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- PDB-9n47: Cryo-EM structure of Candida albicans pH regulated antigen 1 (Pra... -

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Basic information

Entry
Database: PDB / ID: 9n47
TitleCryo-EM structure of Candida albicans pH regulated antigen 1 (Pra1) protein in the absence of Zn2+
ComponentspH-regulated antigen PRA1
KeywordsMETAL BINDING PROTEIN / zinc binding protein / peptidase family M35 structural fold / zinc scavenging 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsSyrjanen, J.L. / Perera, R.L.
Funding support Finland, 1items
OrganizationGrant numberCountry
Other government Finland
Citation
Journal: 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.
#1: Journal: 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, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: pH-regulated antigen PRA1
B: pH-regulated antigen PRA1
C: pH-regulated antigen PRA1
D: pH-regulated antigen PRA1
E: pH-regulated antigen PRA1
F: pH-regulated antigen PRA1


Theoretical massNumber of molelcules
Total (without water)189,4156
Polymers189,4156
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
pH-regulated antigen PRA1 / 58 kDa fibrinogen-binding mannoprotein


Mass: 31569.156 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Gene: PRA1, FBP1, CAALFM_C406980WA, CaO19.10623, CaO19.3111 / Plasmid: pCDNA3.0 / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: P87020
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Hexameric assembly of Pra1 protein in the absence of zinc
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.18921 MDa / Experimental value: NO
Source (natural)Organism: Candida albicans (yeast)
Source (recombinant)Organism: Homo sapiens (human) / Strain: Expi293F / Cell: HEK / Plasmid: pcDNA3.0
Buffer solutionpH: 6 / Details: 20 mM MES pH 6.0, 150 mM NaCl
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMMES1
2150 mMsodium chlorideNaCl1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 63.2 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
7Coot0.9.8.7model fitting
8UCSF Chimera1.16model fitting
10cryoSPARC4.4initial Euler assignment
11cryoSPARC4.4final Euler assignment
13cryoSPARC4.43D reconstruction
14PHENIX1.21.2_5419model refinement
15Coot0.9.8.7model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 607405
Details: Non-uniform refinement in CryoSPARC 4.4 was used for the final reconstruction
Symmetry type: POINT
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 49.5 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003810896
ELECTRON MICROSCOPYf_angle_d0.501314784
ELECTRON MICROSCOPYf_chiral_restr0.04341548
ELECTRON MICROSCOPYf_plane_restr0.00281908
ELECTRON MICROSCOPYf_dihedral_angle_d4.4081463

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