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- EMDB-4800: Cryo-EM structure of the anti-feeding prophage (AFP) baseplate in... -

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Basic information

Entry
Database: EMDB / ID: EMD-4800
TitleCryo-EM structure of the anti-feeding prophage (AFP) baseplate in extended state, 3-fold symmetrised
Map dataCryo-EM structure of the anti-feeding prophage (AFP) baseplate in extended state, 3-fold symmetrised. Scaling by factor of 2 is recommended for visualization
Sample
  • Complex: Cryo-EM structure of the anti-feeding prophage (AFP) baseplate in extended state, 3-fold symmetrised
    • Protein or peptide: Afp7
    • Protein or peptide: Afp8
Function / homologyContractile injection system tube protein, N-terminal domain / Contractile injection system tube protein / 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 / Afp8 / Afp7
Function and homology information
Biological speciesSerratia entomophila (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsDesfosses A
CitationJournal: Nat Microbiol / Year: 2019
Title: Atomic structures of an entire contractile injection system in both the extended and contracted states.
Authors: Ambroise Desfosses / Hariprasad Venugopal / Tapan Joshi / Jan Felix / Matthew Jessop / Hyengseop Jeong / Jaekyung Hyun / J Bernard Heymann / Mark R H Hurst / Irina Gutsche / Alok K Mitra /
Abstract: Contractile injection systems are sophisticated multiprotein nanomachines that puncture target cell membranes. Although the number of atomic-resolution insights into contractile bacteriophage tails, ...Contractile injection systems are sophisticated multiprotein nanomachines that puncture target cell membranes. Although the number of atomic-resolution insights into contractile bacteriophage tails, bacterial type six secretion systems and R-pyocins is rapidly increasing, structural information on the contraction of bacterial phage-like protein-translocation structures directed towards eukaryotic hosts is scarce. Here, we characterize the antifeeding prophage AFP from Serratia entomophila by cryo-electron microscopy. We present the high-resolution structure of the entire AFP particle in the extended state, trace 11 protein chains de novo from the apical cap to the needle tip, describe localization variants and perform specific structural comparisons with related systems. We analyse inter-subunit interactions and highlight their universal conservation within contractile injection systems while revealing the specificities of AFP. Furthermore, we provide the structure of the AFP sheath-baseplate complex in a contracted state. This study reveals atomic details of interaction networks that accompany and define the contraction mechanism of toxin-delivery tailocins, offering a comprehensive framework for understanding their mode of action and for their possible adaptation as biocontrol agents.
History
DepositionApr 10, 2019-
Header (metadata) releaseApr 24, 2019-
Map releaseApr 24, 2019-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6rbk
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6rbk
  • 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_4800.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of the anti-feeding prophage (AFP) baseplate in extended state, 3-fold symmetrised. Scaling by factor of 2 is recommended for visualization
Voxel sizeX=Y=Z: 1.35 Å
Density
Contour LevelBy AUTHOR: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.22256626 - 0.35270968
Average (Standard dev.)0.0010621262 (±0.011780059)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-180-180-180
Dimensions360360360
Spacing360360360
CellA=B=C: 486.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z486.000486.000486.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-180-180-180
NC/NR/NS360360360
D min/max/mean-0.2230.3530.001

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Supplemental data

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Half map: None

Fileemd_4800_half_map_1.map
AnnotationNone
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: None

Fileemd_4800_half_map_2.map
AnnotationNone
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire : Cryo-EM structure of the anti-feeding prophage (AFP) baseplate in...

EntireName: Cryo-EM structure of the anti-feeding prophage (AFP) baseplate in extended state, 3-fold symmetrised
Components
  • Complex: Cryo-EM structure of the anti-feeding prophage (AFP) baseplate in extended state, 3-fold symmetrised
    • Protein or peptide: Afp7
    • Protein or peptide: Afp8

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Supramolecule #1: Cryo-EM structure of the anti-feeding prophage (AFP) baseplate in...

SupramoleculeName: Cryo-EM structure of the anti-feeding prophage (AFP) baseplate in extended state, 3-fold symmetrised
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: A scaling by a factor of 2 is recommended for visualisation
Source (natural)Organism: Serratia entomophila (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: Afp7

MacromoleculeName: Afp7 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Serratia entomophila (bacteria)
Molecular weightTheoretical: 25.259434 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSLLERGLSK LTLNAWKDRE GKIPAGSMSA MYNPETIQLD YQTRFDTEDT INTASQSNRY VISEPVGLNL TLLFDSQMPG NTTPIETQL AMLKSLCAVD AATGSPYFLR ITWGKMRWEN KGWFAGRARD LSVTYTLFDR DATPLRATVQ LSLVADESFV I QQSLKTQS ...String:
MSLLERGLSK LTLNAWKDRE GKIPAGSMSA MYNPETIQLD YQTRFDTEDT INTASQSNRY VISEPVGLNL TLLFDSQMPG NTTPIETQL AMLKSLCAVD AATGSPYFLR ITWGKMRWEN KGWFAGRARD LSVTYTLFDR DATPLRATVQ LSLVADESFV I QQSLKTQS APDRALVSVP DLASLPLLAL SAGGVLASSV DYLSLAWDND LDNLDDFQTG DFLRATKGEE V

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Macromolecule #2: Afp8

MacromoleculeName: Afp8 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Serratia entomophila (bacteria)
Molecular weightTheoretical: 58.091715 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSHITLDIAG QRSTLGIRRL RVQQLINEIP LAQLELHIPT DNHGAADNAV QHEVSRFTLG VRVGIAQDNK PLFDGYLVQK KMQLKGKEW SVRLEARHAL QKLTFLPHSR VFRQQDDSTV MKGLLQSAGV KLTQESAAQL SSKHDQLLQF RLSDWQFIRS R LLSTNCWL ...String:
MSHITLDIAG QRSTLGIRRL RVQQLINEIP LAQLELHIPT DNHGAADNAV QHEVSRFTLG VRVGIAQDNK PLFDGYLVQK KMQLKGKEW SVRLEARHAL QKLTFLPHSR VFRQQDDSTV MKGLLQSAGV KLTQESAAQL SSKHDQLLQF RLSDWQFIRS R LLSTNCWL LPDAASDTVV IRPLSDAAMA SRTLARDSHD YTLYEINLNF DNRFTPDSLS LQGWDIAAQR LTAAQKSPAG AF RPWKPAG KVGQSSAGRQ DYALAFSMLP EATLQTLSNS WLNYQQMTGV QGHIVLAGTR DFAPGESITL SGFGAGLDGT AML SGVNQQ FDTQYGWRSE LVIGLPASML EPAPPVRSLH IGTVAGFTAD PQHLDRIAIH LPALNLPDSL IFARLSKPWA SHAS GFCFY PEPGDEVVVG FIDSDPRYPM ILGALHNPKN TAPFPPDEKN NRKGLIVSQA DQTQALMIDT EEKTLRLMAG DNTLT LTGE GNLTMSTPNA LQLQADTLGL QADSNLSIAG KQQVEITSAK INMKK

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 20.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 46991
CTF correctionSoftware - Name: CTFFIND
Startup modelType of model: OTHER / Details: Previous 20A map of AFP (Heymann et al., 2013)
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 46991
FSC plot (resolution estimation)

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