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Yorodumi- EMDB-13268: Streptococcus pneumoniae choline importer LicB in lipid nanodiscs -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13268 | |||||||||
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Title | Streptococcus pneumoniae choline importer LicB in lipid nanodiscs | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | EamA domain / EamA-like transporter family / membrane => GO:0016020 / LicB protein Function and homology information | |||||||||
Biological species | Streptococcus pneumoniae TIGR4 (bacteria) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.75 Å | |||||||||
Authors | Perez C / Baerland N | |||||||||
Funding support | Switzerland, 1 items
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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 AS / Cebrero G / Hutter CA / Seeger MA / Veening JW / Perez C | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_13268.map.gz | 203.9 MB | EMDB map data format | |
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Header (meta data) | emd-13268-v30.xml emd-13268.xml | 14.5 KB 14.5 KB | Display Display | EMDB header |
Images | emd_13268.png | 59.9 KB | ||
Masks | emd_13268_msk_1.map | 216 MB | Mask map | |
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13268 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13268 | HTTPS FTP |
-Related structure data
Related structure data | 7pafMC 7b0kC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_13268.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 0.878 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_13268_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Choline importer in nanodiscs bound to nanobody
Entire | Name: Choline importer in nanodiscs bound to nanobody |
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Components |
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-Supramolecule #1: Choline importer in nanodiscs bound to nanobody
Supramolecule | Name: Choline importer in nanodiscs bound to nanobody / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Streptococcus pneumoniae TIGR4 (bacteria) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Molecular weight | Experimental: 260 KDa |
-Macromolecule #1: Nanobody
Macromolecule | Name: Nanobody / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 16.802365 KDa |
Recombinant expression | Organism: Escherichia coli MC1061 (bacteria) |
Sequence | String: GSSSQVQLVE SGGGSVQAGG SLRLSCAASG TIHAIGYLGW FRQAPGKERE GVAALTTYDG WTYYADSVKG RFTVSLDNAK NTVYLQMNS LKPEDTALYY CAAADDGWMF PLYHNHYEYW GQGTQVTVSA GRAGEQKLIS EEDLNSAVDH HHHHH |
-Macromolecule #2: LicB protein
Macromolecule | Name: LicB protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Streptococcus pneumoniae TIGR4 (bacteria) / Strain: ATCC BAA-334 / TIGR4 |
Molecular weight | Theoretical: 31.647631 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MKSKNGVPFG LLSGIFWGLG LTVSAYIFSI FTDLSPFVVA ATHDFLSIFI LLAFLLVKEG KVRLSIFLNI RNVSVIIGAL LAGPIGMQA NLYAVKYIGS SLASSVSAIY PAISVLLAFF FLKHKISKNT VFGIVLIIGG IIAQTYKVEQ VNSFYIGILC A LVCAIAWG ...String: MKSKNGVPFG LLSGIFWGLG LTVSAYIFSI FTDLSPFVVA ATHDFLSIFI LLAFLLVKEG KVRLSIFLNI RNVSVIIGAL LAGPIGMQA NLYAVKYIGS SLASSVSAIY PAISVLLAFF FLKHKISKNT VFGIVLIIGG IIAQTYKVEQ VNSFYIGILC A LVCAIAWG SESVLSSFAM ESELSEIEAL LIRQVTSFLS YLVIVLFSHQ SFTAVANGQL LGLMIVFAAF DMISYLAYYI AI NRLQPAK ATGLNVSYVV WTVLFAVVFL GAPLDMLTIM TSLVVIAGVY IIIKE |
-Macromolecule #3: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...
Macromolecule | Name: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE type: ligand / ID: 3 / Number of copies: 1 / Formula: PGT |
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Molecular weight | Theoretical: 751.023 Da |
Chemical component information | ChemComp-PGT: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.0 µm |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: OTHER |
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Output model | PDB-7paf: |