7YUY | pdb_00007yuy

Structure of a mutated membrane-bound glycosyltransferase


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7YUY

This is version 1.4 of the entry. See complete history

Literature

Structural and mechanistic insights into fungal beta-1,3-glucan synthase FKS1.

Hu, X.Yang, P.Chai, C.Liu, J.Sun, H.Wu, Y.Zhang, M.Zhang, M.Liu, X.Yu, H.

(2023) Nature 616: 190-198

  • DOI: https://doi.org/10.1038/s41586-023-05856-5
  • Primary Citation Related Structures: 
    7XE4, 7YUY

  • PubMed Abstract: 

    The membrane-integrated synthase FKS is involved in the biosynthesis of β-1,3-glucan, the core component of the fungal cell wall 1,2 . FKS is the target of widely prescribed antifungal drugs, including echinocandin and ibrexafungerp 3,4 . Unfortunately, the mechanism of action of FKS remains enigmatic and this has hampered development of more effective medicines targeting the enzyme. Here we present the cryo-electron microscopy structures of Saccharomyces cerevisiae FKS1 and the echinocandin-resistant mutant FKS1(S643P). These structures reveal the active site of the enzyme at the membrane-cytoplasm interface and a glucan translocation path spanning the membrane bilayer. Multiple bound lipids and notable membrane distortions are observed in the FKS1 structures, suggesting active FKS1-membrane interactions. Echinocandin-resistant mutations are clustered at a region near TM5-6 and TM8 of FKS1. The structure of FKS1(S643P) reveals altered lipid arrangements in this region, suggesting a drug-resistant mechanism of the mutant enzyme. The structures, the catalytic mechanism and the molecular insights into drug-resistant mutations of FKS1 revealed in this study advance the mechanistic understanding of fungal β-1,3-glucan biosynthesis and establish a foundation for developing new antifungal drugs by targeting FKS.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.

Macromolecule Content 

  • Total Structure Weight: 219.84 kDa 
  • Atom Count: 12,391 
  • Modeled Residue Count: 1,503 
  • Deposited Residue Count: 1,876 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
1,3-beta-glucan synthase component FKS1A [auth F]1,876Saccharomyces cerevisiaeMutation(s): 1 
Gene Names: FKS1CND1CWH53ETG1GLS1GSC1PBR1YLR342WL8300.6
EC: 2.4.1.34
Membrane Entity: Yes 
UniProt
Find proteins for P38631 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38631 
Go to UniProtKB:  P38631
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38631
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseB [auth A]2N/A
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose
C
4N/A
Glycosylation Resources
GlyTouCan: G87841AX
GlyCosmos: G87841AX
GlyGen: G87841AX

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XKP

Query on XKP



Download:Ideal Coordinates CCD File
BA [auth F](11R,14S)-17-amino-14-hydroxy-8,14-dioxo-9,13,15-trioxa-14lambda~5~-phosphaheptadecan-11-yl decanoate
C23 H46 N O8 P
VYUSSAVVRCGYLY-OAQYLSRUSA-N
C14

Query on C14



Download:Ideal Coordinates CCD File
Q [auth F]TETRADECANE
C14 H30
BGHCVCJVXZWKCC-UHFFFAOYSA-N
D12

Query on D12



Download:Ideal Coordinates CCD File
AA [auth F],
Y [auth F],
Z [auth F]
DODECANE
C12 H26
SNRUBQQJIBEYMU-UHFFFAOYSA-N
D10

Query on D10



Download:Ideal Coordinates CCD File
K [auth F]
L [auth F]
M [auth F]
N [auth F]
O [auth F]
K [auth F],
L [auth F],
M [auth F],
N [auth F],
O [auth F],
P [auth F]
DECANE
C10 H22
DIOQZVSQGTUSAI-UHFFFAOYSA-N
DD9

Query on DD9



Download:Ideal Coordinates CCD File
D [auth F]
E [auth F]
F
G [auth F]
H [auth F]
D [auth F],
E [auth F],
F,
G [auth F],
H [auth F],
I [auth F],
J [auth F]
nonane
C9 H20
BKIMMITUMNQMOS-UHFFFAOYSA-N
HP6

Query on HP6



Download:Ideal Coordinates CCD File
R [auth F]
S [auth F]
T [auth F]
U [auth F]
V [auth F]
R [auth F],
S [auth F],
T [auth F],
U [auth F],
V [auth F],
W [auth F],
X [auth F]
HEPTANE
C7 H16
IMNFDUFMRHMDMM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-29
    Type: Initial release
  • Version 1.1: 2023-04-05
    Changes: Database references
  • Version 1.2: 2023-04-19
    Changes: Database references
  • Version 1.3: 2024-10-16
    Changes: Data collection, Structure summary
  • Version 1.4: 2025-06-18
    Changes: Data collection