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- EMDB-54524: Cryo-EM structure of Candida albicans Vrg4 bound to an inhibitory... -

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Basic information

Entry
Database: EMDB / ID: EMD-54524
TitleCryo-EM structure of Candida albicans Vrg4 bound to an inhibitory nanobody and GDP-Mannose.
Map dataUnsharpened map
Sample
  • Complex: Nanobody bound to C.albicans Vrg4 transporter
    • Protein or peptide: GDP-mannose transporter
    • Protein or peptide: lama nanobody
  • Ligand: GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE
KeywordsGDP-Mannose transporter / Membrane Protein / Nucleotide Sugar Transporter / TRANSPORT PROTEIN
Function / homology
Function and homology information


GDP-mannose transmembrane transporter activity / GDP-mannose transmembrane transport / hyphal growth / protein N-linked glycosylation via asparagine / antiporter activity / cytoplasmic vesicle membrane / Golgi membrane / endoplasmic reticulum membrane / Golgi apparatus
Similarity search - Function
GDP-mannose transporter
Similarity search - Component
Biological speciesCandida albicans (yeast) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsDeme JC / Parker JL / Lea SM / Newstead S
Funding support United States, United Kingdom, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)Intramural Research Program United States
Wellcome Trust215519/Z/19/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MR/S021043/1 United Kingdom
CitationJournal: Res Sq / Year: 2025
Title: Structural basis for transport and inhibition of nucleotide sugar transport in pathogenic fungi.
Authors: Joanne L Parker / Justin C Deme / Bjarne Feddersen / Susan M Lea / Simon Newstead /
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 ...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 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.
History
DepositionJul 23, 2025-
Header (metadata) releaseSep 3, 2025-
Map releaseSep 3, 2025-
UpdateSep 3, 2025-
Current statusSep 3, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54524.png

Downloads & links

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Map

FileDownload / File: emd_54524.map.gz / Format: CCP4 / Size: 229.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened map
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 392 pix.
= 286.944 Å		0.73 Å/pix.
x 392 pix.
= 286.944 Å		0.73 Å/pix.
x 392 pix.
= 286.944 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.732 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.266
Minimum - Maximum-0.6145677 - 1.1929257
Average (Standard dev.)0.00047433568 (±0.020553231)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions392392392
Spacing392392392
CellA=B=C: 286.944 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54524_msk_1.map
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Additional map: deepEMhancer map

Fileemd_54524_additional_1.map
AnnotationdeepEMhancer map
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Additional map: Sharpened map

Fileemd_54524_additional_2.map
AnnotationSharpened map
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Half map: #2

Fileemd_54524_half_map_1.map
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Half map: #1

Fileemd_54524_half_map_2.map
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Sample components

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Entire : Nanobody bound to C.albicans Vrg4 transporter

EntireName: Nanobody bound to C.albicans Vrg4 transporter
Components
  • Complex: Nanobody bound to C.albicans Vrg4 transporter
    • Protein or peptide: GDP-mannose transporter
    • Protein or peptide: lama nanobody
  • Ligand: GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE

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Supramolecule #1: Nanobody bound to C.albicans Vrg4 transporter

SupramoleculeName: Nanobody bound to C.albicans Vrg4 transporter / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Candida albicans (yeast)

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Macromolecule #1: GDP-mannose transporter

MacromoleculeName: GDP-mannose transporter / type: protein_or_peptide / ID: 1 / Details: Candida albicans Vrg4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Candida albicans (yeast)
Molecular weightTheoretical: 37.183223 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MDSKHSTSSS SSGSLATRIS NSGPISIAAY CLSSILMTVT NKYVLSGFSF NLNFFLLAVQ SIVCIVTIGS LKSLNIITYR QFNKDEAKK WSPIAFLLVA MIYTSSKALQ YLSIPVYTIF KNLTIILIAY GEVIWFGGKV TTMALSSFLL MVLSSVIAYY G DNAAVKSH ...String:
MDSKHSTSSS SSGSLATRIS NSGPISIAAY CLSSILMTVT NKYVLSGFSF NLNFFLLAVQ SIVCIVTIGS LKSLNIITYR QFNKDEAKK WSPIAFLLVA MIYTSSKALQ YLSIPVYTIF KNLTIILIAY GEVIWFGGKV TTMALSSFLL MVLSSVIAYY G DNAAVKSH DDAFALYLGY FWMLTNCFAS AAFVLIMRKR IKLTNFKDFD TMYYNNLLSI PILLICSFIF EDWSSANVSL NF PADNRVT TITAMILSGA SSVGISYCSA WCVRVTSSTT YSMVGALNKL PIALSGLIFF EAAVNFWSVS SIFVGFGAGL VYA VAKQKQ QKEQSQQLPT TK

UniProtKB: GDP-mannose transporter

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Macromolecule #2: lama nanobody

MacromoleculeName: lama nanobody / type: protein_or_peptide / ID: 2 / Details: lama nanobody / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 13.78135 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
QVQLVESGGG LVQAGGSLRL SCAASGRTFR SYTLGWFRQA PGKEREFVAA IKWSTDTTYY ADSVKGRFTI SGDNAKNTVY LQMNSLKPE DTAVYFCAAR SLSTVIAGPE IPWPYNSWGQ GTQVTVSS

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Macromolecule #3: GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE / type: ligand / ID: 3 / Number of copies: 1 / Formula: GDD
Molecular weightTheoretical: 605.341 Da
Chemical component information

ChemComp-GDD:
GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 53.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5oge

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 51142
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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