Structure of CNAG_02591 from Cryptococcus neoformans

Experimental Data Snapshot

  • Resolution: 1.49 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.139 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


A Small Protein Associated with Fungal Energy Metabolism Affects the Virulence of Cryptococcus neoformans in Mammals.

McClelland, E.E.Ramagopal, U.A.Rivera, J.Cox, J.Nakouzi, A.Prabu, M.M.Almo, S.C.Casadevall, A.

(2016) PLoS Pathog 12: e1005849-e1005849

  • DOI: https://doi.org/10.1371/journal.ppat.1005849
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The pathogenic yeast Cryptococcus neoformans causes cryptococcosis, a life-threatening fungal disease. C. neoformans has multiple virulence mechanisms that are non-host specific, induce damage and interfere with immune clearance. Microarray analysis of C. neoformans strains serially passaged in mice associated a small gene (CNAG_02591) with virulence. This gene, hereafter identified as HVA1 (hypervirulence-associated protein 1), encodes a protein that has homologs of unknown function in plant and animal fungi, consistent with a conserved mechanism. Expression of HVA1 was negatively correlated with virulence and was reduced in vitro and in vivo in both mouse- and Galleria-passaged strains of C. neoformans. Phenotypic analysis in hva1Δ and hva1Δ+HVA1 strains revealed no significant differences in established virulence factors. Mice infected intravenously with the hva1Δ strain had higher fungal burden in the spleen and brain, but lower fungal burden in the lungs, and died faster than mice infected with H99W or the hva1Δ+HVA1 strain. Metabolomics analysis demonstrated a general increase in all amino acids measured in the disrupted strain and a block in the TCA cycle at isocitrate dehydrogenase, possibly due to alterations in the nicotinamide cofactor pool. Macrophage fungal burden experiments recapitulated the mouse hypervirulent phenotype of the hva1Δ strain only in the presence of exogenous NADPH. The crystal structure of the Hva1 protein was solved, and a comparison of structurally similar proteins correlated with the metabolomics data and potential interactions with NADPH. We report a new gene that modulates virulence through a mechanism associated with changes in fungal metabolism.

  • Organizational Affiliation

    Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, United States of America.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hypothetical protein CNAG_02591
A, B
77Cryptococcus neoformans var. grubii H99Mutation(s): 0 
Gene Names: CNAG_02591
Find proteins for J9VKY2 (Cryptococcus neoformans var. grubii serotype A (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487))
Explore J9VKY2 
Go to UniProtKB:  J9VKY2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupJ9VKY2
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CD

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
J [auth B]
K [auth B]
L [auth B]
C [auth A],
D [auth A],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth B]
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
O [auth B]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
O [auth B],
P [auth B],
Q [auth B]
O4 S
Query on GOL

Download Ideal Coordinates CCD File 
C3 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 1.49 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.139 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.775α = 73.93
b = 34.686β = 72.85
c = 38.253γ = 79.46
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-28
    Type: Initial release
  • Version 1.1: 2016-09-28
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Derived calculations, Refinement description
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations