[English] 日本語
Yorodumi- EMDB-9764: Cryo-EM Structure of an Extracellular Contractile Injection Syste... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9764 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM Structure of an Extracellular Contractile Injection System, PVC baseplate in extended state (reconstructed with C3 symmetry) | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Keywords | assembly / Photorhabdus asymbiotica / PVC / contractile injection system / bacteriophage-like / PROTEIN TRANSPORT | |||||||||
Function / homology | 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 / Phage_base_V domain-containing protein Function and homology information | |||||||||
Biological species | Photorhabdus asymbiotica (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Jiang F / Li N | |||||||||
Citation | Journal: Cell / Year: 2019 Title: Cryo-EM Structure and Assembly of an Extracellular Contractile Injection System. Authors: Feng Jiang / Ningning Li / Xia Wang / Jiaxuan Cheng / Yaoguang Huang / Yun Yang / Jianguo Yang / Bin Cai / Yi-Ping Wang / Qi Jin / Ning Gao / Abstract: Contractile injection systems (CISs) are cell-puncturing nanodevices that share ancestry with contractile tail bacteriophages. Photorhabdus virulence cassette (PVC) represents one group of ...Contractile injection systems (CISs) are cell-puncturing nanodevices that share ancestry with contractile tail bacteriophages. Photorhabdus virulence cassette (PVC) represents one group of extracellular CISs that are present in both bacteria and archaea. Here, we report the cryo-EM structure of an intact PVC from P. asymbiotica. This over 10-MDa device resembles a simplified T4 phage tail, containing a hexagonal baseplate complex with six fibers and a capped 117-nanometer sheath-tube trunk. One distinct feature of the PVC is the presence of three variants for both tube and sheath proteins, indicating a functional specialization of them during evolution. The terminal hexameric cap docks onto the topmost layer of the inner tube and locks the outer sheath in pre-contraction state with six stretching arms. Our results on the PVC provide a framework for understanding the general mechanism of widespread CISs and pave the way for using them as delivery tools in biological or therapeutic applications. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_9764.map.gz | 95.9 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-9764-v30.xml emd-9764.xml | 9.6 KB 9.6 KB | Display Display | EMDB header |
Images | emd_9764.png | 172.2 KB | ||
Filedesc metadata | emd-9764.cif.gz | 5.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9764 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9764 | HTTPS FTP |
-Related structure data
Related structure data | 6j0mMC 9760C 9761C 9762C 9763C 9765C 6j0bC 6j0cC 6j0fC 6j0nC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_9764.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.121 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : baseplate in extended state
Entire | Name: baseplate in extended state |
---|---|
Components |
|
-Supramolecule #1: baseplate in extended state
Supramolecule | Name: baseplate in extended state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: Photorhabdus asymbiotica (bacteria) |
-Macromolecule #1: Pvc8
Macromolecule | Name: Pvc8 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Photorhabdus asymbiotica (bacteria) |
Molecular weight | Theoretical: 60.029703 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSHQLKIIAD GKALSLLAAV DVDTCYRVNS IPSATLKLSV PDRPLSSFSQ TDVQTELAHC QVGKTLRLEL IDGSKKWVLF NGLITRKAL RIKNKQLLLT LVVKHRLQLM VDTQHSQLFK DKSEKAILST LLNQTGINAR FGKIAALDQK HEQMVQFRCS D WHFLLCRL ...String: MSHQLKIIAD GKALSLLAAV DVDTCYRVNS IPSATLKLSV PDRPLSSFSQ TDVQTELAHC QVGKTLRLEL IDGSKKWVLF NGLITRKAL RIKNKQLLLT LVVKHRLQLM VDTQHSQLFK DKSEKAILST LLNQTGINAR FGKIAALDQK HEQMVQFRCS D WHFLLCRL SATGAWLLPA IEDVQFVQPD ALKSNSAYTL KSRGDENKDI VVKDAYWQFD NQINPALLEV SGWDISKQQV QS GGRYGKI ALGKAALSPD GLASLNKTGW DICYSSPLTT QESGYLAQGL LLNQRISGVT GEFLLKGDGR YQLGDNIQLT GFG SQLDGT ASITEVRHRL NRRIDWETTV SIGLQHEYLP ILPDAPELHI ATVAKYQQDS AVLNRIPIIL PVLNRPNEFL WARL GKPYA SHESGFCFYP EPGDEVIIGF FENDPRYPVI LGAMHNPKNK APFEPTQDNR EKVLIVKKGE AQQQLVIDGK EKMIR INAG ENQIMLQQDK DISLSTKKEL TLKAQTMNAT MDKSLAMSGK NSVEIKGAKI NLTQ |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | helical array |
-Sample preparation
Buffer | pH: 7.4 |
---|---|
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 46.4 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
---|---|
Final reconstruction | Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 63000 |
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: PROJECTION MATCHING |