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Yorodumi- EMDB-4800: Cryo-EM structure of the anti-feeding prophage (AFP) baseplate in... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4800 | |||||||||
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Title | Cryo-EM structure of the anti-feeding prophage (AFP) baseplate in extended state, 3-fold symmetrised | |||||||||
Map data | Cryo-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 |
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Keywords | Anti-feeding prophage / secretion system / AFP / contractile / VIRUS LIKE PARTICLE / baseplate | |||||||||
Function / homology | Contractile 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 species | Serratia entomophila (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 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_4800.map.gz | 22.1 MB | EMDB map data format | |
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Header (meta data) | emd-4800-v30.xml emd-4800.xml | 16.1 KB 16.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4800_fsc.xml | 12.7 KB | Display | FSC data file |
Images | emd_4800.png | 112 KB | ||
Filedesc metadata | emd-4800.cif.gz | 6 KB | ||
Others | emd_4800_half_map_1.map.gz emd_4800_half_map_2.map.gz | 140.6 MB 140.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4800 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4800 | HTTPS FTP |
-Validation report
Summary document | emd_4800_validation.pdf.gz | 904.5 KB | Display | EMDB validaton report |
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Full document | emd_4800_full_validation.pdf.gz | 904 KB | Display | |
Data in XML | emd_4800_validation.xml.gz | 20.1 KB | Display | |
Data in CIF | emd_4800_validation.cif.gz | 26.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4800 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4800 | HTTPS FTP |
-Related structure data
Related structure data | 6rbkMC 4782C 4783C 4784C 4801C 4802C 4803C 4859C 4871C 4876C 6raoC 6rapC 6rbnC 6rc8C 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_4800.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-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 size | X=Y=Z: 1.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: None
File | emd_4800_half_map_1.map | ||||||||||||
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Annotation | None | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: None
File | emd_4800_half_map_2.map | ||||||||||||
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Annotation | None | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cryo-EM structure of the anti-feeding prophage (AFP) baseplate in...
Entire | Name: Cryo-EM structure of the anti-feeding prophage (AFP) baseplate in extended state, 3-fold symmetrised |
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Components |
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-Supramolecule #1: Cryo-EM structure of the anti-feeding prophage (AFP) baseplate in...
Supramolecule | Name: 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 |
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Source (natural) | Organism: Serratia entomophila (bacteria) |
-Macromolecule #1: Afp7
Macromolecule | Name: Afp7 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Serratia entomophila (bacteria) |
Molecular weight | Theoretical: 25.259434 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: 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 UniProtKB: Afp7 |
-Macromolecule #2: Afp8
Macromolecule | Name: Afp8 / 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: 58.091715 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: 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 UniProtKB: Afp8 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-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: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 20.0 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 |