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- EMDB-9764: Cryo-EM Structure of an Extracellular Contractile Injection Syste... -

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Basic information

Entry
Database: EMDB / ID: EMD-9764
TitleCryo-EM Structure of an Extracellular Contractile Injection System, PVC baseplate in extended state (reconstructed with C3 symmetry)
Map data
Sample
  • Complex: baseplate in extended state
    • Protein or peptide: Pvc8
Keywordsassembly / Photorhabdus asymbiotica / PVC / contractile injection system / bacteriophage-like / PROTEIN TRANSPORT
Function / homologyPhage tail baseplate hub (GPD) / Gp5/Type VI secretion system Vgr protein, OB-fold domain / Type VI secretion system/phage-baseplate injector OB domain / Vgr protein, OB-fold domain superfamily / Gp5/Type VI secretion system Vgr protein OB-fold domain-containing protein
Function and homology information
Biological speciesPhotorhabdus asymbiotica (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 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 24, 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: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6j0m
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6j0m
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9764.png

Downloads & links

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Map

FileDownload / File: emd_9764.map.gz / Format: CCP4 / Size: 103 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 300 pix.
= 336.3 Å		1.12 Å/pix.
x 300 pix.
= 336.3 Å		1.12 Å/pix.
x 300 pix.
= 336.3 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: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.12706022 - 0.20124087
Average (Standard dev.)0.00063644344 (±0.013196937)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 336.30002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1211.1211.121
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z336.300336.300336.300
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.1270.2010.001

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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 state
Components
  • Complex: baseplate in extended state
    • Protein or peptide: Pvc8

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Supramolecule #1: baseplate in extended state

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

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Macromolecule #1: Pvc8

MacromoleculeName: Pvc8 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus asymbiotica (bacteria)
Molecular weightTheoretical: 60.029703 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSHQLKIIAD GKALSLLAAV DVDTCYRVNS IPSATLKLSV PDRPLSSFSQ TDVQTELAHC QVGKTLRLEL IDGSKKWVLF NGLITRKAL RIKNKQLLLT LVVKHRLQLM VDTQHSQLFK DKSEKAILST LLNQTGINAR FGKIAALDQK HEQMVQFRCS D WHFLLCRL ...String:
MSHQLKIIAD GKALSLLAAV DVDTCYRVNS IPSATLKLSV PDRPLSSFSQ TDVQTELAHC QVGKTLRLEL IDGSKKWVLF NGLITRKAL RIKNKQLLLT LVVKHRLQLM VDTQHSQLFK DKSEKAILST LLNQTGINAR FGKIAALDQK HEQMVQFRCS D WHFLLCRL SATGAWLLPA IEDVQFVQPD ALKSNSAYTL KSRGDENKDI VVKDAYWQFD NQINPALLEV SGWDISKQQV QS GGRYGKI ALGKAALSPD GLASLNKTGW DICYSSPLTT QESGYLAQGL LLNQRISGVT GEFLLKGDGR YQLGDNIQLT GFG SQLDGT ASITEVRHRL NRRIDWETTV SIGLQHEYLP ILPDAPELHI ATVAKYQQDS AVLNRIPIIL PVLNRPNEFL WARL GKPYA SHESGFCFYP EPGDEVIIGF FENDPRYPVI LGAMHNPKNK APFEPTQDNR EKVLIVKKGE AQQQLVIDGK EKMIR INAG ENQIMLQQDK DISLSTKKEL TLKAQTMNAT MDKSLAMSGK NSVEIKGAKI NLTQ

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7.4
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

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 63000
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: PROJECTION MATCHING

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