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- EMDB-76827: Structure of Class II chitin synthase, Chs1, from Candida albican... -

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Basic information

Entry
Database: EMDB / ID: EMD-76827
TitleStructure of Class II chitin synthase, Chs1, from Candida albicans (CaChs1), state 1 (post UDP hydrolysis) after 5 min reaction
Map data
Sample
  • Complex: Structure of Class II chitin synthase, Chs1, from Candida albicans (CaChs1), state 1 (post UDP hydrolysis) after 5 min reaction
    • Protein or peptide: Chitin synthase
  • Ligand: MAGNESIUM ION
  • Ligand: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: URIDINE-5'-DIPHOSPHATE
  • Ligand: water
KeywordsEnzyme / chitin synthesis / MEMBRANE PROTEIN
Function / homology:
Function and homology information
Biological speciesCandida albicans (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.38 Å
AuthorsRen Z / Lee SY
Funding support United States, 1 items
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, 2026-
Header (metadata) releaseOct 14, 2026-
Map releaseOct 14, 2026-
UpdateOct 14, 2026-
Current statusOct 14, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76827.png

Downloads & links

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Map

FileDownload / File: emd_76827.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 320 pix.
= 297.6 Å		0.93 Å/pix.
x 320 pix.
= 297.6 Å		0.93 Å/pix.
x 320 pix.
= 297.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.1
Minimum - Maximum-0.4455219 - 0.6477454
Average (Standard dev.)0.0008952407 (±0.016192202)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 297.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_76827_msk_1.map
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Half map: #1

Fileemd_76827_half_map_1.map
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Half map: #2

Fileemd_76827_half_map_2.map
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Sample components

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Entire : Structure of Class II chitin synthase, Chs1, from Candida albican...

EntireName: Structure of Class II chitin synthase, Chs1, from Candida albicans (CaChs1), state 1 (post UDP hydrolysis) after 5 min reaction
Components
  • Complex: Structure of Class II chitin synthase, Chs1, from Candida albicans (CaChs1), state 1 (post UDP hydrolysis) after 5 min reaction
    • Protein or peptide: Chitin synthase
  • Ligand: MAGNESIUM ION
  • Ligand: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: URIDINE-5'-DIPHOSPHATE
  • Ligand: water

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Supramolecule #1: Structure of Class II chitin synthase, Chs1, from Candida albican...

SupramoleculeName: Structure of Class II chitin synthase, Chs1, from Candida albicans (CaChs1), state 1 (post UDP hydrolysis) after 5 min reaction
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Candida albicans (yeast)

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Macromolecule #1: Chitin synthase

MacromoleculeName: Chitin synthase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: chitin synthase
Source (natural)Organism: Candida albicans (yeast)
Molecular weightTheoretical: 120.059891 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKNPFDSGSD DEDPFLSNPQ SAPSMPYAAY TSDRTSPRKT YQPLNFDSED EDAKESEFMA FPSSTSGSPF HQQQSPRQSP NIFSRSTAR AATSKSNMSI YDNTPNLQFN KSGAATPRAQ FTSKESPKRQ KTTEVTIDFD NDDDNNHTLE FENGSPRRSF R SSAISSER ...String:
MKNPFDSGSD DEDPFLSNPQ SAPSMPYAAY TSDRTSPRKT YQPLNFDSED EDAKESEFMA FPSSTSGSPF HQQQSPRQSP NIFSRSTAR AATSKSNMSI YDNTPNLQFN KSGAATPRAQ FTSKESPKRQ KTTEVTIDFD NDDDNNHTLE FENGSPRRSF R SSAISSER FLPPPQPIFS RETFAEANSR EEEKSADQET LDEKYDYDSY QKGYEEVETL HSEGTAYSGS SYLSDDASPE TT DYFGASI DGNIMHNINN GYVPNREKTI TKRKVRLVGG KAGNLVLENP VPTELRKVLT RTESPFGEFT NMTYTACTSQ PDT FSAEGF TLRAAKYGRE TEIVICITMY NEDEVAFART MHGVMKNIAH LCSRHKSKIW GKDSWKKVQV IIVADGRNKV QQSV LELLT ATGCYQENLA RPYVNNSKVN AHLFEYTTQI SIDENLKFKG DEKNLAPVQV LFCLKESNQK KINSHRWLFN AFCPV LDPN VIVLLDVGTK PDNHAIYNLW KAFDRDSNVA GAAGEIKAMK GKGWINLTNP LVASQNFEYK LSNILDKPLE SLFGYI SVL PGALSAYRYI ALKNHDDGTG PLASYFKGED LLCSHDKDKE NTKANFFEAN MYLAEDRILC WELVSKRNDN WVLKFVK SA TGETDVPETI AEFLSQRRRW INGAFFAALY SLYHFRKIWT TDHSYARKFW LHVEFIYQLV SLLFSFFSLS NFYLTFYF L TGSLVSYKSL GKKGGFWIFT LFNYLCIGVL TSLFIVSIGN RPHASKNIFK TLIILLTICA LYALVVGFVF VINTIATFG TGGTSTYVLV SIVVSLLSTY GLYTLMSILY LDPWHMLTCS VQYFLMIPSY TCTLQIFAFC NTHDVSWGTK GDNNPKEDLS NQYIIEKNA SGEFEAVIVD TNIDEDYLET LYNIRSKRSN KKVALGHSEK TPLDGDDYAK DVRTRVVLFW MIANLVFIMT M VQVYEPGD TGRNIYLAFI LWAVAVLALV RAIGSLGYLI QTYARFFVES KSKWMKRGYT APSHNPLNSN SLEVLFQGPA AD YKDDDDK AHHHHHHHHH H

UniProtKB: UNIPROTKB: G1UA94

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #3: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine

MacromoleculeName: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / type: ligand / ID: 3 / Number of copies: 2 / Formula: PEE
Molecular weightTheoretical: 744.034 Da
Chemical component information

ChemComp-PEE:
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE, phospholipid*YM

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #5: URIDINE-5'-DIPHOSPHATE

MacromoleculeName: URIDINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 2 / Formula: UDP
Molecular weightTheoretical: 404.161 Da
Chemical component information

ChemComp-UDP:
URIDINE-5'-DIPHOSPHATE / UDP*YM

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 2 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 39122
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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