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- PDB-9ztc: Beta-1,3-glucan synthase Fks1 S643P from Saccharomyces Cerevisiae -

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Basic information

Entry
Database: PDB / ID: 9ztc
TitleBeta-1,3-glucan synthase Fks1 S643P from Saccharomyces Cerevisiae
Components1,3-beta-glucan synthase component FKS1
KeywordsMEMBRANE PROTEIN / Enzyme
Function / homology
Function and homology information


fungal-type cell wall polysaccharide biosynthetic process / 1,3-beta-glucan synthase / 1,3-beta-D-glucan synthase activity / (1->3)-beta-D-glucan biosynthetic process / 1,3-beta-D-glucan synthase complex / fungal-type cell wall biogenesis / cellular bud / ascospore wall assembly / actin cortical patch / cellular bud tip ...fungal-type cell wall polysaccharide biosynthetic process / 1,3-beta-glucan synthase / 1,3-beta-D-glucan synthase activity / (1->3)-beta-D-glucan biosynthetic process / 1,3-beta-D-glucan synthase complex / fungal-type cell wall biogenesis / cellular bud / ascospore wall assembly / actin cortical patch / cellular bud tip / fungal-type cell wall / cellular bud neck / regulation of cell size / positive regulation of endocytosis / cell periphery / mitochondrion / plasma membrane
Similarity search - Function
: / 1,3-beta-glucan synthase component FKS1, second domain / Glycosyl transferase, family 48 / 1,3-beta-glucan synthase subunit FKS1-like, domain-1 / 1,3-beta-glucan synthase component / 1,3-beta-glucan synthase subunit FKS1, domain-1 / 1,3-beta-glucan synthase subunit FKS1
Similarity search - Domain/homology
CHOLESTEROL HEMISUCCINATE / 1,3-beta-glucan synthase component FKS1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsRen, Z. / Lee, S.Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI170906 United States
CitationJournal: Nature / Year: 2026
Title: Structural basis of fungal β-1,3-glucan synthase inhibition by caspofungin.
Authors: Zhenning Ren / Abhishek Chhetri / Chang Liu / ShuYu Offner / Kedar Sharma / Mario J Borgnia / Wonpil Im / Kenichi Yokoyama / Seok-Yong Lee /
Abstract: Invasive fungal infections pose life-threatening risks to the increasing population of immunocompromised patients. Treatment remains challenging due to limited antifungal drugs and increasing ...Invasive fungal infections pose life-threatening risks to the increasing population of immunocompromised patients. Treatment remains challenging due to limited antifungal drugs and increasing resistance. β-1,3-D-glucan synthase (GS), comprising the catalytic Fks1 and the regulatory small GTPase, Rho1 (refs. ), is the target of clinically important echinocandin antifungals. Despite recent studies, the mechanisms of GS catalysis, Rho1 regulation and echinocandin inhibition and resistance remain elusive. Here we present cryo-electron microscopy structures of native Saccharomyces cerevisiae Fks1 (ScFks1) solved under catalytically relevant conditions, revealing its interactions with the antifungal caspofungin (CFN), glucan product from the translocation channel and Rho1. CFN forms a ternary complex with nascent glucan and Fks1 at the membrane-protein interface, suggesting an unexpected role of CFN in stalling polymer translocation. Our echinocandin-resistant S643P structure suggests a resistance mechanism: the substitution destabilizes CFN and glucan binding through both allosteric structural perturbation and direct steric clash. Rho1 binding induces active site rearrangements essential for catalysis, including that of the 'latch loop' for donor substrate coordination. Furthermore, we identify YMR295C as an auxiliary subunit. These findings elucidate the mechanisms of GS-mediated glucan synthesis and its inhibition and resistance by echinocandins, laying the groundwork for rational antifungal design.
History
DepositionDec 23, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 1,3-beta-glucan synthase component FKS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,8234
Polymers221,2631
Non-polymers1,5603
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 1,3-beta-glucan synthase component FKS1 / 1 / 3-beta-D-glucan-UDP glucosyltransferase / Calcineurin dependent protein 1 / Calcofluor white ...1 / 3-beta-D-glucan-UDP glucosyltransferase / Calcineurin dependent protein 1 / Calcofluor white hypersensitivity protein 53 / Echinocandin target gene protein 1 / FK506 sensitivity protein 1 / Glucan synthase of cerevisiae protein 1 / Papulacandin B resistance protein 1


Mass: 221262.531 Da / Num. of mol.: 1 / Mutation: S643P / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38631, 1,3-beta-glucan synthase
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H50O4
Has ligand of interestN
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: Beta-1,3-glucan synthase Fks1 S643P from Saccharomyces Cerevisiae
Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.5
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 194636 / Symmetry type: POINT
RefinementHighest resolution: 3.5 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00210451
ELECTRON MICROSCOPYf_angle_d0.51914273
ELECTRON MICROSCOPYf_dihedral_angle_d11.513464
ELECTRON MICROSCOPYf_chiral_restr0.0371620
ELECTRON MICROSCOPYf_plane_restr0.0041809

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