9S35 | pdb_00009s35

Cryo-EM structure of Candida albicans Vrg4 bound to an inhibitory nanobody.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural basis for transport and inhibition of nucleotide sugar transport in pathogenic fungi.

Newstead, S.Parker, J.Deme, J.Feddersen, B.Lea, S.

(2025) Res Sq 

  • DOI: https://doi.org/10.21203/rs.3.rs-7213965/v1
  • Primary Citation of Related Structures:  
    9S35, 9S36

  • PubMed Abstract: 

    GDP-Mannose transporters are Golgi-localised solute carriers that are essential for the virulence of pathogenic fungi, serving as critical components of fungal glycosylation pathways. However, the mechanism by which nucleotide sugars are recognised and transported across the Golgi membrane remains unclear, hindering efforts to develop effective inhibitors that could serve as novel antifungal agents. Here, we present cryo-EM structures of the GDP-Mannose transporter, Vrg4, from Candida albicans in complex with nanobodies and in both the cytoplasmic and Golgi-facing states. Structural comparisons between these two states, in addition to a GDP-mannose bound structure, demonstrate the importance of ligand movement during transport. Additionally, we demonstrate the ability of the nanobodies to specifically inhibit Vrg4, presenting proof-of-principle that nanobodies can be used as effective inhibitors of nucleotide sugar transport and glycosylation in cells.


  • Organizational Affiliation
    • Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Llama NanobodyA [auth B]123Lama 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: 2
MoleculeChains Sequence LengthOrganismDetailsImage
GDP-mannose transporterB [auth A]338Candida albicansMutation(s): 0 
Gene Names: VRG4CAALFM_C107700CACaO19.1232CaO19.8817
Membrane Entity: Yes 
UniProt
Find proteins for Q5A477 (Candida albicans (strain SC5314 / ATCC MYA-2876))
Explore Q5A477 
Go to UniProtKB:  Q5A477
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5A477
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesIntramural Research Program
Wellcome TrustUnited Kingdom215519/Z/19/Z
Medical Research Council (MRC, United Kingdom)United KingdomMR/S021043/1

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-03
    Type: Initial release