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- EMDB-48872: Cryo-EM structure of Candida albicans pH regulated antigen 1 (Pra... -

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Basic information

Entry
Database: EMDB / ID: EMD-48872
TitleCryo-EM structure of Candida albicans pH regulated antigen 1 (Pra1) protein in complex with Zn2+
Map dataSharpened map used for model building
Sample
  • Complex: Hexameric assembly of Pra1 protein in complex with zinc
    • Protein or peptide: pH-regulated antigen PRA1
  • Ligand: ZINC ION
Keywordszinc binding protein / peptidase family M35 structural fold / zinc scavenging protein / METAL BINDING PROTEIN
Function / homology
Function and homology information


symbiont-mediated perturbation of host T-cell mediated immune response / symbiont-mediated suppression of host T-cell mediated immune response / adhesion of symbiont to host via host extracellular matrix / high molecular weight kininogen binding / symbiont-mediated suppression of host complement activation by activation of host proteases / symbiont-mediated suppression of host complement activation by recruitment of complement control protein / symbiont-mediated suppression of host complement activation / iron acquisition from host / hyphal tip / negative regulation of complement activation ...symbiont-mediated perturbation of host T-cell mediated immune response / symbiont-mediated suppression of host T-cell mediated immune response / adhesion of symbiont to host via host extracellular matrix / high molecular weight kininogen binding / symbiont-mediated suppression of host complement activation by activation of host proteases / symbiont-mediated suppression of host complement activation by recruitment of complement control protein / symbiont-mediated suppression of host complement activation / iron acquisition from host / hyphal tip / negative regulation of complement activation / hyphal cell wall / adhesion of symbiont to host / fungal-type cell wall / symbiont-mediated evasion of host immune response / fibrinogen binding / leukocyte cell-cell adhesion / integrin binding / metallopeptidase activity / cell surface / extracellular region / zinc ion binding
Similarity search - Function
Putative peptidase domain, HRXXH / Fungal antigen PRA1-like / Putative peptidase family / Metallopeptidase, catalytic domain superfamily
Similarity search - Domain/homology
pH-regulated antigen PRA1
Similarity search - Component
Biological speciesCandida albicans (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsSyrjanen JL
Funding support Finland, 1 items
OrganizationGrant numberCountry
Other government Finland
CitationJournal: Nat Commun / Year: 2025
Title: Structural insights into mechanisms of zinc scavenging by the Candida albicans zincophore Pra1.
Authors: Alexandre Nore / Elena Roselletti / Tanmoy Chakraborty / Nicha Särkkä / Rajika L Perera / Duncan Wilson / Johanna L Syrjänen /
Abstract: Candida albicans causes over 400,000 life-threatening, and an additional half a billion of mucosal infections annually. In response to infection, the host limits essential micronutrient availability, ...Candida albicans causes over 400,000 life-threatening, and an additional half a billion of mucosal infections annually. In response to infection, the host limits essential micronutrient availability, including zinc, to restrict growth of the invading pathogen. As assimilation of zinc is essential for C. albicans pathogenicity, limitation induces secretion of the zincophore protein Pra1 to scavenge zinc from the host. Pra1 also plays a number of important roles in host-pathogen interactions and is conserved in most fungi. However, the structure of fungal zincophores is unknown. Here, we present cryo-EM structures of C. albicans Pra1 in apo- and zinc-bound states, at 2.8 and 2.5 Å resolution respectively. Our work reveals a hexameric ring with multiple zinc binding sites. Through genetic studies, we show that these sites are essential for C. albicans growth under zinc restriction but do not affect the inflammatory properties of Pra1. These data create a foundation for future work to explore the structural basis of Pra1-mediated host-pathogen interactions, C. albicans zinc uptake, as well as therapeutics development.
History
DepositionFeb 2, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48872.png

Downloads & links

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Map

FileDownload / File: emd_48872.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map used for model building
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 320 pix.
= 275.52 Å		0.86 Å/pix.
x 320 pix.
= 275.52 Å		0.86 Å/pix.
x 320 pix.
= 275.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.861 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.28
Minimum - Maximum-1.0458235 - 2.0026815
Average (Standard dev.)0.0009320997 (±0.042783447)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 275.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened map, generated in CryoSPARC

Fileemd_48872_additional_1.map
AnnotationUnsharpened map, generated in CryoSPARC
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A, generated in CryoSPARC

Fileemd_48872_half_map_1.map
AnnotationHalf map A, generated in CryoSPARC
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B, generated in CryoSPARC

Fileemd_48872_half_map_2.map
AnnotationHalf map B, generated in CryoSPARC
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Hexameric assembly of Pra1 protein in complex with zinc

EntireName: Hexameric assembly of Pra1 protein in complex with zinc
Components
  • Complex: Hexameric assembly of Pra1 protein in complex with zinc
    • Protein or peptide: pH-regulated antigen PRA1
  • Ligand: ZINC ION

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Supramolecule #1: Hexameric assembly of Pra1 protein in complex with zinc

SupramoleculeName: Hexameric assembly of Pra1 protein in complex with zinc
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Candida albicans (yeast)
Molecular weightTheoretical: 189.21 KDa

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Macromolecule #1: pH-regulated antigen PRA1

MacromoleculeName: pH-regulated antigen PRA1 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Candida albicans (yeast)
Molecular weightTheoretical: 31.569156 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GSAPVTVTRF VDASPTGYDW RADWVKGFPI DSSCNATQYN QLSTGLQEAQ LLAEHARDHT LRFGSKSPFF RKYFGNETAS AEVVGHFDN VVGADKSSIL FLCDDLDDKC KNDGWAGYWR GSNHSDQTII CDLSFVTRRY LTQLCSSGYT VSKSKTNIFW A GDLLHRFW ...String:
GSAPVTVTRF VDASPTGYDW RADWVKGFPI DSSCNATQYN QLSTGLQEAQ LLAEHARDHT LRFGSKSPFF RKYFGNETAS AEVVGHFDN VVGADKSSIL FLCDDLDDKC KNDGWAGYWR GSNHSDQTII CDLSFVTRRY LTQLCSSGYT VSKSKTNIFW A GDLLHRFW HLKSIGQLVI EHYADTYEEV LELAQENSTY AVRNSNSLIY YALDVYAYDV TIPGEGCNGD GTSYKKSDFS SF EDSDSGS DSGASSTASS SHQHTDSNPS ATTDANSHCH THADGEVHC

UniProtKB: pH-regulated antigen PRA1

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 6 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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: 8
Component:
ConcentrationNameFormula
20.0 mMTris
150.0 mMsodium chlorideNaCl
1.0 mMzinc sulphateZnSO4

Details: 20 mM Tris-HCl pH 8.0, 150 mM NaCl, 1 mM ZnSO4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 63.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4) / Number images used: 1102286
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-9n4d:
Cryo-EM structure of Candida albicans pH regulated antigen 1 (Pra1) protein in complex with Zn2+

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