9LAD | pdb_00009lad

Crystal structure of the complex between Neuronal Pentraxin 2 (NP2 PTX) and antibody fragment VHH N1

• PDB DOI: https://doi.org/10.2210/pdb9LAD/pdb

• Classification: PROTEIN BINDING
• Organism(s): Vicugna pacos, Homo sapiens
• Expression System: Escherichia coli BL21(DE3), Homo sapiens
• Mutation(s): No 


• Deposited: 2025-01-02 Released: 2025-12-10 
• Deposition Author(s): Caaveiro, J.M.M., Yokoo, T., Tsumoto, K.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 
  0.220 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.189 (DCC) 

Starting Model: in silico

Literature

Development of a VHH that inhibits the binding of neuronal pentraxin 2 to a postsynaptic glutamate receptor, AMPAR.

Yokoo, T., Nakakido, M., Matsuda, K., Caaveiro, J.M.M., Fernandez-Perez, J., Yuzaki, M., Tsumoto, K.

(2025) J Biological Chem 302: 110975-110975

• PubMed: 41308985 
• DOI: https://doi.org/10.1016/j.jbc.2025.110975
• Primary Citation Related Structures: 
  9LAD


• PubMed Abstract: 
  

  Neurons connect to each other via synapses to form neural circuits. Recent research has shown that neuropsychiatric disorders and neurological disorders such as autism spectrum disorders and Alzheimer's disease (AD) are synaptic diseases caused by abnormality of synapses. Synaptic organizers are molecules responsible for synapse formation. Neuronal pentraxin 2 (NP2) is synaptic organizer and a secreted protein that is expressed mainly in the hippocampus and cerebellum, and it contributes to synaptic plasticity. NP2 forms clusters with its family proteins NP1 and NPR and binds to postsynaptic amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid-type receptors (AMPARs). In recent years, research has revealed the disease relevance of NP2. For example, it can be a biomarker of AD, and its overexpression in the peripheral nervous system has been reported to cause chronic itch. However, the mechanism of NP2 function has not been well described at the molecular level. In this study, we developed a variable domain of heavy chain of heavy chain antibody (VHH) against NP2 to elucidate its molecular mechanism of action and to regulate its function of NP2. The obtained VHH N1 showed high specificity and affinity to NP2, and its binding mechanism was elucidated by X-ray crystallography. Furthermore, VHH N1 inhibited the binding of NP2 to AMPARs, and this inhibitory activity was confirmed in cells. These results provide useful insights into the molecular mechanism of NP2 function and highlight the potential application of VHH N1 as a detection agent for NP2 or as a therapeutic agent for chronic itch.

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Organizational Affiliation: 
• Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.
Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan; Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan. Electronic address: [e-mail].
Department of physiology, School of Medicine, Keio University, 35, Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan.
Department of Protein Drug Discovery, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan.
Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.
Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan; Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan; The institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content 

• Total Structure Weight: 38.56 kDa 
• Atom Count: 2,702 
• Modeled Residue Count: 326 
• Deposited Residue Count: 345 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N1 VHH	A [auth B]	126	Vicugna pacos	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuronal pentraxin-2	B [auth C]	219	Homo sapiens	Mutation(s): 0  Gene Names: Nptx2, Narp
UniProt
Find proteins for P97738 (Rattus norvegicus) Explore P97738  Go to UniProtKB:  P97738

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	G [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
AZI	C [auth B]	AZIDE ION N3 IVRMZWNICZWHMI-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)	D [auth C], E [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	F [auth C], H [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free:  0.220 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.189 (DCC) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.574	α = 90
b = 118.234	β = 90
c = 39.464	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-12-10 
Deposition Author(s): Caaveiro, J.M.M., Yokoo, T., Tsumoto, K.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	21H05090
Japan Society for the Promotion of Science (JSPS)	Japan	20H02531
Japan Society for the Promotion of Science (JSPS)	Japan	23KJ0516
Japan Agency for Medical Research and Development (AMED)	Japan	18ak0101100
Japan Agency for Medical Research and Development (AMED)	Japan	JP223fa627001
Japan Agency for Medical Research and Development (AMED)	Japan	JP223fa727002
Japan Agency for Medical Research and Development (AMED)	Japan	JP22ama121033
Japan Agency for Medical Research and Development (AMED)	Japan	JP24ama121031

Revision History  

• Version 1.0: 2025-12-10
  Type: Initial release
  
• Version 1.1: 2026-01-07
  Changes: Database references