9G9P | pdb_00009g9p

Lipid III flippase WzxE with NB10 and NB7 nanobodies in inward-facing conformation - crystal 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.274 (Depositor), 0.271 (DCC) 
  • R-Value Work: 
    0.220 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 
    0.223 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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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 of 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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NB10 Nanobody140Lama glamaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NB7 Nanobody136Lama glamaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.274 (Depositor), 0.271 (DCC) 
  • R-Value Work:  0.220 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 0.223 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.884α = 90
b = 191.681β = 90
c = 102.087γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata scaling
xia2data reduction
PHASERphasing

Structure Validation

View Full Validation Report



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