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- PDB-9o4g: Cryo-EM structure of the CHSY3-CHPF1 chondroitin synthase heterodimer -

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Basic information

Entry
Database: PDB / ID: 9o4g
TitleCryo-EM structure of the CHSY3-CHPF1 chondroitin synthase heterodimer
Components
  • Chondroitin sulfate synthase 2
  • Chondroitin sulfate synthase 3
KeywordsSUGAR BINDING PROTEIN / TRANSFERASE / Chondroitin sulfate / Chondroitin sulfate synthase
Function / homology
Function and homology information


glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase / N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase / glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity / N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity / CS-GAG biosynthesis / chondroitin sulfate proteoglycan biosynthetic process / Golgi cisterna membrane / mitochondrial matrix / Golgi membrane / metal ion binding / cytosol
Similarity search - Function
Chondroitin N-acetylgalactosaminyltransferase / : / Chondroitin N-acetylgalactosaminyltransferase / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
: / URIDINE-5'-DIPHOSPHATE / Chondroitin sulfate synthase 3 / Chondroitin sulfate synthase 2
Similarity search - Component
Biological speciesHuman adenovirus sp.
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.42 Å
AuthorsTehari, D. / Cortiella, N. / Perez, C. / Moremen, K.
Funding support United States, Switzerland, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM154846 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM130915 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103390 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM158187 United States
Swiss National Science Foundation310030_207974 Switzerland
CitationJournal: To Be Published
Title: Structural basis of chondroitin sulfate backbone polymer synthesis
Authors: Tehari, D. / Cortiella, N. / Perez, C. / Moremen, K.W.
History
DepositionApr 8, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chondroitin sulfate synthase 3
B: Chondroitin sulfate synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,5985
Polymers179,0842
Non-polymers5143
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Chondroitin sulfate synthase 3 / Carbohydrate synthase 2 / Chondroitin glucuronyltransferase 3 / Chondroitin synthase 2 / ChSy-2 / ...Carbohydrate synthase 2 / Chondroitin glucuronyltransferase 3 / Chondroitin synthase 2 / ChSy-2 / Glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase II / N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase 3 / N-acetylgalactosaminyltransferase 3


Mass: 97018.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus sp. / Gene: CHSY3, CHSY2, CSS3 / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
References: UniProt: Q70JA7, glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase, N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase
#2: Protein Chondroitin sulfate synthase 2 / Chondroitin glucuronyltransferase 2 / Chondroitin-polymerizing factor / ChPF / Glucuronosyl-N- ...Chondroitin glucuronyltransferase 2 / Chondroitin-polymerizing factor / ChPF / Glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase II / N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase II / N-acetylgalactosaminyltransferase 2


Mass: 82065.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHPF, CSS2, UNQ651/PRO1281 / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
References: UniProt: Q8IZ52, glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase, N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: CHSY3-CHPF1 heterocomplex / Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Strain: HEK293
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS TALOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 54.9 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
4cryoSPARC4.5.1CTF correction
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 163527 / Symmetry type: POINT
RefinementHighest resolution: 3.42 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00311266
ELECTRON MICROSCOPYf_angle_d0.53815273
ELECTRON MICROSCOPYf_dihedral_angle_d4.6751525
ELECTRON MICROSCOPYf_chiral_restr0.0411636
ELECTRON MICROSCOPYf_plane_restr0.0052004

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