9G95 | pdb_00009g95

Lipid III flippase WzxE with NB10 nanobody in outward-facing conformation at 2.7552 A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.289 (Depositor), 0.289 (DCC) 
  • R-Value Work: 
    0.236 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 
    0.238 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 9G95

Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history

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

  • 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.


  • Organizational Affiliation
    • Rosalind Franklin Institute, Harwell Campus, Didcot, UK.

Macromolecule Content 

  • Total Structure Weight: 63.95 kDa 
  • Atom Count: 4,309 
  • Modeled Residue Count: 543 
  • Deposited Residue Count: 565 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Lipid III flippase425Escherichia coliMutation(s): 0 
Gene Names: wzxEwzxyifJb3792JW3766
Membrane Entity: Yes 
UniProt
Find proteins for P0AAA7 (Escherichia coli (strain K12))
Explore P0AAA7 
Go to UniProtKB:  P0AAA7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AAA7
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
NB10 Nanobody140Lama glamaMutation(s): 0 

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MPG

Query on MPG



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A]
[(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate
C21 H40 O4
JPJYKWFFJCWMPK-GDCKJWNLSA-N
OCT

Query on OCT



Download:Ideal Coordinates CCD File
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A]
N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
M [auth A],
N [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN

Query on ZN



Download:Ideal Coordinates CCD File
O [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
P [auth A],
Q [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.289 (Depositor), 0.289 (DCC) 
  • R-Value Work:  0.236 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 0.238 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 271.54α = 90
b = 38.45β = 93.09
c = 56.96γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction
CRANK2phasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom--

Revision History  (Full details and data files)

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