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- EMDB-54523: Cryo-EM structure of Candida albicans Vrg4 bound to an inhibitory... -

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Basic information

Entry
Database: EMDB / ID: EMD-54523
TitleCryo-EM structure of Candida albicans Vrg4 bound to an inhibitory nanobody.
Map dataUnsharpened EM map
Sample
  • Complex: Nanobody bound to C.albicans Vrg4 transporter
    • Protein or peptide: Llama Nanobody
    • Protein or peptide: GDP-mannose transporter
  • Ligand: water
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: 3.0 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_54523.png

Downloads & links

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Map

FileDownload / File: emd_54523.map.gz / Format: CCP4 / Size: 229.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened EM map
Projections & slices

Image control

Size
Brightness
Contrast
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.732 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.417
Minimum - Maximum-0.92443717 - 1.4518816
Average (Standard dev.)0.0003991672 (±0.021011861)
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_54523_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened EM map

Fileemd_54523_additional_1.map
AnnotationSharpened EM map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_54523_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_54523_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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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: Llama Nanobody
    • Protein or peptide: GDP-mannose transporter
  • Ligand: water

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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: Llama Nanobody

MacromoleculeName: Llama Nanobody / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 13.376 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
QVQLVESGGG LVQPGGSLRL SCAASGSISE INVMGWYRQA PGKQRELVAR ITTGGSTNYA DSVKGRFTIS RDNAKNTVYL QMNSLKPED TAVYMCNAHR RVVMEWGPLG YDYWGQGTQV TVSS

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Macromolecule #2: GDP-mannose transporter

MacromoleculeName: GDP-mannose transporter / type: protein_or_peptide / ID: 2 / 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 #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 7 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 55.0 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: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 348612
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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