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Yorodumi- PDB-7oko: Structure of the outer-membrane core complex (outer ring) from a ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7oko | ||||||
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Title | Structure of the outer-membrane core complex (outer ring) from a conjugative type IV secretion system | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / Type IV secretion system / F plasmid / outer-membrane core complex / conjugation | ||||||
Function / homology | Pilus assembly TraK / Type-F conjugative transfer system secretin TraK / TraK protein / Type IV conjugative transfer system protein TraV / Type IV conjugative transfer system lipoprotein (TraV) / Prokaryotic membrane lipoprotein lipid attachment site profile. / Type-F conjugative transfer system secretin TraK / Type IV conjugative transfer system lipoprotein TraV Function and homology information | ||||||
Biological species | Salmonella enterica (bacteria) Salmonella enterica subsp. salamae serovar 58:l z13 z28:z6 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||
Authors | Amin, H. / Ilangovan, A. / Costa, T.R.D. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nat Commun / Year: 2021 Title: Architecture of the outer-membrane core complex from a conjugative type IV secretion system. Authors: Himani Amin / Aravindan Ilangovan / Tiago R D Costa / Abstract: Conjugation is one of the most important processes that bacteria utilize to spread antibiotic resistance genes among bacterial populations. Interbacterial DNA transfer requires a large double ...Conjugation is one of the most important processes that bacteria utilize to spread antibiotic resistance genes among bacterial populations. Interbacterial DNA transfer requires a large double membrane-spanning nanomachine called the type 4 secretion system (T4SS) made up of the inner-membrane complex (IMC), the outer-membrane core complex (OMCC) and the conjugative pilus. The iconic F plasmid-encoded T4SS has been central in understanding conjugation for several decades, however atomic details of its structure are not known. Here, we report the structure of a complete conjugative OMCC encoded by the pED208 plasmid from E. coli, solved by cryo-electron microscopy at 3.3 Å resolution. This 2.1 MDa complex has a unique arrangement with two radial concentric rings, each having a different symmetry eventually contributing to remarkable differences in protein stoichiometry and flexibility in comparison to other OMCCs. Our structure suggests that F-OMCC is a highly dynamic complex, with implications for pilus extension and retraction during conjugation. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7oko.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7oko.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7oko.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7oko_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7oko_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7oko_validation.xml.gz | 165.9 KB | Display | |
Data in CIF | 7oko_validation.cif.gz | 260.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ok/7oko ftp://data.pdbj.org/pub/pdb/validation_reports/ok/7oko | HTTPS FTP |
-Related structure data
Related structure data | 12963MC 7oknC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 20928.650 Da / Num. of mol.: 26 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica (bacteria) / Gene: traV, GND40_003952 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A753A8N9 #2: Protein/peptide | Mass: 1128.233 Da / Num. of mol.: 13 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica (bacteria) / Production host: Escherichia coli (E. coli) #3: Protein | Mass: 23312.551 Da / Num. of mol.: 26 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. salamae serovar 58:l,z13,z28:z6 (bacteria) Gene: traK, G4J24_003123 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A734HNY4 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Outer-membrane core complex (outer ring) / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Salmonella enterica (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 1.3 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 298235 / Symmetry type: POINT |