9Q8Z | pdb_00009q8z

Human chondroitin sulfate polymerase complex CHSY3-CHPF


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for human chondroitin sulfate chain polymerization.

Dutta, P.Cordeiro, R.L.Friedel-Arboleas, M.Bourgeais, M.Vallet, S.D.Weber, M.Molinas, M.Shu, H.Gronset, M.N.N.Miller, R.L.Boeri Erba, E.Wild, R.

(2025) Nat Commun 16: 11663-11663

  • DOI: https://doi.org/10.1038/s41467-025-66787-5
  • Primary Citation of Related Structures:  
    9Q8Z

  • PubMed Abstract: 

    Chondroitin sulfates are complex polysaccharide chains that regulate various biological processes at the cell surface and within the extracellular matrix. Here, we identify four heterodimeric complexes responsible for chondroitin sulfate chain polymerization in humans: CHSY1-CHPF, CHSY1-CHPF2, CHSY3-CHPF, and CHSY3-CHPF2. Using a custom-tailored in vitro glycosylation assay based on chemo-enzymatically synthesized fluorescent substrates, we demonstrate that all four complexes exhibit chain polymerization activity. The cryo-EM structure of the CHSY3-CHPF complex provides molecular insights into the chondroitin sulfate chain polymerization reaction. The architecture of the catalytic sites suggests that CHSY1 and CHSY3 are enzymatically active, while CHPF and CHPF2 primarily play a stabilizing role. Mutational analysis of purified enzyme complexes, combined with an in cellulo complementation assay, confirms that only CHSY1 and CHSY3 have bifunctional glycosyltransferase activities. Based on the spatial arrangement of the catalytic sites, we propose that chondroitin sulfate chain polymerization follows a non-processive, distributive mechanism.


  • Organizational Affiliation
    • Institut de Biologie Structurale, UMR 5075, University Grenoble Alpes, CNRS, CEA, Grenoble, France.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chondroitin sulfate synthase 2710Homo sapiensMutation(s): 0 
Gene Names: CHPFCSS2UNQ651/PRO1281
EC: 2.4.1.175 (PDB Primary Data), 2.4.1.226 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IZ52 (Homo sapiens)
Explore Q8IZ52 
Go to UniProtKB:  Q8IZ52
PHAROS:  Q8IZ52
GTEx:  ENSG00000123989 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IZ52
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q8IZ52-1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Chondroitin sulfate synthase 3753Homo sapiensMutation(s): 0 
Gene Names: CHSY3CHSY2CSS3
EC: 2.4.1.175 (PDB Primary Data), 2.4.1.226 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q70JA7 (Homo sapiens)
Explore Q70JA7 
Go to UniProtKB:  Q70JA7
PHAROS:  Q70JA7
GTEx:  ENSG00000198108 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ70JA7
Glycosylation
Glycosylation Sites: 2Go to GlyGen: Q70JA7-1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UDP (Subject of Investigation/LOI)
Query on UDP

Download Ideal Coordinates CCD File 
D [auth B]URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B],
F [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
MN (Subject of Investigation/LOI)
Query on MN

Download Ideal Coordinates CCD File 
G [auth B],
H [auth B]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARCv.3.3.1
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateImpulscience Program of the Bettencourt Schueller Foundation
Agence Nationale de la Recherche (ANR)FranceANR-23-CE44-0011
Laboratories of Excellence (LabEx)FranceANR-17-EURE-0003
Agence Nationale de la Recherche (ANR)FranceANR-21-ESRE-0046

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-03
    Type: Initial release
  • Version 1.1: 2025-12-10
    Changes: Data collection, Database references
  • Version 1.2: 2026-01-07
    Changes: Data collection, Database references