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Yorodumi- EMDB-4803: Cryo-EM structure of the anti-feeding prophage (AFP) helical shea... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4803 | |||||||||
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Title | Cryo-EM structure of the anti-feeding prophage (AFP) helical sheath in contracted state | |||||||||
Map data | None | |||||||||
Sample |
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Keywords | Anti-feeding prophage / secretion system / AFP / contractile / VIRUS LIKE PARTICLE / sheath / 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 / Afp3 / Afp2 Function and homology information | |||||||||
Biological species | Serratia entomophila (bacteria) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Desfosses A | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4803.map.gz | 34.4 MB | EMDB map data format | |
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Header (meta data) | emd-4803-v30.xml emd-4803.xml | 12.6 KB 12.6 KB | Display Display | EMDB header |
Images | emd_4803.png | 250.8 KB | ||
Filedesc metadata | emd-4803.cif.gz | 5.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4803 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4803 | HTTPS FTP |
-Validation report
Summary document | emd_4803_validation.pdf.gz | 694.1 KB | Display | EMDB validaton report |
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Full document | emd_4803_full_validation.pdf.gz | 693.7 KB | Display | |
Data in XML | emd_4803_validation.xml.gz | 6.3 KB | Display | |
Data in CIF | emd_4803_validation.cif.gz | 7.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4803 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4803 | HTTPS FTP |
-Related structure data
Related structure data | 6rc8MC 4782C 4783C 4784C 4800C 4801C 4802C 4859C 4871C 4876C 6raoC 6rapC 6rbkC 6rbnC 6rglC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_4803.map.gz / Format: CCP4 / Size: 46.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.397 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Cryo-EM structure of the anti-feeding prophage (AFP) helical shea...
Entire | Name: Cryo-EM structure of the anti-feeding prophage (AFP) helical sheath in contracted state |
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Components |
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-Supramolecule #1: Cryo-EM structure of the anti-feeding prophage (AFP) helical shea...
Supramolecule | Name: Cryo-EM structure of the anti-feeding prophage (AFP) helical sheath in contracted state type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Serratia entomophila (bacteria) |
-Macromolecule #1: Afp2
Macromolecule | Name: Afp2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Serratia entomophila (bacteria) |
Molecular weight | Theoretical: 38.784355 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: 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 |
-Macromolecule #2: Afp3
Macromolecule | Name: Afp3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Serratia entomophila (bacteria) |
Molecular weight | Theoretical: 48.777566 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 27.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 34.97 Å Applied symmetry - Helical parameters - Δ&Phi: 3.14 ° Applied symmetry - Helical parameters - Axial symmetry: C6 (6 fold cyclic) Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPRING / Number images used: 45567 |
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Segment selection | Number selected: 45567 / Software - Name: EMAN2 |
Startup model | Type of model: OTHER / Details: Previous 20A map of AFP (Heymann et al., 2013) |
Final angle assignment | Type: PROJECTION MATCHING |