+Open data
-Basic information
Entry | Database: PDB / ID: 8k3v | ||||||
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Title | S. cerevisiae Chs1 in complex with UDP-GlcNAc | ||||||
Components | Chitin synthase 1 | ||||||
Keywords | ANTIFUNGAL PROTEIN/INHIBITOR / ANTIFUNGAL PROTEIN-INHIBITOR complex | ||||||
Function / homology | Function and homology information chitosome / chitin synthase / chitin synthase activity / : / septum digestion after cytokinesis / cell septum / cell periphery / cell wall organization / plasma membrane Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||
Authors | Bai, L. / Chen, D. | ||||||
Funding support | China, 1items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8k3v.cif.gz | 274.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8k3v.ent.gz | 208.4 KB | Display | PDB format |
PDBx/mmJSON format | 8k3v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8k3v_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8k3v_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8k3v_validation.xml.gz | 52.6 KB | Display | |
Data in CIF | 8k3v_validation.cif.gz | 74.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k3/8k3v ftp://data.pdbj.org/pub/pdb/validation_reports/k3/8k3v | HTTPS FTP |
-Related structure data
Related structure data | 36862MC 8k3pC 8k3qC 8k3rC 8k3tC 8k3uC 8k3wC 8k3xC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 130001.141 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: CHS1 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P08004, chitin synthase #2: Chemical | #3: Chemical | #4: Chemical | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: S. cerevisiae Chs1 in complex with UDP-GlcNAc / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Source (recombinant) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software | Name: PHENIX / Version: 1.18.2_3874: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 250346 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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