Pvc2 / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 39.374281 kDa
SourceSpecies: Photorhabdus asymbiotica subsp. asymbiotica (strain ATCC 43949 / 3105-77) (bacteria)
Strain: ATCC 43949 / 3105-77
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #8: protein, Pvc5

ProteinName: Pvc5 / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 17.506895 kDa
SourceSpecies: Photorhabdus asymbiotica subsp. asymbiotica (strain ATCC 43949 / 3105-77) (bacteria)
Strain: ATCC 43949 / 3105-77
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #9: protein, Pvc1

ProteinName: Pvc1 / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 16.532557 kDa
SourceSpecies: Photorhabdus asymbiotica subsp. asymbiotica (strain ATCC 43949 / 3105-77) (bacteria)
Strain: ATCC 43949 / 3105-77
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #10: protein, Pvc3

ProteinName: Pvc3 / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 48.794949 kDa
SourceSpecies: Photorhabdus asymbiotica subsp. asymbiotica (strain ATCC 43949 / 3105-77) (bacteria)
Strain: ATCC 43949 / 3105-77
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 46.4 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C6 (6 fold cyclic) / Number of projections: 63000
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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