9DFT | pdb_00009dft

G1 domain of human aggrecan

• PDB DOI: https://doi.org/10.2210/pdb9DFT/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2024-08-30 Released: 2025-04-30 
• Deposition Author(s): Bouyains, S.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 
  0.244 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.213 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: in silico

Literature

Aggrecan immobilizes to perineuronal nets through hyaluronan-dependent and hyaluronan-independent binding activities.

Otsuka, M.Y., Essel, L.B., Sinha, A., Nickerson, G., Mejia, S.M., Edge, A., Matthews, R.T., Bouyain, S.

(2025) J Biological Chem 301: 108525-108525

• PubMed: 40273987 
• DOI: https://doi.org/10.1016/j.jbc.2025.108525
• Primary Citation of Related Structures:  
  9DFF, 9DFT


• PubMed Abstract: 
  

  Aggrecan (ACAN) is a large, secreted chondroitin sulfate proteoglycan that includes three globular regions named G1, G2, G3, and is decorated with multiple glycosaminoglycan attachments between its G2 and G3 domains. The N-terminal G1 region interacts with the glycosaminoglycan hyaluronan (HA), which is an essential component of the vertebrate extracellular matrix. In the central nervous system, ACAN is found in perineuronal nets (PNNs), honeycomb-like structures that localize to the surface of parvalbumin-positive neurons in specific neural circuits. PNNs regulate the plasticity of the central nervous system, and it is believed that association between ACAN and HA is a foundational event in the assembly of these reticular structures. Here, we report the co-crystal structure of the G1 region of ACAN in the absence and presence of a HA decasaccharide and analyze the importance of the HA-binding activity of ACAN for its integration into PNNs. We demonstrate that the single immunoglobulin domain and the two Link modules that comprise the G1 region form a single structural unit, and that HA is clamped inside a groove that spans the length of the tandem Link domains. Introducing point mutations in the glycosaminoglycan-binding site eliminates HA-binding activity in ACAN, but, surprisingly, only decreases the integration of ACAN into PNNs. Thus, these results suggest that ACAN can be recruited into PNNs independently of its HA-binding activity.

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Organizational Affiliation: 
• Division of Biological and Biomedical Systems, School of Science and Engineering, University of Missouri-Kansas City, Kansas City, Missouri, 64110.
Department of Neuroscience and Physiology, State University of New York Upstate Medical University, Syracuse, New York, 13210.
Department of Neuroscience and Physiology, State University of New York Upstate Medical University, Syracuse, New York, 13210. Electronic address: [e-mail].
Division of Biological and Biomedical Systems, School of Science and Engineering, University of Missouri-Kansas City, Kansas City, Missouri, 64110. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 75.62 kDa 
• Atom Count: 4,758 
• Modeled Residue Count: 595 
• Deposited Residue Count: 670 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aggrecan core protein	A, B	335	Homo sapiens	Mutation(s): 0  Gene Names: ACAN, AGC1, CSPG1, MSK16
UniProt & NIH Common Fund Data Resources
Find proteins for P16112 (Homo sapiens) Explore P16112  Go to UniProtKB:  P16112
PHAROS:  P16112 GTEx:  ENSG00000157766
Glycosylation
Glycosylation Sites: 3		Go to GlyGen: P16112-1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	H [auth B], I [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free:  0.244 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.213 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.48	α = 90
b = 121.48	β = 90
c = 213.39	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-30 
Deposition Author(s): Bouyains, S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM143757

Revision History  

• Version 1.0: 2025-04-30
  Type: Initial release
  
• Version 1.1: 2025-05-07
  Changes: Database references
• Version 1.2: 2025-06-11
  Changes: Database references