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Yorodumi- PDB-7sax: Structure of GldLM, the proton-powered motor that drives Type IX ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7sax | |||||||||||||||
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Title | Structure of GldLM, the proton-powered motor that drives Type IX protein secretion and gliding motility in Sphingobacterium wenxiniae | |||||||||||||||
Components |
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Keywords | MOTOR PROTEIN / type IX secretion system | |||||||||||||||
Function / homology | Function and homology information | |||||||||||||||
Biological species | Sphingobacterium wenxiniae (bacteria) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | |||||||||||||||
Authors | Hennell James, R. / Deme, J.C. / Lea, S.M. | |||||||||||||||
Funding support | European Union, 4items
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Citation | Journal: mBio / Year: 2022 Title: Structures of the Type IX Secretion/Gliding Motility Motor from across the Phylum . Authors: Rory Hennell James / Justin C Deme / Alicia Hunter / Ben C Berks / Susan M Lea / Abstract: Gliding motility using cell surface adhesins, and export of proteins by the type IX secretion system (T9SS) are two phylum-specific features of the Bacteroidetes. Both of these processes are ...Gliding motility using cell surface adhesins, and export of proteins by the type IX secretion system (T9SS) are two phylum-specific features of the Bacteroidetes. Both of these processes are energized by the GldLM motor complex, which transduces the proton motive force at the inner membrane into mechanical work at the outer membrane. We previously used cryo-electron microscopy to solve the structure of the GldLM motor core from Flavobacterium johnsoniae at 3.9-Å resolution (R. Hennell James, J. C. Deme, A. Kjaer, F. Alcock, et al., Nat Microbiol 6:221-233, 2021, https://dx.doi.org/10.1038/s41564-020-00823-6). Here, we present structures of homologous complexes from a range of pathogenic and environmental species at up to 3.0-Å resolution. These structures show that the architecture of the GldLM motor core is conserved across the phylum, although there are species-specific differences at the N terminus of GldL. The resolution improvements reveal a cage-like structure that ties together the membrane-proximal cytoplasmic region of GldL and influences gliding function. These findings add detail to our structural understanding of bacterial ion-driven motors that drive the T9SS and gliding motility. Many bacteria in the phylum use the type IX secretion system to secrete proteins across their outer membrane. Most of these bacteria can also glide across surfaces using adhesin proteins that are propelled across the cell surface. Both secretion and gliding motility are driven by the GldLM protein complex, which forms a nanoscale electrochemical motor. We used cryo-electron microscopy to study the structure of the GldLM protein complex from different species, including the human pathogens Porphyromonas gingivalis and Capnocytophaga canimorsus. The organization of the motor is conserved across species, but we find species-specific structural differences and resolve motor features at higher resolution. This work improves our understanding of the type IX secretion system, which is a virulence determinant in human and animal diseases. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7sax.cif.gz | 136.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7sax.ent.gz | 101.7 KB | Display | PDB format |
PDBx/mmJSON format | 7sax.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7sax_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 7sax_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7sax_validation.xml.gz | 33.4 KB | Display | |
Data in CIF | 7sax_validation.cif.gz | 48.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sa/7sax ftp://data.pdbj.org/pub/pdb/validation_reports/sa/7sax | HTTPS FTP |
-Related structure data
Related structure data | 24958MC 7satC 7sauC 7sazC 7sb2C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 28533.041 Da / Num. of mol.: 2 / Fragment: C-terminal TEV cleavage site and TwinStrep Tag Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sphingobacterium wenxiniae (bacteria) / Gene: SAMN05660206_103134 / Plasmid: pT12 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A1I6R6I5 #2: Protein | Mass: 23072.148 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sphingobacterium wenxiniae (bacteria) / Gene: SAMN05660206_103135 / Plasmid: pT12 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A1I6R6J4 Sequence details | C-terminal TEV cleavage site and TwinStrep Tag | |
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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: Type IX Secretion System/gliding motility GldLM motor complex Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | |||||||||||||||||||||||||
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Molecular weight | Value: 0.1725 MDa / Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: Sphingobacterium wenxiniae (bacteria) | |||||||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) / Strain: BL21 / Plasmid: pT12 | |||||||||||||||||||||||||
Buffer solution | pH: 8 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Details: 15 mA / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K / Details: Wait time 10 s Blot time 2 s |
-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 |
Image recording | Electron dose: 56 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 7167266 | |||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 111727 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 63.2 / Protocol: AB INITIO MODEL / Space: REAL Details: A homology model based on the structure of FjoGldLM (PDB 6YS8) was used as a starting model and modified to fit the EM density using Coot. Refinement was carried out using Phenix. |