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- PDB-7b0k: membrane protein structure -

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Basic information

Entry
Database: PDB / ID: 7b0k
Titlemembrane protein structure
ComponentsDrug/metabolite transporter (DMT) superfamily permease
KeywordsTRANSPORT PROTEIN / choline transporter
Function / homology: / EamA domain / EamA-like transporter family / membrane / CHOLINE ION / Drug/metabolite transporter (DMT) superfamily permease
Function and homology information
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.8 Å
AuthorsBaerland, N. / Perez, C.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science FoundationPP00P3_198903 Switzerland
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
DepositionNov 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation / Item: _citation.journal_id_ISSN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Drug/metabolite transporter (DMT) superfamily permease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7522
Polymers31,6481
Non-polymers1041
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area360 Å2
ΔGint7 kcal/mol
Surface area12310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.900, 43.440, 126.820
Angle α, β, γ (deg.)90.000, 120.431, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

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Components

#1: Protein Drug/metabolite transporter (DMT) superfamily permease / EamA family transporter


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
#2: Chemical ChemComp-CHT / CHOLINE ION


Mass: 104.171 Da / Num. of mol.: 1 / Fragment: ligand / Source method: obtained synthetically / Formula: C5H14NO / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.84 Å3/Da / Density % sol: 74.57 %
Crystal growTemperature: 289 K / Method: vapor diffusion / Details: 30 % PEG 400, 50 mM HEPES pH 6.4

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 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

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
3.83-3.953.520.5712.321960.8510.67737.2
3.95-4.083.5270.8151.732940.7950.96161.1
4.08-4.223.5010.6711.744530.8830.79689.5
4.22-4.383.4370.552.194740.9220.65499
4.38-4.563.4250.4132.664350.9550.49498
4.56-4.763.3690.3653.024260.9720.43797.5
4.76-4.993.2750.3473.293960.950.41597.8
4.99-5.263.2410.3033.574020.9670.36396.9
5.26-5.583.1790.2683.523580.9750.32394.2
5.58-5.9730.2513.723320.9540.30695.7
5.97-6.443.3240.2134.683390.9640.25598.8
6.44-7.063.3240.1665.793150.9840.19798.4
7.06-7.892.9740.1027.072690.990.12498.5
7.89-9.112.9480.0678.392490.9950.08294.7
9.11-11.162.5650.078.871860.990.08687.7
11.16-15.792.7720.069.241490.9950.07289.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.3267 513 9.97 %
Rwork0.3091 4634 -
obs0.311 5147 86.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 101.62 Å2
Refinement stepCycle: LAST / Resolution: 3.8→10.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1938 0 7 0 1945
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00261984
X-RAY DIFFRACTIONf_angle_d0.56372701
X-RAY DIFFRACTIONf_chiral_restr0.0402343
X-RAY DIFFRACTIONf_plane_restr0.0039314
X-RAY DIFFRACTIONf_dihedral_angle_d14.70541137
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8-4.170.4071820.3653718X-RAY DIFFRACTION55.17
4.17-4.720.31441430.32341295X-RAY DIFFRACTION97.96
4.72-5.80.34871450.31271281X-RAY DIFFRACTION96.29
5.8-10.960.29591430.28381340X-RAY DIFFRACTION96.86

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