9DZV | pdb_00009dzv

Cryo-EM structure of the C. neoformans lipid flippase Apt1-Cdc50 in the E1 state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.27 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Butyrolactol A is a phospholipid flippase inhibitor that potentiates the bioactivity of caspofungin against resistant fungi.

Chen, X.Duan, H.D.Hoy, M.J.Koteva, K.Spitzer, M.Guitor, A.K.Puumala, E.Hu, G.Yiu, B.Chou, S.Bian, Z.Guo, A.B.Y.Sun, S.Robbins, N.Cook, M.A.Truant, R.MacNeil, L.T.Brown, E.D.Kronstad, J.W.Cowen, L.E.Heitman, J.Li, H.Wright, G.D.

(2025) bioRxiv 

  • DOI: https://doi.org/10.1101/2025.01.06.630955
  • Primary Citation of Related Structures:  
    9DZU, 9DZV, 9OMV

  • PubMed Abstract: 

    Fungal infections cause millions of deaths annually and are challenging to treat due to limited antifungal options and increasing drug resistance. Cryptococci are intrinsically resistant to the latest generation of antifungals, echinocandins, while Candida auris , a notorious global threat, is also increasingly resistant. We performed a natural product extract screen for rescue of the activity of the echinocandin caspofungin against Cryptococcus neoformans H99, identifying butyrolactol A, which restores echinocandin efficacy against resistant fungal pathogens, including C. auris . Mode of action studies revealed that butyrolactol A inhibits the phospholipid flippase Apt1-Cdc50, blocking phospholipid transport. Cryoelectron-microscopy analysis of the Apt1●butyrolactol A complex revealed that the flippase is locked in a dead-end state. Apt1 inhibition disrupts membrane asymmetry, vesicular trafficking, and cytoskeletal organization, thereby enhancing echinocandin uptake and potency. This study identifies flippases as promising antifungal targets and demonstrates the potential of revisiting natural products to expand the antifungal arsenal and combat resistance.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription regulatorA [auth B]411Cryptococcus neoformans H99Mutation(s): 0 
Gene Names: CNAG_06465
Membrane Entity: Yes 
UniProt
Find proteins for J9VW44 (Cryptococcus neoformans (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487))
Explore J9VW44 
Go to UniProtKB:  J9VW44
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupJ9VW44
Glycosylation
Glycosylation Sites: 4
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Phospholipid-transporting ATPaseB [auth A]1,570Cryptococcus neoformans H99Mutation(s): 0 
Gene Names: CNAG_06469
EC: 7.6.2.1
Membrane Entity: Yes 
UniProt
Find proteins for J9VZ19 (Cryptococcus neoformans (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487))
Explore J9VZ19 
Go to UniProtKB:  J9VZ19
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupJ9VZ19
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC [auth D],
E [auth G]
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD [auth E]6N-Glycosylation
Glycosylation Resources
GlyTouCan:  G34220DL
GlyCosmos:  G34220DL
GlyGen:  G34220DL
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.27 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA231466

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-05
    Type: Initial release