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- PDB-7wjn: CryoEM structure of chitin synthase 1 mutant E495A from Phytophth... -
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Basic information
Entry | Database: PDB / ID: 7wjn | |||||||||
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Title | CryoEM structure of chitin synthase 1 mutant E495A from Phytophthora sojae complexed with UDP-GlcNAc | |||||||||
![]() | Chitin synthase | |||||||||
![]() | TRANSFERASE / carbohydate / biosynthetic protein / membrane protein | |||||||||
Function / homology | ![]() chitin synthase / chitin synthase activity / : / cell septum / cell periphery / membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
![]() | Chen, W. / Cao, P. / Gong, Y. / Yang, Q. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for directional chitin biosynthesis. Authors: Wei Chen / Peng Cao / Yuansheng Liu / Ailing Yu / Dong Wang / Lei Chen / Rajamanikandan Sundarraj / Zhiguang Yuchi / Yong Gong / Hans Merzendorfer / Qing Yang / ![]() ![]() Abstract: Chitin, the most abundant aminopolysaccharide in nature, is an extracellular polymer consisting of N-acetylglucosamine (GlcNAc) units. The key reactions of chitin biosynthesis are catalysed by chitin ...Chitin, the most abundant aminopolysaccharide in nature, is an extracellular polymer consisting of N-acetylglucosamine (GlcNAc) units. The key reactions of chitin biosynthesis are catalysed by chitin synthase, a membrane-integrated glycosyltransferase that transfers GlcNAc from UDP-GlcNAc to a growing chitin chain. However, the precise mechanism of this process has yet to be elucidated. Here we report five cryo-electron microscopy structures of a chitin synthase from the devastating soybean root rot pathogenic oomycete Phytophthora sojae (PsChs1). They represent the apo, GlcNAc-bound, nascent chitin oligomer-bound, UDP-bound (post-synthesis) and chitin synthase inhibitor nikkomycin Z-bound states of the enzyme, providing detailed views into the multiple steps of chitin biosynthesis and its competitive inhibition. The structures reveal the chitin synthesis reaction chamber that has the substrate-binding site, the catalytic centre and the entrance to the polymer-translocating channel that allows the product polymer to be discharged. This arrangement reflects consecutive key events in chitin biosynthesis from UDP-GlcNAc binding and polymer elongation to the release of the product. We identified a swinging loop within the chitin-translocating channel, which acts as a 'gate lock' that prevents the substrate from leaving while directing the product polymer into the translocating channel for discharge to the extracellular side of the cell membrane. This work reveals the directional multistep mechanism of chitin biosynthesis and provides a structural basis for inhibition of chitin synthesis. | |||||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 295.3 KB | Display | ![]() |
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PDB format | ![]() | 236.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 881.7 KB | Display | ![]() |
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Full document | ![]() | 889.9 KB | Display | |
Data in XML | ![]() | 44.9 KB | Display | |
Data in CIF | ![]() | 67.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 32546MC ![]() 7wjmC ![]() 7wjoC ![]() 7x05C ![]() 7x06C M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 103088.664 Da / Num. of mol.: 2 / Mutation: E495A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: P6497 / Gene: PHYSODRAFT_557500 / Cell line (production host): HEK293 / Production host: ![]() #2: Chemical | #3: 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 |
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Sample preparation
Component | Name: Chitin synthase 1 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 8 |
Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 60 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 350132 / Symmetry type: POINT | ||||||||||||||||||||||||
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