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- EMDB-4802: Cryo-EM structure of the anti-feeding prophage (AFP) helical shea... -

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Basic information

Entry
Database: EMDB / ID: EMD-4802
TitleCryo-EM structure of the anti-feeding prophage (AFP) helical sheath-tube complex in extended state
Map dataNone
Sample
  • Complex: Cryo-EM structure of the anti-feeding prophage (AFP) helical sheath-tube complex in extended state
    • Protein or peptide: Afp1
    • Protein or peptide: Afp2
    • Protein or peptide: Afp3
KeywordsAnti-feeding prophage / secretion system / AFP / contractile / VIRUS LIKE PARTICLE / sheath / tube
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
Biological speciesSerratia entomophila (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 2.8 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 11, 2019-
Header (metadata) releaseApr 24, 2019-
Map releaseApr 24, 2019-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / 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-6rbn
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6rbn
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4802.png

Downloads & links

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Map

FileDownload / File: emd_4802.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 360 pix.
= 486. Å		1.35 Å/pix.
x 360 pix.
= 486. Å		1.35 Å/pix.
x 360 pix.
= 486. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.05
Minimum - Maximum-0.12793036 - 0.2058465
Average (Standard dev.)0.00038390022 (±0.007163424)
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-0.1280.2060.000

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Supplemental data

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Half map: None

Fileemd_4802_half_map_1.map
AnnotationNone
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: None

Fileemd_4802_half_map_2.map
AnnotationNone
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of the anti-feeding prophage (AFP) helical shea...

EntireName: Cryo-EM structure of the anti-feeding prophage (AFP) helical sheath-tube complex in extended state
Components
  • Complex: Cryo-EM structure of the anti-feeding prophage (AFP) helical sheath-tube complex in extended state
    • Protein or peptide: Afp1
    • Protein or peptide: Afp2
    • Protein or peptide: Afp3

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

SupramoleculeName: Cryo-EM structure of the anti-feeding prophage (AFP) helical sheath-tube complex in extended state
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)

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Macromolecule #1: Afp1

MacromoleculeName: Afp1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Serratia entomophila (bacteria)
Molecular weightTheoretical: 16.449449 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAITADDIAV QYPIPTYRFI VTLGDEQVPF TSASGLDINF DTIEYRDGTG NWFKMPGQRQ APNITLSKGV FPGKNAMYEW INAIQLNQV EKKDIMISLT NEAGTEVLVS WNVSNAFPTS LTSPSFDATS NEIAVQQITL MADRVTIQTA

UniProtKB: Afp1

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Macromolecule #2: Afp2

MacromoleculeName: Afp2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Serratia entomophila (bacteria)
Molecular weightTheoretical: 38.784355 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTVTTTYPGV YLSEDAVSSF SVNSAATAVP LFAYDSENTN TINKPIQVFR NWAEFTVEYP TPLEDAFYTS LSLWFMHGGG KCYLVNEAN IADAVAQYDD ITLIVAAGTD TTTYTAFTTV VGQGYRIFGL FDGPKEKIAG TAKPDEVMEE YPTSPFGAVF Y PWGTLASG ...String:
MTVTTTYPGV YLSEDAVSSF SVNSAATAVP LFAYDSENTN TINKPIQVFR NWAEFTVEYP TPLEDAFYTS LSLWFMHGGG KCYLVNEAN IADAVAQYDD ITLIVAAGTD TTTYTAFTTV VGQGYRIFGL FDGPKEKIAG TAKPDEVMEE YPTSPFGAVF Y PWGTLASG AAVPPSAIAA ASITQTDRTR GVWKAPANQA VNGVTPAFAV SDDFQGKYNQ GKALNMIRTF SGQGTVVWGA RT LEDSDNW RYIPVRRLFN AVERDIQKSL NKLVFEPNSQ PTWQRVKAAV DSYLHSLWQQ GALAGNTPAD AWFVQVGKDL TMT QEEINQ GKMIIKIGLA AVRPAEFIIL QFSQDIAQ

UniProtKB: Afp2

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Macromolecule #3: Afp3

MacromoleculeName: Afp3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Serratia entomophila (bacteria)
Molecular weightTheoretical: 48.777566 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MATVTSVPGV YIEEDASPAM SVSASATAVP LFVARFTPLK PELAGVITRI GSWLDYTILF DSNVPSSARV TVSSTAVEPS PEFDALETA SSKATTTYTY QIDDTEVVDP TASVALRLYF QNGGGPCYLY PLEKADDNGP LAALPDLIDE VGEITLLASP D PDETYRTA ...String:
MATVTSVPGV YIEEDASPAM SVSASATAVP LFVARFTPLK PELAGVITRI GSWLDYTILF DSNVPSSARV TVSSTAVEPS PEFDALETA SSKATTTYTY QIDDTEVVDP TASVALRLYF QNGGGPCYLY PLEKADDNGP LAALPDLIDE VGEITLLASP D PDETYRTA VYGALAASLD QHKGYFLLAD SVNGDAPSAV GGSAQVAVYY PNVEVPHTRK LDDAEVAIDG YLDDEGKAVT TL AALRVVN TEFAGEIAQS LSGDLSAPLS LPPSALIAGV YGKTDGERGV WKAPANVVLN GVSDVSVRVT NEQQAELNPK GIN VIRHFS DRGLVVWGSR TQKDDDDWRY IPVRRLFDAA ERDIKKALQP MVFEPNSQLT WKRVQTAIDN YLYRLWQQGA LAGN KAEEA YFVRVGKGIT MTQDEINQGK MIIQVGMAAV RPAEFIILKF TQDMSQ

UniProtKB: Afp3

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

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

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 78.6436 Å
Applied symmetry - Helical parameters - Δ&Phi: 40.2722 °
Applied symmetry - Helical parameters - Axial symmetry: C6 (6 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 123368
Segment selectionNumber selected: 123368 / Software - Name: EMAN2
Startup modelType of model: OTHER / Details: Previous 20A map of AFP (Heymann et al., 2013)
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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