+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36855 | |||||||||
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Title | S. cerevisiae Chs1 in complex with polyoxin B | |||||||||
Map data | map | |||||||||
Sample |
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Keywords | ANTIFUNGAL PROTEIN-INHIBITOR complex | |||||||||
Function / homology | Function and homology information chitosome / chitin synthase / chitin synthase activity / cell wall chitin biosynthetic process / septum digestion after cytokinesis / cell septum / cell periphery / cell wall organization / plasma membrane Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae S288C (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.64 Å | |||||||||
Authors | Bai L / Chen DD | |||||||||
Funding support | China, 1 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Structure, catalysis, chitin transport, and selective inhibition of chitin synthase. Authors: Dan-Dan Chen / Zhao-Bin Wang / Le-Xuan Wang / Peng Zhao / Cai-Hong Yun / Lin Bai / Abstract: Chitin is one of the most abundant natural biopolymers and serves as a critical structural component of extracellular matrices, including fungal cell walls and insect exoskeletons. As a linear ...Chitin is one of the most abundant natural biopolymers and serves as a critical structural component of extracellular matrices, including fungal cell walls and insect exoskeletons. As a linear polymer of β-(1,4)-linked N-acetylglucosamine, chitin is synthesized by chitin synthases, which are recognized as targets for antifungal and anti-insect drugs. In this study, we determine seven different cryo-electron microscopy structures of a Saccharomyces cerevisiae chitin synthase in the absence and presence of glycosyl donor, acceptor, product, or peptidyl nucleoside inhibitors. Combined with functional analyses, these structures show how the donor and acceptor substrates bind in the active site, how substrate hydrolysis drives self-priming, how a chitin-conducting transmembrane channel opens, and how peptidyl nucleoside inhibitors inhibit chitin synthase. Our work provides a structural basis for understanding the function and inhibition of chitin synthase. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_36855.map.gz | 37.5 MB | EMDB map data format | |
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Header (meta data) | emd-36855-v30.xml emd-36855.xml | 15 KB 15 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_36855_fsc.xml | 9.2 KB | Display | FSC data file |
Images | emd_36855.png | 77.2 KB | ||
Filedesc metadata | emd-36855.cif.gz | 6.1 KB | ||
Others | emd_36855_half_map_1.map.gz emd_36855_half_map_2.map.gz | 37.2 MB 37.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36855 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36855 | HTTPS FTP |
-Related structure data
Related structure data | 8k3pMC 8k3qC 8k3rC 8k3tC 8k3uC 8k3vC 8k3wC 8k3xC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_36855.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: half map
File | emd_36855_half_map_1.map | ||||||||||||
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Annotation | half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map
File | emd_36855_half_map_2.map | ||||||||||||
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Annotation | half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : S. cerevisiae Chs1 in complex with polyoxin B
Entire | Name: S. cerevisiae Chs1 in complex with polyoxin B |
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Components |
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-Supramolecule #1: S. cerevisiae Chs1 in complex with polyoxin B
Supramolecule | Name: S. cerevisiae Chs1 in complex with polyoxin B / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
-Macromolecule #1: Chitin synthase 1
Macromolecule | Name: Chitin synthase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c |
Molecular weight | Theoretical: 133.307375 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | String: 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 |
-Macromolecule #2: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...
Macromolecule | Name: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate type: ligand / ID: 2 / Number of copies: 2 / Formula: POV |
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Molecular weight | Theoretical: 760.076 Da |
Chemical component information | ChemComp-POV: |
-Macromolecule #3: (2S)-2-[[(2S,3S,4S)-5-aminocarbonyloxy-2-azanyl-3,4-bis(oxidanyl)...
Macromolecule | Name: (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 |
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Molecular weight | Theoretical: 507.406 Da |
Chemical component information | ChemComp-VDG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 4 mg/mL |
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Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |