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- EMDB-36855: S. cerevisiae Chs1 in complex with polyoxin B -

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Basic information

Entry
Database: EMDB / ID: EMD-36855
TitleS. cerevisiae Chs1 in complex with polyoxin B
Map datamap
Sample
  • Complex: S. cerevisiae Chs1 in complex with polyoxin B
    • Protein or peptide: Chitin synthase 1
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: (2S)-2-[[(2S,3S,4S)-5-aminocarbonyloxy-2-azanyl-3,4-bis(oxidanyl)pentanoyl]amino]-2-[(2R,3S,4R,5R)-5-[5-(hydroxymethyl)-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]ethanoic acid
KeywordsANTIFUNGAL PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


chitosome / cell wall chitin biosynthetic process / chitin synthase / chitin synthase activity / septum digestion after cytokinesis / cell septum / cell periphery / cell wall organization / plasma 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 speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.64 Å
AuthorsBai L / Chen DD
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171212 China
CitationJournal: Nat Commun / Year: 2023
Title: Structure, catalysis, chitin transport, and selective inhibition of chitin synthase
Authors: Chen DD / Wang ZB / Wang LX / Zhao P / Yun CH / Bai L
History
DepositionJul 16, 2023-
Header (metadata) releaseOct 18, 2023-
Map releaseOct 18, 2023-
UpdateNov 1, 2023-
Current statusNov 1, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36855.png

Downloads & links

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Map

FileDownload / File: emd_36855.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.117
Minimum - Maximum-0.3818312 - 0.58118665
Average (Standard dev.)-0.000015902717 (±0.022665331)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 233.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map

Fileemd_36855_half_map_1.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map

Fileemd_36855_half_map_2.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : S. cerevisiae Chs1 in complex with polyoxin B

EntireName: S. cerevisiae Chs1 in complex with polyoxin B
Components
  • Complex: S. cerevisiae Chs1 in complex with polyoxin B
    • Protein or peptide: Chitin synthase 1
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: (2S)-2-[[(2S,3S,4S)-5-aminocarbonyloxy-2-azanyl-3,4-bis(oxidanyl)pentanoyl]amino]-2-[(2R,3S,4R,5R)-5-[5-(hydroxymethyl)-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]ethanoic acid

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Supramolecule #1: S. cerevisiae Chs1 in complex with polyoxin B

SupramoleculeName: S. cerevisiae Chs1 in complex with polyoxin B / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Chitin synthase 1

MacromoleculeName: Chitin synthase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 133.307375 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSDQNNRSRN EYHSNRKNEP SYELQNAHSG LFHSSNEELT NRNQRYTNQN ASMGSFTPVQ SLQFPEQSQQ TNMLYNGDDG NNNTINDNE RDIYGGFVNH HRQRPPPATA EYNDVFNTNS QQLPSEHQYN NVPSYPLPSI NVIQTTPELI HNGSQTMATP I ERPFFNEN ...String:
MSDQNNRSRN EYHSNRKNEP SYELQNAHSG LFHSSNEELT NRNQRYTNQN ASMGSFTPVQ SLQFPEQSQQ TNMLYNGDDG NNNTINDNE RDIYGGFVNH HRQRPPPATA EYNDVFNTNS QQLPSEHQYN NVPSYPLPSI NVIQTTPELI HNGSQTMATP I ERPFFNEN DYYYNNRNSR TSPSIASSSD GYADQEARPI LEQPNNNMNS GNIPQYHDQP FGYNNGYHGL QAKDYYDDPE GG YIDQRGD DYQINSYLGR NGEMVDPYDY ENSLRHMTPM ERREYLHDDS RPVNDGKEEL DSVKSGYSHR DLGEYDKDDF SRD DEYDDL NTIDKLQFQA NGVPASSSVS SIGSKESDII VSNDNLTANR ALKRSGTEIR KFKLWNGNFV FDSPISKTLL DQYA TTTEN ANTLPNEFKF MRYQAVTCEP NQLAEKNFTV RQLKYLTPRE TELMLVVTMY NEDHILLGRT LKGIMDNVKY MVKKK NSST WGPDAWKKIV VCIISDGRSK INERSLALLS SLGCYQDGFA KDEINEKKVA MHVYEHTTMI NITNISESEV SLECNQ GTV PIQLLFCLKE QNQKKINSHR WAFEGFAELL RPNIVTLLDA GTMPGKDSIY QLWREFRNPN VGGACGEIRT DLGKRFV KL LNPLVASQNF EYKMSNILDK TTESNFGFIT VLPGAFSAYR FEAVRGQPLQ KYFYGEIMEN EGFHFFSSNM YLAEDRIL C FEVVTKKNCN WILKYCRSSY ASTDVPERVP EFILQRRRWL NGSFFASVYS FCHFYRVWSS GHNIGRKLLL TVEFFYLFF NTLISWFSLS SFFLVFRILT VSIALAYHSA FNVLSVIFLW LYGICTLSTF ILSLGNKPKS TEKFYVLTCV IFAVMMIYMI FCSIFMSVK SFQNILKNDT ISFEGLITTE AFRDIVISLG STYCLYLISS IIYLQPWHML TSFIQYILLS PSYINVLNIY A FCNVHDLS WGTKGAMANP LGKINTTEDG TFKMEVLVSS SEIQANYDKY LKVLNDFDPK SESRPTEPSY DEKKTGYYAN VR SLVIIFW VITNFIIVAV VLETGGIADY IAMKSISTDD TLETAKKAEI PLMTSKASIY FNVILWLVAL SALIRFIGCS IYM IVRFFK KVTFRGGSGG DYKDDDDKDY KDDDDKDYKD DDDK

UniProtKB: Chitin synthase 1

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Macromolecule #2: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 2 / Number of copies: 2 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM / POPC

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Macromolecule #3: (2S)-2-[[(2S,3S,4S)-5-aminocarbonyloxy-2-azanyl-3,4-bis(oxidanyl)...

MacromoleculeName: (2S)-2-[[(2S,3S,4S)-5-aminocarbonyloxy-2-azanyl-3,4-bis(oxidanyl)pentanoyl]amino]-2-[(2R,3S,4R,5R)-5-[5-(hydroxymethyl)-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]ethanoic acid
type: ligand / ID: 3 / Number of copies: 2 / Formula: VDG
Molecular weightTheoretical: 507.406 Da
Chemical component information

ChemComp-VDG:
(2S)-2-[[(2S,3S,4S)-5-aminocarbonyloxy-2-azanyl-3,4-bis(oxidanyl)pentanoyl]amino]-2-[(2R,3S,4R,5R)-5-[5-(hydroxymethyl)-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]ethanoic acid

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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

Concentration4 mg/mL
BufferpH: 7.4
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: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.64 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 113713
FSC plot (resolution estimation)

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