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Yorodumi- PDB-6r6b: Structure of the core Shigella flexneri type III secretion system... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6r6b | ||||||||||||||||||
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Title | Structure of the core Shigella flexneri type III secretion system export gate complex SctRST (Spa24/Spa9/Spa29). | ||||||||||||||||||
Components |
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Keywords | PROTEIN TRANSPORT / Type III secretion / T3SS / Flagella / Cryo-EM / Membrane protein | ||||||||||||||||||
Function / homology | Function and homology information | ||||||||||||||||||
Biological species | Shigella flexneri (bacteria) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||||||||||||||
Authors | Johnson, S. / Kuhlen, L. / Deme, J.C. / Abrusci, P. / Lea, S.M. | ||||||||||||||||||
Funding support | United Kingdom, 5items
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Citation | Journal: mBio / Year: 2019 Title: The Structure of an Injectisome Export Gate Demonstrates Conservation of Architecture in the Core Export Gate between Flagellar and Virulence Type III Secretion Systems. Authors: Steven Johnson / Lucas Kuhlen / Justin C Deme / Patrizia Abrusci / Susan M Lea / Abstract: Export of proteins through type III secretion systems (T3SS) is critical for motility and virulence of many major bacterial pathogens. Proteins are exported through a genetically defined export gate ...Export of proteins through type III secretion systems (T3SS) is critical for motility and virulence of many major bacterial pathogens. Proteins are exported through a genetically defined export gate complex consisting of three proteins. We have recently shown at 4.2 Å that the flagellar complex of these three putative membrane proteins (FliPQR in flagellar systems, SctRST in virulence systems) assembles into an extramembrane helical assembly that likely seeds correct assembly of the rod. Here we present the structure of an equivalent complex from the virulence system at 3.5 Å by cryo-electron microscopy. This higher-resolution structure yields a more precise description of the structure and confirms the prediction of structural conservation in this core complex. Analysis of particle heterogeneity also suggests how the SctS/FliQ subunits sequentially assemble in the complex. Although predicted on the basis of sequence conservation, the work presented here formally demonstrates that all classes of type III secretion systems, flagellar or virulence, share the same architecture at the level of the core structures. This absolute conservation of the unusual extramembrane structure of the core export gate complex now allows work to move to focusing on both mechanistic studies of type III but also on fundamental studies of how such a complex is assembled. #1: Journal: Nat Struct Mol Biol / Year: 2018 Title: Structure of the core of the type III secretion system export apparatus. Authors: Lucas Kuhlen / Patrizia Abrusci / Steven Johnson / Joseph Gault / Justin Deme / Joseph Caesar / Tobias Dietsche / Mehari Tesfazgi Mebrhatu / Tariq Ganief / Boris Macek / Samuel Wagner / ...Authors: Lucas Kuhlen / Patrizia Abrusci / Steven Johnson / Joseph Gault / Justin Deme / Joseph Caesar / Tobias Dietsche / Mehari Tesfazgi Mebrhatu / Tariq Ganief / Boris Macek / Samuel Wagner / Carol V Robinson / Susan M Lea / Abstract: Export of proteins through type III secretion systems is critical for motility and virulence of many major bacterial pathogens. Three putative integral membrane proteins (FliP, FliQ, FliR) are ...Export of proteins through type III secretion systems is critical for motility and virulence of many major bacterial pathogens. Three putative integral membrane proteins (FliP, FliQ, FliR) are suggested to form the core of an export gate in the inner membrane, but their structure, assembly and location within the final nanomachine remain unclear. Here, we present the cryoelectron microscopy structure of the Salmonella Typhimurium FliP-FliQ-FliR complex at 4.2 Å. None of the subunits adopt canonical integral membrane protein topologies, and common helix-turn-helix structural elements allow them to form a helical assembly with 5:4:1 stoichiometry. Fitting of the structure into reconstructions of intact secretion systems, combined with cross-linking, localize the export gate as a core component of the periplasmic portion of the machinery. This study thereby identifies the export gate as a key element of the secretion channel and implies that it primes the helical architecture of the components assembling downstream. | ||||||||||||||||||
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 | 6r6b.cif.gz | 259.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6r6b.ent.gz | 208.1 KB | Display | PDB format |
PDBx/mmJSON format | 6r6b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6r6b_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 6r6b_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6r6b_validation.xml.gz | 53.1 KB | Display | |
Data in CIF | 6r6b_validation.cif.gz | 80.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r6/6r6b ftp://data.pdbj.org/pub/pdb/validation_reports/r6/6r6b | HTTPS FTP |
-Related structure data
Related structure data | 4734MC 4733C 6r69C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 24215.562 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: spaP, spa24, CP0153 / Production host: Escherichia coli (E. coli) / Variant (production host): MT56 / References: UniProt: P0A1L3 #2: Protein | | Mass: 32644.086 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: spaR, spa29, CP0155 / Production host: Escherichia coli (E. coli) / Variant (production host): MT56 / References: UniProt: P0A1M6 #3: Protein | Mass: 9433.338 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: spaQ, spa9, CP0154 / Production host: Escherichia coli (E. coli) / Variant (production host): MT56 / References: UniProt: P0A1M4 |
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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: Shigella flexneri type III secretion export gate (Spa24Spa9Spa29) Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | ||||||||||||||||
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Molecular weight | Value: 0.191 MDa / Experimental value: YES | ||||||||||||||||
Source (natural) | Organism: Shigella flexneri (bacteria) | ||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) / Strain: MT56 | ||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||
Buffer component |
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Specimen | Conc.: 8.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil, UltrAuFoil, R1.2/1.3 | ||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K |
-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 |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 8 sec. / Electron dose: 48 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 3741 |
Image scans | Movie frames/image: 20 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 775073 | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 212561 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL |