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- EMDB-25432: Chitin Synthase 2 from Candida albicans at the apo state -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-25432
TitleChitin Synthase 2 from Candida albicans at the apo state
Map data
Sample
  • Complex: Chitin synthase 2 from Candida albicans in the apo state
    • Protein or peptide: Chitin synthase
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
Function / homology
Function and homology information


cell wall chitin biosynthetic process / chitin synthase / chitin synthase activity / cell septum / cell periphery / membrane
Similarity search - Function
Chitin synthase N-terminal / Chitin synthase N-terminal / Fungal chitin synthase / Chitin synthase / Chitin synthase / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
Biological speciesCandida albicans (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsRen Z / Chhetri A / Lee S / Yokoyama K
Funding support1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM115729
CitationJournal: Nat Struct Mol Biol / Year: 2022
Title: Structural basis for inhibition and regulation of a chitin synthase from Candida albicans.
Authors: Zhenning Ren / Abhishek Chhetri / Ziqiang Guan / Yang Suo / Kenichi Yokoyama / Seok-Yong Lee /
Abstract: Chitin is an essential component of the fungal cell wall. Chitin synthases (Chss) catalyze chitin formation and translocation across the membrane and are targets of antifungal agents, including ...Chitin is an essential component of the fungal cell wall. Chitin synthases (Chss) catalyze chitin formation and translocation across the membrane and are targets of antifungal agents, including nikkomycin Z and polyoxin D. Lack of structural insights into the action of these inhibitors on Chs has hampered their further development to the clinic. We present the cryo-EM structures of Chs2 from Candida albicans (CaChs2) in the apo, substrate-bound, nikkomycin Z-bound, and polyoxin D-bound states. CaChs2 adopts a unique domain-swapped dimer configuration where a conserved motif in the domain-swapped region controls enzyme activity. CaChs2 has a dual regulation mechanism where the chitin translocation tunnel is closed by the extracellular gate and plugged by a lipid molecule in the apo state to prevent non-specific leak. Analyses of substrate and inhibitor binding provide insights into the chemical logic of Chs inhibition, which can guide Chs-targeted antifungal development.
History
DepositionNov 14, 2021-
Header (metadata) releaseJul 13, 2022-
Map releaseJul 13, 2022-
UpdateJul 27, 2022-
Current statusJul 27, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25432.png

Downloads & links

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Map

FileDownload / File: emd_25432.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.08270019 - 0.16553248
Average (Standard dev.)0.0006679817 (±0.005386267)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions216216216
Spacing216216216
CellA=B=C: 233.28001 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Chitin synthase 2 from Candida albicans in the apo state

EntireName: Chitin synthase 2 from Candida albicans in the apo state
Components
  • Complex: Chitin synthase 2 from Candida albicans in the apo state
    • Protein or peptide: Chitin synthase
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine

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Supramolecule #1: Chitin synthase 2 from Candida albicans in the apo state

SupramoleculeName: Chitin synthase 2 from Candida albicans in the apo state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Candida albicans (yeast)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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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: 119.298227 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSYNNPNNSN SHLRPHAYNN SRRDDSDGDE SSIEFLNQRS NTPLTQGTYN YHNTSTNSLN FQQPEPIYRN QTRTSLSDSY YDHPIFDTS QTQIQPPHDN PFTESYEMTD TSYQGNDHHY RTGQPNHLMN PTYNQAFIPH VYDEEDNDEQ EYDQRIQYNQ F QGDHFDLA ...String:
MSYNNPNNSN SHLRPHAYNN SRRDDSDGDE SSIEFLNQRS NTPLTQGTYN YHNTSTNSLN FQQPEPIYRN QTRTSLSDSY YDHPIFDTS QTQIQPPHDN PFTESYEMTD TSYQGNDHHY RTGQPNHLMN PTYNQAFIPH VYDEEDNDEQ EYDQRIQYNQ F QGDHFDLA AISYADDESQ SQLDYVPTER VIPEGEEEEE EGETSFEKEP GSETISGPFG EERSFEEPPP QQEVRSKKLT RA TGLNGHL VLDCPVADEL LSKFPDYNPA EKSGGLSREF AFMRYTAVTC GPSNFYRDAY ILRPVHYPIP RQTELMIVIT MYN EDDILL GRTLKGVFKN IKYLESKARS STWGKDSWKK IVVCIVSDGR TKINERAQAL LAGLGVYQEG LAKSRVDDKK VQAH MFEYT TRVGISKVTD DVVKLTTEKV VPVQMLFCLK ETNAKKINSH RWCFQAIGQV LDPKIVVLLD CGTQPSGRSL YELWK EFDR DHRVAGACGE ITTSLKKRQM ITNPLVYGQN FEYKISNILD KPTESSFGFI SVLPGAFSAY RFIALQNDIN GVGPLE KYF KGEFLHSSGE LDPNDDEFQM KHLMLKEEAG IFTSNMYLAE DRILCFELVA KRGCNWLLRY CKSARAETDV PEGLAEF IL QRRRWLNGSF FAAIYSLVHF YKVWTSSHSF GRKIFLHIEF FYQLINLIVS WFSIGSYFLV FRILTTSLGD KALGFAPG K ILSVIFLWLY LASIVTTFVL SFGNKPKGTE KFYVTIVIFF AILMAYMIFA AIFMAVHSIQ DIYRSGTRIT VSLFFQNSE FRDLVVATSS TYALYFLASF LYFEPWHMFT SFVQYILLSP SYVNVLNIYA FCNIDDISWG TKGEVGGKSL GEAKLREDGT FDVSVPISK EQINQSYLDQ LEKIRDPAPP EEKVLVTNTE DYYAFIRSMT VLVWMFTNFV VIALVLETGG FNQFVEATDL A NLKSNRAA VFLTVILWTV AFMALFRFIG CIYYLITRLG REIKASEHAT KANSLEVLFQ GPDYKDDDDK AHHHHHHHHH H

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Macromolecule #2: 1,2-Distearoyl-sn-glycerophosphoethanolamine

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 2 / Number of copies: 8 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da
Chemical component information

ChemComp-3PE:
1,2-Distearoyl-sn-glycerophosphoethanolamine / phospholipid*YM / Phosphatidylethanolamine

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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

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: From Ab initio
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 385452

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