9G9M | pdb_00009g9m

Lipid III flippase WzxE with NB10 and NB7 nanobodies in outward-facing conformation - crystal 1

• PDB DOI: https://doi.org/10.2210/pdb9G9M/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Escherichia coli, Lama glama
• Expression System: Escherichia coli BL21(DE3), Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMmpstruc


• Deposited: 2024-07-25 Released: 2025-01-22 
• Deposition Author(s): Le Bas, A., Naismith, J.H.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.287 (Depositor), 0.287 (DCC) 
• R-Value Work: 
  0.235 (Depositor), 0.234 (DCC) 
• R-Value Observed: 
  0.237 (Depositor) 

Starting Model: experimental

Literature

Structure of WzxE the lipid III flippase for Enterobacterial Common Antigen polysaccharide.

Le Bas, A., Clarke, B.R., Teelucksingh, T., Lee, M., El Omari, K., Giltrap, A.M., McMahon, S.A., Liu, H., Beale, J.H., Mykhaylyk, V., Duman, R., Paterson, N.G., Ward, P.N., Harrison, P.J., Weckener, M., Pardon, E., Steyaert, J., Liu, H., Quigley, A., Davis, B.G., Wagner, A., Whitfield, C., Naismith, J.H.

(2025) Open Biol 15: 240310-240310

• PubMed: 39772807 
• DOI: https://doi.org/10.1098/rsob.240310
• Primary Citation Related Structures: 
  9G95, 9G97, 9G9M, 9G9N, 9G9O, 9G9P


• PubMed Abstract: 
  

  The enterobacterial common antigen (ECA) is conserved in Gram-negative bacteria of the Enterobacterales order although its function is debated. ECA biogenesis depends on the Wzx/Wzy-dependent strategy whereby the newly synthesized lipid-linked repeat units, lipid III, are transferred across the inner membrane by the lipid III flippase WzxE. WzxE is part of the Wzx family and required in many glycan assembly systems, but an understanding of its molecular mechanism is hindered due to a lack of structural evidence. Here, we present the first X-ray structures of WzxE from Escherichia coli in complex with nanobodies. Both inward- and outward-facing conformations highlight two pairs of arginine residues that move in a reciprocal fashion, enabling flipping. One of the arginine pairs coordinated to a glutamate residue is essential for activity along with the C-terminal arginine rich tail located close to the entrance of the lumen. This work helps understand the translocation mechanism of the Wzx flippase family.

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Organizational Affiliation: 
• Rosalind Franklin Institute, Harwell Campus, Didcot, UK.
Division of Structural Biology, University of Oxford, Roosevelt Drive, Oxford, UK.
Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada.
Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK.
Department of Pharmacology, University of Oxford, Oxford, UK.
Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, UK.
Biomedical Sciences Research Complex, North Haugh, University of St Andrews, St Andrews, UK.
Membrane Protein Laboratory, Diamond Light Source, Research Complex at Harwell, Didcot, UK.
Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Pleinlaan 2, Brussels B-1050, Belgium.
VIB-VUB Center for Structural Biology, VIB, Pleinlaan 2, Brussels B-1050, Belgium.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 76.58 kDa 
• Atom Count: 5,137 
• Modeled Residue Count: 666 
• Deposited Residue Count: 701 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipid III flippase	A	425	Escherichia coli	Mutation(s): 0  Gene Names: wzxE, wzx, yifJ, b3792, JW3766 Membrane Entity: Yes
UniProt
Find proteins for P0AAA7 (Escherichia coli (strain K12)) Explore P0AAA7  Go to UniProtKB:  P0AAA7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NB10 Nanobody	B	140	Lama glama	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
NB7 Nanobody	C	136	Lama glama	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.287 (Depositor), 0.287 (DCC) 
• R-Value Work:  0.235 (Depositor), 0.234 (DCC) 
• R-Value Observed: 0.237 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.855	α = 90
b = 152.687	β = 90
c = 287.5	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data scaling
xia2	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-01-22 
Deposition Author(s): Le Bas, A., Naismith, J.H.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	--

Revision History  

• Version 1.0: 2025-01-22
  Type: Initial release