+Open data
-Basic information
Entry | Database: PDB / ID: 7b0k | ||||||
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Title | membrane protein structure | ||||||
Components | Drug/metabolite transporter (DMT) superfamily permease | ||||||
Keywords | TRANSPORT PROTEIN / choline transporter | ||||||
Function / homology | EamA domain / EamA-like transporter family / membrane => GO:0016020 / CHOLINE ION / Drug/metabolite transporter (DMT) superfamily permease Function and homology information | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.8 Å | ||||||
Authors | Baerland, N. / Perez, C. | ||||||
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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7b0k.cif.gz | 125.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7b0k.ent.gz | 88.9 KB | Display | PDB format |
PDBx/mmJSON format | 7b0k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b0/7b0k ftp://data.pdbj.org/pub/pdb/validation_reports/b0/7b0k | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31647.631 Da / Num. of mol.: 1 / Fragment: membrane protein Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) Gene: ERS021280_00207, ERS409062_01153, GM533_00320, SAMEA104035127_01235, SAMEA104035134_01163, SAMEA104154639_01167, SAMEA104154682_01012, SAMEA2204024_01167, SAMEA3232645_00550, SAMEA3354337_ ...Gene: ERS021280_00207, ERS409062_01153, GM533_00320, SAMEA104035127_01235, SAMEA104035134_01163, SAMEA104154639_01167, SAMEA104154682_01012, SAMEA2204024_01167, SAMEA3232645_00550, SAMEA3354337_01417, SAMEA3389964_01659, SAMEA3390019_01836, SAMEA3714202_00443 Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: A0A0E7XN74 |
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#2: Chemical | ChemComp-CHT / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.84 Å3/Da / Density % sol: 74.57 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion / Details: 30 % PEG 400, 50 mM HEPES pH 6.4 |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 2, 2018 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.53→12.995 Å / Num. obs: 5593 / % possible obs: 72.1 % / Redundancy: 3.259 % / Biso Wilson estimate: 114.86 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.121 / Rrim(I) all: 0.146 / Χ2: 0.821 / Net I/σ(I): 3.94 / Num. measured all: 18226 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: other Resolution: 3.8→10.96 Å / SU ML: 0.7292 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 38.1135 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 101.62 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.8→10.96 Å
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Refine LS restraints |
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LS refinement shell |
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