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- EMDB-4876: Cryo-EM structure of the anti-feeding prophage (AFP) baseplate in... -

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Basic information

Entry
Database: EMDB / ID: EMD-4876
TitleCryo-EM structure of the anti-feeding prophage (AFP) baseplate in contracted state
Map dataNone
Sample
  • Complex: Cryo-EM structure of the anti-feeding prophage (AFP) baseplate in contracted state
    • Protein or peptide: Afp2
    • Protein or peptide: Afp3
    • Protein or peptide: Afp4
KeywordsAnti-feeding prophage / secretion system / AFP / contractile / VIRUS LIKE PARTICLE / baseplate / contracted
Function / homology: / 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 / Afp4 / Afp3 / Afp2
Function and homology information
Biological speciesSerratia entomophila (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.4 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 16, 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: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6rgl
  • Surface level: 0.085
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6rgl
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4876.png

Downloads & links

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Map

FileDownload / File: emd_4876.map.gz / Format: CCP4 / Size: 129.7 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.)
1.4 Å/pix.
x 324 pix.
= 452.628 Å		1.4 Å/pix.
x 324 pix.
= 452.628 Å		1.4 Å/pix.
x 324 pix.
= 452.628 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.397 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.085 / Movie #1: 0.03
Minimum - Maximum-0.1524302 - 0.32065934
Average (Standard dev.)0.0016152955 (±0.019030623)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-162-162-162
Dimensions324324324
Spacing324324324
CellA=B=C: 452.628 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3971.3971.397
M x/y/z324324324
origin x/y/z0.0000.0000.000
length x/y/z452.628452.628452.628
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-162-162-162
NC/NR/NS324324324
D min/max/mean-0.1520.3210.002

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Supplemental data

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Supplemental map: emd 4876 half map 1.map

Fileemd_4876_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Supplemental map: emd 4876 half map 2.map

Fileemd_4876_half_map_2.map
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) baseplate in...

EntireName: Cryo-EM structure of the anti-feeding prophage (AFP) baseplate in contracted state
Components
  • Complex: Cryo-EM structure of the anti-feeding prophage (AFP) baseplate in contracted state
    • Protein or peptide: Afp2
    • Protein or peptide: Afp3
    • Protein or peptide: Afp4

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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 contracted state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Serratia entomophila (bacteria)

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Macromolecule #1: Afp2

MacromoleculeName: Afp2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / 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 #2: Afp3

MacromoleculeName: Afp3 / type: protein_or_peptide / ID: 2 / 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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Macromolecule #3: Afp4

MacromoleculeName: Afp4 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Serratia entomophila (bacteria)
Molecular weightTheoretical: 45.565633 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTMVLPGVSY NETLLTQASN DDPVTMPLFI GYTPPDTAIP VTVMQPVSVG SLTQANSLFG QRGTLAYSLR HFFENGGLQC YVLPLGPGK GEPAARLQEL IAALQTPQML ETLLADDKTG LVLVPELSEL NEVSSTSLSA EGVDAAEVDA DALWYQGWQV L LTLCRQAP ...String:
MTMVLPGVSY NETLLTQASN DDPVTMPLFI GYTPPDTAIP VTVMQPVSVG SLTQANSLFG QRGTLAYSLR HFFENGGLQC YVLPLGPGK GEPAARLQEL IAALQTPQML ETLLADDKTG LVLVPELSEL NEVSSTSLSA EGVDAAEVDA DALWYQGWQV L LTLCRQAP QRFALLELPE DPASAVTLTQ QSFSADQCQR GAAWWPRLET SYQDESSAPV VLSPLPAVAA AIQRSAHDNG VW KAPANIA LAKTRRPTQS ILTSQALLDN QGVSCNLIRS FVGKGVRLWG CRTLLNEENT AWRYIQIRLL VSSVEHYLSK LAR AYLFEP NTAPTWMKLK GQVWTWLRQQ WLAGAFFGTV EDEAFSLSIG LDETMTEDDI RHGKMILQVR LALLAPAEFI AISL TLDLR DGTASAQTGG QS

UniProtKB: Afp4

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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
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 27.0 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

Particle selectionNumber selected: 30378
Startup modelType of model: OTHER / Details: Previous 20A map of AFP (Heymann et al., 2013)
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 5.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Details: Very large anisotropy in resolution / Number images used: 3816
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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