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- EMDB-39709: Cryo-EM structure of chitin synthase -

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Basic information

Entry
Database: EMDB / ID: EMD-39709
TitleCryo-EM structure of chitin synthase
Map data
Sample
  • Complex: a membrane-integrated glycosyltransferase that transfers GlcNAc from UDP-GlcNAc to a growing chitin chain
    • Protein or peptide: chitin synthase
  • Ligand: URIDINE-5'-DIPHOSPHATE
  • Ligand: MANGANESE (II) ION
Keywordschitin synthase / membrane-integrated glycosyltransferase / TRANSFERASE
Function / homology
Function and homology information


chitin synthase / chitin synthase activity / chitin biosynthetic process / cell wall organization / plasma membrane
Similarity search - Function
Fungal chitin synthase / Chitin synthase-like glycosyltransferase domain / Chitin synthase / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
Biological speciesPhytophthora sojae strain P6497 (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsZhang X / Niu S / Li P / Bi Y
Funding support1 items
OrganizationGrant numberCountry
Other government
CitationJournal: Int J Mol Sci / Year: 2024
Title: Chitin Translocation Is Functionally Coupled with Synthesis in Chitin Synthase.
Authors: Suhao Niu / Lei Qi / Xiaoyue Zhang / Dongfang He / Pengwei Li / Hao Wang / Yunchen Bi /
Abstract: Chitin, an extracellular polysaccharide, is synthesized by membrane-embedded chitin synthase (CHS) utilizing intracellular substrates. The mechanism of the translocation of synthesized chitin across ...Chitin, an extracellular polysaccharide, is synthesized by membrane-embedded chitin synthase (CHS) utilizing intracellular substrates. The mechanism of the translocation of synthesized chitin across the membrane to extracellular locations remains unresolved. We prove that the chitin synthase from (CHS) is a processive glycosyltransferase, which can rapidly produce and tightly bind with the highly polymerized chitin. We further demonstrate that CHS is a bifunctional enzyme, which is necessary and sufficient to translocate the synthesized chitin. CHS was purified and then reconstituted into proteoliposomes (PLs). The nascent chitin is generated and protected from chitinase degradation unless detergent solubilizes the PLs, showing that CHS translocates the newly produced chitin into the lumen of the PLs. We also attempted to resolve the CHS structure of the synthesized chitin-bound state, although it was not successful; the obtained high-resolution structure of the UDP/Mn-bound state could still assist in describing the characterization of the CHS's transmembrane channel. Consistently, we demonstrate that CHS is indispensable and capable of translocating chitin in a process that is tightly coupled to chitin synthesis.
History
DepositionApr 10, 2024-
Header (metadata) releaseDec 4, 2024-
Map releaseDec 4, 2024-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39709.png

Downloads & links

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Map

FileDownload / File: emd_39709.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 300 pix.
= 276. Å		0.92 Å/pix.
x 300 pix.
= 276. Å		0.92 Å/pix.
x 300 pix.
= 276. Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.7687176 - 2.8725579
Average (Standard dev.)0.0034363698 (±0.0817445)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 276.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_39709_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_39709_half_map_2.map
Projections & Slices
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Sample components

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Entire : a membrane-integrated glycosyltransferase that transfers GlcNAc f...

EntireName: a membrane-integrated glycosyltransferase that transfers GlcNAc from UDP-GlcNAc to a growing chitin chain
Components
  • Complex: a membrane-integrated glycosyltransferase that transfers GlcNAc from UDP-GlcNAc to a growing chitin chain
    • Protein or peptide: chitin synthase
  • Ligand: URIDINE-5'-DIPHOSPHATE
  • Ligand: MANGANESE (II) ION

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Supramolecule #1: a membrane-integrated glycosyltransferase that transfers GlcNAc f...

SupramoleculeName: a membrane-integrated glycosyltransferase that transfers GlcNAc from UDP-GlcNAc to a growing chitin chain
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Phytophthora sojae strain P6497 (eukaryote)
Molecular weightTheoretical: 103 kDa/nm

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Macromolecule #1: chitin synthase

MacromoleculeName: chitin synthase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: chitin synthase
Source (natural)Organism: Phytophthora sojae strain P6497 (eukaryote)
Molecular weightTheoretical: 104.586328 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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 SSAALVPRGS HHHHHH

UniProtKB: Chitin synthase 1

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Macromolecule #2: URIDINE-5'-DIPHOSPHATE

MacromoleculeName: URIDINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: UDP
Molecular weightTheoretical: 404.161 Da
Chemical component information

ChemComp-UDP:
URIDINE-5'-DIPHOSPHATE / UDP*YM

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Macromolecule #3: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: MN
Molecular weightTheoretical: 54.938 Da

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7wjn

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 561823
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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