7B0K

membrane protein structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.327 
  • R-Value Work: 0.309 
  • R-Value Observed: 0.311 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Mechanistic basis of choline import involved in teichoic acids and lipopolysaccharide modification.

Barland, N.Rueff, A.S.Cebrero, G.Hutter, C.A.J.Seeger, M.A.Veening, J.W.Perez, C.

(2022) Sci Adv 8: eabm1122-eabm1122

  • DOI: https://doi.org/10.1126/sciadv.abm1122
  • Primary Citation of Related Structures:  
    7B0K, 7PAF

  • PubMed 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. Bacteria carrying the operon that performs phosphocholine decoration synthesize phosphocholine after uptake of the choline precursor by LicB, a conserved transporter among divergent species. Streptococcus pneumoniae is a prominent pathogen where phosphocholine decoration plays a fundamental role in virulence. Here, we present cryo-electron microscopy and crystal structures of S. pneumoniae 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.


  • Organizational Affiliation

    Biozentrum, University of Basel, Basel 4056, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Drug/metabolite transporter (DMT) superfamily permease292Streptococcus pneumoniaeMutation(s): 0 
Gene Names: 
Membrane Entity: Yes 
UniProt
Find proteins for A0A0E7XN74 (Streptococcus pneumoniae)
Explore A0A0E7XN74 
Go to UniProtKB:  A0A0E7XN74
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0E7XN74
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CHT (Subject of Investigation/LOI)
Query on CHT

Download Ideal Coordinates CCD File 
B [auth A]CHOLINE ION
C5 H14 N O
OEYIOHPDSNJKLS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.327 
  • R-Value Work: 0.309 
  • R-Value Observed: 0.311 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.9α = 90
b = 43.44β = 120.431
c = 126.82γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerlandPP00P3_198903

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-16
    Type: Initial release