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- EMDB-32918: CryoEM structure of chitin synthase 1 from Phytophthora sojae com... -
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Open data
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Basic information
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Title | CryoEM structure of chitin synthase 1 from Phytophthora sojae complexed with UDP | ||||||||||||
![]() | CryoEM map of chitin synthase 1 from Phytophthora sojae complexed with UDP | ||||||||||||
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![]() | carbohydate / biosynthetic protein / membrane protein / transferase | ||||||||||||
Function / homology | ![]() chitin synthase / chitin synthase activity / : / cell septum / cell periphery / membrane Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||
![]() | Chen W / Cao P | ||||||||||||
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. | ||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 7.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 12.6 KB 12.6 KB | Display Display | ![]() |
Images | ![]() | 151.2 KB | ||
Filedesc metadata | ![]() | 5.8 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7x06MC ![]() 7wjmC ![]() 7wjnC ![]() 7wjoC ![]() 7x05C C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | CryoEM map of chitin synthase 1 from Phytophthora sojae complexed with UDP | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
-Entire : Chitin synthase 1
Entire | Name: Chitin synthase 1 |
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Components |
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-Supramolecule #1: Chitin synthase 1
Supramolecule | Name: Chitin synthase 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Chitin synthase
Macromolecule | Name: Chitin synthase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: chitin synthase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 103.146703 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MSGAPPPSSG FAPRSYGQQP LSHAPRSSMM SVEYDGIPLP PPSIRSCGSQ QYVTSYIPTG AAFPPSSVQD MISSMKSYAS ATDLVRTYS EIPSVEEALS TLDRAAAALN ARRYRDALKL YLEGGYAMAN VAERQANPKI CNLLTSKGFE TLNWCARLCD W IEGRIKEK ...String: MSGAPPPSSG FAPRSYGQQP LSHAPRSSMM SVEYDGIPLP PPSIRSCGSQ QYVTSYIPTG AAFPPSSVQD MISSMKSYAS ATDLVRTYS EIPSVEEALS TLDRAAAALN ARRYRDALKL YLEGGYAMAN VAERQANPKI CNLLTSKGFE TLNWCARLCD W IEGRIKEK HPRPGVHKVG IPVSNWDEDW VGPFMDEEEA RRMWYTPVYC PHPIDFSNLG YRLRCVETGR RPRLMICITM YN EGPQQLK ATLKKLANNL AYLKEQMPGD EKSLTGAFAG DDVWQNVLVC IVADGREQVH PKTLDYLEAI GLYDEDLLTI NSA GIGAQC HLFEHTLQLS VNGKCLLPIQ TVFALKENKA SKLDSHHWYF NAFAEQIQPE YTAVMDVGTM LTKSALYHLL FAFE RNHQI GGACGQLTVD NPFENLSNWV ISAQHFEYKI SNILDKSLES CFGFISVLPG AFSAYRYEAI RGAPLDAYFQ TLNIE LDVL GPFIGNMYLA EDRILSFEVV ARKNCNWTMH YVKDAVARTD VPHDLVGLIS QRKRWLNGAF FATLFSIWNW GRIYSE SKH TFVRKMAFLV FYVYHLLYTA FGFFLPANLY LALFFIVFQG FQQNRLEFID TSEYSQTVLD CAVYIYNFSY LFGLLML II IGLGNNPKHM KLTYYFVGAV FGLMMMLSSL VGAGIFFSTP ATVHSIVVSI LTVGVYFIAS ALHGEVHHIF MTFTHYTA L IPSFVNIFTI YSFCNLQDLS WGTKGLHDDP LLAASLDETE KGDFKDVIAK RRALEELRRE EKERVENRKK NFEAFRTNV LLTWAFSNLI FALFVVYFAS SSTYMPVLYI FVASLNTCRL LGSIGHWVYI HTEGLRGRVI DKSECGNGTG RYPQNSYVQL EEHYAALAE DQRTYASGRT NASVRTVNDV SSAA UniProtKB: chitin synthase |
-Macromolecule #2: URIDINE-5'-DIPHOSPHATE
Macromolecule | Name: URIDINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: UDP |
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Molecular weight | Theoretical: 404.161 Da |
Chemical component information | ![]() ChemComp-UDP: |
-Macromolecule #3: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 5 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Final reconstruction | Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 224465 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |