+Open data
-Basic information
Entry | Database: PDB / ID: 6u9e | ||||||
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Title | Structure of PdpA-VgrG Complex, Lidless | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / T6SS Central Spike / Complex | ||||||
Function / homology | Uncharacterized protein / PdpA Function and homology information | ||||||
Biological species | Francisella novicida (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.21 Å | ||||||
Authors | Yang, X. / Clemens, D.L. / Lee, B.-Y. / Cui, Y. / Zhou, Z.H. / Horwitz, M.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Structure / Year: 2019 Title: Atomic Structure of the Francisella T6SS Central Spike Reveals a Unique α-Helical Lid and a Putative Cargo. Authors: Xue Yang / Daniel L Clemens / Bai-Yu Lee / Yanxiang Cui / Z Hong Zhou / Marcus A Horwitz / Abstract: Francisella bacteria rely on a phylogenetically distinct type VI secretion system (T6SS) to escape host phagosomes and cause the fatal disease tularemia, but the structural and molecular mechanisms ...Francisella bacteria rely on a phylogenetically distinct type VI secretion system (T6SS) to escape host phagosomes and cause the fatal disease tularemia, but the structural and molecular mechanisms involved are unknown. Here we report the atomic structure of the Francisella T6SS central spike complex, obtained by cryo-electron microscopy. Our structural and functional studies demonstrate that, unlike the single-protein spike composition of other T6SS subtypes, Francisella T6SS's central spike is formed by two proteins, PdpA and VgrG, akin to T4-bacteriophage gp27 and gp5, respectively, and that PdpA has unique characteristics, including a putative cargo within its cavity and an N-terminal helical lid. Structure-guided mutagenesis demonstrates that the PdpA N-terminal lid and C-terminal spike are essential to Francisella T6SS function. PdpA is thus both an adaptor, connecting VgrG to the tube, and a likely carrier of secreted cargo. These findings are important to understanding Francisella pathogenicity and designing therapeutics to combat tularemia. | ||||||
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 | 6u9e.cif.gz | 387.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6u9e.ent.gz | 312.8 KB | Display | PDB format |
PDBx/mmJSON format | 6u9e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u9/6u9e ftp://data.pdbj.org/pub/pdb/validation_reports/u9/6u9e | HTTPS FTP |
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-Related structure data
Related structure data | 20695MC 6u9fC 6u9gC 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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-Components
#1: Protein | Mass: 95469.961 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Francisella novicida (bacteria) / Gene: pdpA / Production host: Escherichia coli (E. coli) / References: UniProt: Q7X3I9 #2: Protein | Mass: 20539.779 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Francisella novicida (bacteria) / Gene: B4919_03525 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7X3I8 |
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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: PdpA-VgrG complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Francisella novicida (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 |
Specimen support | Details: unspecified |
Vitrification | Instrument: FEI VITROBOT MARK IV / 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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 47 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING ONLY |
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3D reconstruction | Resolution: 4.21 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16889 / Symmetry type: POINT |
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL |