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- EMDB-48869: Cryo-EM structure of Candida albicans pH regulated antigen 1 (Pra... -

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Basic information

Entry
Database: EMDB / ID: EMD-48869
TitleCryo-EM structure of Candida albicans pH regulated antigen 1 (Pra1) protein in the absence of Zn2+
Map dataSharpened map used for model building, generated in cryosparc
Sample
  • Complex: Hexameric assembly of Pra1 protein in the absence of zinc
    • Protein or peptide: pH-regulated antigen PRA1
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: 2.8 Å
AuthorsSyrjanen JL
Funding support Finland, 1 items
OrganizationGrant numberCountry
Other government Finland
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
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_48869.png

Downloads & links

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Map

FileDownload / File: emd_48869.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map used for model building, generated in cryosparc
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: 0.376
Minimum - Maximum-1.1355629 - 1.8234076
Average (Standard dev.)0.0015312505 (±0.044900943)
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_48869_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_48869_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_48869_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 the absence of zinc

EntireName: Hexameric assembly of Pra1 protein in the absence of zinc
Components
  • Complex: Hexameric assembly of Pra1 protein in the absence of zinc
    • Protein or peptide: pH-regulated antigen PRA1

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Supramolecule #1: Hexameric assembly of Pra1 protein in the absence of zinc

SupramoleculeName: Hexameric assembly of Pra1 protein in the absence of zinc
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 6
Component:
ConcentrationNameFormula
20.0 mMMES
150.0 mMsodium chlorideNaCl

Details: 20 mM MES pH 6.0, 150 mM NaCl
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
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: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4)
Details: Non-uniform refinement in CryoSPARC 4.4 was used for the final reconstruction
Number images used: 607405
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-9n47:
Cryo-EM structure of Candida albicans pH regulated antigen 1 (Pra1) protein in the absence of Zn2+

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