Download MendeleyStructural basis for human chondroitin sulfate chain polymerization
Dutta, P., Cordeiro, R.L., Friedel, M., Bourgeais, M., Vallet, S., Weber, M., Molinas, M., Shu, H., Gronset, M., Miller, R., Boeri-Erba, E., Wild, R.(2025) Nat Commun
9Q8Z | pdb_00009q8z
Human chondroitin sulfate polymerase complex CHSY3-CHPF
- PDB DOI: https://doi.org/10.2210/pdb9Q8Z/pdb
- EM Map EMD-52913: EMDB EMDataResource
- Classification: TRANSFERASE
- Organism(s): Homo sapiens
- Expression System: Homo sapiens
- Mutation(s): No
- Deposited: 2025-02-25 Released: 2025-12-03
- Funding Organization(s): Other private, Agence Nationale de la Recherche (ANR), Laboratories of Excellence (LabEx)
Experimental Data Snapshot
- Method: ELECTRON MICROSCOPY
- Resolution: 3.00 Å
- Aggregation State: PARTICLE
- Reconstruction Method: SINGLE PARTICLE
Starting Model: in silico
View more details
wwPDB Validation 3D Report Full Report
This is version 1.0 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Chondroitin sulfate synthase 2 | 710 | Homo sapiens | Mutation(s): 0 Gene Names: CHPF, CSS2, UNQ651/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 Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q8IZ52 | ||||
Glycosylation | |||||
| Glycosylation Sites: 1 | Go to GlyGen: Q8IZ52-1 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Chondroitin sulfate synthase 3 | 753 | Homo sapiens | Mutation(s): 0 Gene Names: CHSY3, CHSY2, CSS3 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 Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q70JA7 | ||||
Glycosylation | |||||
| Glycosylation Sites: 2 | Go to GlyGen: Q70JA7-1 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| UDP (Subject of Investigation/LOI) Query on UDP | D [auth B] | URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N |  | ||
| NAG Query on NAG | 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 | 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
| Task | Software Package | Version |
|---|---|---|
| RECONSTRUCTION | cryoSPARC | v.3.3.1 |
| MODEL REFINEMENT | PHENIX |
Entry History & Funding Information
Deposition Data
- Released Date: 2025-12-03 Deposition Author(s): Dutta, P., Cordeiro, R.L., Wild, R.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Other private | Impulscience Program of the Bettencourt Schueller Foundation | |
| Agence Nationale de la Recherche (ANR) | France | ANR-23-CE44-0011 |
| Laboratories of Excellence (LabEx) | France | ANR-17-EURE-0003 |
| Agence Nationale de la Recherche (ANR) | France | ANR-21-ESRE-0046 |
Revision History (Full details and data files)
- Version 1.0: 2025-12-03
Type: Initial release
