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- PDB-12xp: Candida albicans Chitin synthase 1 (CaChs1) intermediate state (D... -

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Basic information

Entry
Database: PDB / ID: 12xp
TitleCandida albicans Chitin synthase 1 (CaChs1) intermediate state (DA-6), bound to UDP and diynyl arylamine (DA, aka RO-09-3143)
ComponentsChitin synthase
KeywordsMEMBRANE PROTEIN / Enzyme / chitin synthesis
Function / homology: / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / URIDINE-5'-DIPHOSPHATE / :
Function and homology information
Biological speciesCandida albicans (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.29 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: Nat Microbiol / Year: 2026
Title: Cryo-EM structures of Candida albicans chitin synthase Chs1 reveal a druggable translocation channel.
Authors: Zhenning Ren / Abhishek Chhetri / Chang Liu / Ziqiang Guan / ShuYu Offner / Dmitry Kozhanov / Mario J Borgnia / Wonpil Im / Kenichi Yokoyama / Seok-Yong Lee /
Abstract: Invasive candidiasis is a leading cause of hospital-acquired bloodstream infections with high mortality. While the fungal cell wall is an excellent therapeutic target, inhibitor development against ...Invasive candidiasis is a leading cause of hospital-acquired bloodstream infections with high mortality. While the fungal cell wall is an excellent therapeutic target, inhibitor development against the essential chitin synthase (Chs) has been hampered by the absence of structural and mechanistic understanding of class II Chs, which contribute to fungal viability. Here we present cryo-electron microscopy structures of Candida albicans class II Chs (CaChs1) at 2.93-3.38 Å resolution, providing insights into its mechanisms of early elongation, chito-oligomer translocation and inhibition by the CaChs1-specific non-competitive inhibitor diynyl arylamine (DA). Chitin elongation and translocation are coupled to coordinated motion of the glycosyltransferase domain and the dimer interface. Notably, DA binds within the chitin translocation channel where a regulatory lipid resides and inhibits the enzyme by occluding product polymer extrusion. Importantly, DA showed potent synergy with the class I Chs inhibitor nikkomycin Z against C. albicans and Candida auris. These findings establish the chitin translocation channel as a druggable site for rational antifungal design.
History
DepositionApr 21, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 14, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chitin synthase
B: Chitin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,0098
Polymers240,1202
Non-polymers2,8896
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Chitin synthase / CaChs1


Mass: 120059.891 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Gene: CaJ7.0315, CaO19.5188 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: G1UA94, chitin synthase
#2: Chemical ChemComp-A1DEH / 8-[(6,6-dimethylhepta-2,4-diyn-1-yl)(methyl)amino]-2H-1,4-benzoxazin-3(4H)-one


Mass: 296.364 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H20N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE


Mass: 744.034 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H78NO8P / Comment: DOPE, phospholipid*YM
#4: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
Has ligand of interestY
Has protein modificationN

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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: Candida albicans Chitin synthase 1 (CaChs1) intermediate state (DA-6), bound to UDP and diynyl arylamine (DA, aka RO-09-3143)
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Candida albicans (yeast)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
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: TFS FALCON 4i (4k 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: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 79366 / Symmetry type: POINT
RefinementHighest resolution: 3.29 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00211347
ELECTRON MICROSCOPYf_angle_d0.46515477
ELECTRON MICROSCOPYf_dihedral_angle_d14.4793753
ELECTRON MICROSCOPYf_chiral_restr0.0381768
ELECTRON MICROSCOPYf_plane_restr0.0041938

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