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- EMDB-4784: Cryo-EM structure of the anti-feeding prophage cap (AFP tube term... -

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Basic information

Entry
Database: EMDB / ID: EMD-4784
TitleCryo-EM structure of the anti-feeding prophage cap (AFP tube terminating cap)
Map dataCryo-EM structure of the anti-feeding prophage cap (AFP tube terminating cap)
Sample
  • Complex: Cryo-EM structure of the anti-feeding prophage cap (AFP tube terminating cap)
    • Protein or peptide: Afp1
    • Protein or peptide: Afp2
    • Protein or peptide: Afp3
    • Protein or peptide: Afp16
KeywordsAnti-feeding prophage / secretion system / AFP / contractile / VIRUS LIKE PARTICLE / cap / tube terminating protein
Function / homology
Function and homology information


structural molecule activity
Similarity search - Function
Pvc16, N-terminal / Pvc16 N-terminal domain / 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
Afp16 / Afp3 / Afp2 / Afp1
Similarity search - Component
Biological speciesSerratia entomophila (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 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 7, 2019-
Header (metadata) releaseApr 17, 2019-
Map releaseApr 17, 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: 0.07
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6rap
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6rap
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4784.png

Downloads & links

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Map

FileDownload / File: emd_4784.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of the anti-feeding prophage cap (AFP tube terminating cap)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 320 pix.
= 432. Å		1.35 Å/pix.
x 320 pix.
= 432. Å		1.35 Å/pix.
x 320 pix.
= 432. 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: 0.07 / Movie #1: 0.07
Minimum - Maximum-0.23562716 - 0.38158214
Average (Standard dev.)0.00069911976 (±0.011597042)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-160-160-160
Dimensions320320320
Spacing320320320
CellA=B=C: 432.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z432.000432.000432.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-160-160-160
NC/NR/NS320320320
D min/max/mean-0.2360.3820.001

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Supplemental data

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Half map: None

Fileemd_4784_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_4784_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 cap (AFP tube term...

EntireName: Cryo-EM structure of the anti-feeding prophage cap (AFP tube terminating cap)
Components
  • Complex: Cryo-EM structure of the anti-feeding prophage cap (AFP tube terminating cap)
    • Protein or peptide: Afp1
    • Protein or peptide: Afp2
    • Protein or peptide: Afp3
    • Protein or peptide: Afp16

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Supramolecule #1: Cryo-EM structure of the anti-feeding prophage cap (AFP tube term...

SupramoleculeName: Cryo-EM structure of the anti-feeding prophage cap (AFP tube terminating cap)
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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Macromolecule #4: Afp16

MacromoleculeName: Afp16 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Serratia entomophila (bacteria)
Molecular weightTheoretical: 32.250184 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSMSNYQTLV DVNNAMNKML RAYVNEAVAI RFDLPDVDAT QADAAISVFL YDIHEDLQLR TAESRGFNAG AGRLLPGWVN VKCNYLITY WESTGPATDA DNPDSQPDNQ AIQVMSQVLA ALINNRQLAD IPGAYTQVMP PKENLNSLGN FWQSLGNRPR L SLNYCVTV ...String:
MSMSNYQTLV DVNNAMNKML RAYVNEAVAI RFDLPDVDAT QADAAISVFL YDIHEDLQLR TAESRGFNAG AGRLLPGWVN VKCNYLITY WESTGPATDA DNPDSQPDNQ AIQVMSQVLA ALINNRQLAD IPGAYTQVMP PKENLNSLGN FWQSLGNRPR L SLNYCVTV PISLSDKGEE MTPVKSLSTT VEPKAPLSPL VITDALREQL RVALGGDYDA CLAMTHVNLD SSPVANSDGS AA EIRVSLR VYGMTPTEYL APMNTVFNEW EKSEAAAVTP DGYRVYINAV DKTDLTGI

UniProtKB: Afp16

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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: GATAN K2 SUMMIT (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

Particle selectionNumber selected: 30858
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: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 23797
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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