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Yorodumi- PDB-7paf: Streptococcus pneumoniae choline importer LicB in lipid nanodiscs -
+Open data
-Basic information
Entry | Database: PDB / ID: 7paf | ||||||
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Title | Streptococcus pneumoniae choline importer LicB in lipid nanodiscs | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / Importer / Choline / nanodisc / Nanobody | ||||||
Function / homology | EamA domain / EamA-like transporter family / membrane => GO:0016020 / Chem-PGT / LicB protein Function and homology information | ||||||
Biological species | synthetic construct (others) Streptococcus pneumoniae TIGR4 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.75 Å | ||||||
Authors | Perez, C. / Baerland, N. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: Sci Adv / Year: 2022 Title: Mechanistic basis of choline import involved in teichoic acids and lipopolysaccharide modification. Authors: Natalie Bärland / Anne-Stéphanie Rueff / Gonzalo Cebrero / Cedric A J Hutter / Markus A Seeger / Jan-Willem Veening / Camilo Perez / Abstract: Phosphocholine molecules decorating bacterial cell wall teichoic acids and outer-membrane lipopolysaccharide have fundamental roles in adhesion to host cells, immune evasion, and persistence. ...Phosphocholine molecules decorating bacterial cell wall teichoic acids and outer-membrane lipopolysaccharide have fundamental roles in adhesion to host cells, immune evasion, and persistence. Bacteria carrying the operon that performs phosphocholine decoration synthesize phosphocholine after uptake of the choline precursor by LicB, a conserved transporter among divergent species. is a prominent pathogen where phosphocholine decoration plays a fundamental role in virulence. Here, we present cryo-electron microscopy and crystal structures of LicB, revealing distinct conformational states and describing architectural and mechanistic elements essential to choline import. Together with in vitro and in vivo functional characterization, we found that LicB displays proton-coupled import activity and promiscuous selectivity involved in adaptation to choline deprivation conditions, and describe LicB inhibition by synthetic nanobodies (sybodies). Our results provide previously unknown insights into the molecular mechanism of a key transporter involved in bacterial pathogenesis and establish a basis for inhibition of the phosphocholine modification pathway across bacterial phyla. #1: Journal: Biorxiv / Year: 2021 Title: Mechanistic basis of choline import involved in teichoic acids and lipopolysaccharide modification Authors: Barland, N. / Rueff, A.S. / Cebrero, G. / Hutter, C.A. / Seeger, M.A. / Veening, J.W. / Perez, C. | ||||||
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 | 7paf.cif.gz | 145.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7paf.ent.gz | 118.8 KB | Display | PDB format |
PDBx/mmJSON format | 7paf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pa/7paf ftp://data.pdbj.org/pub/pdb/validation_reports/pa/7paf | HTTPS FTP |
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-Related structure data
Related structure data | 13268MC 7b0kC 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: Antibody | Mass: 16802.365 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli MC1061 (bacteria) #2: Protein | Mass: 31647.631 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae TIGR4 (bacteria) Strain: ATCC BAA-334 / TIGR4 / Gene: licB, SP_1268 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H2UQH5 #3: Chemical | ChemComp-PGT / ( | Has ligand of interest | N | |
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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: Choline importer in nanodiscs bound to nanobody / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Molecular weight | Value: 0.260 MDa / Experimental value: YES |
Source (natural) | Organism: Streptococcus pneumoniae TIGR4 (bacteria) |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 95 % |
-Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 0 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.15.2_3472: / Classification: refinement | ||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 78649 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER | ||||||||||||||||||||||||||||
Refine LS restraints |
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