Crystal structure of the human neuronal pentraxin 1 (NP1) pentraxin (PTX) domain.

Experimental Data Snapshot

  • Resolution: 1.45 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


A synthetic synaptic organizer protein restores glutamatergic neuronal circuits.

Suzuki, K.Elegheert, J.Song, I.Sasakura, H.Senkov, O.Matsuda, K.Kakegawa, W.Clayton, A.J.Chang, V.T.Ferrer-Ferrer, M.Miura, E.Kaushik, R.Ikeno, M.Morioka, Y.Takeuchi, Y.Shimada, T.Otsuka, S.Stoyanov, S.Watanabe, M.Takeuchi, K.Dityatev, A.Aricescu, A.R.Yuzaki, M.

(2020) Science 369

  • DOI: https://doi.org/10.1126/science.abb4853
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Neuronal synapses undergo structural and functional changes throughout life, which are essential for nervous system physiology. However, these changes may also perturb the excitatory-inhibitory neurotransmission balance and trigger neuropsychiatric and neurological disorders. Molecular tools to restore this balance are highly desirable. Here, we designed and characterized CPTX, a synthetic synaptic organizer combining structural elements from cerebellin-1 and neuronal pentraxin-1. CPTX can interact with presynaptic neurexins and postsynaptic AMPA-type ionotropic glutamate receptors and induced the formation of excitatory synapses both in vitro and in vivo. CPTX restored synaptic functions, motor coordination, spatial and contextual memories, and locomotion in mouse models for cerebellar ataxia, Alzheimer's disease, and spinal cord injury, respectively. Thus, CPTX represents a prototype for structure-guided biologics that can efficiently repair or remodel neuronal circuits.

  • Organizational Affiliation

    Department of Physiology, Keio University School of Medicine, Tokyo 160-8582, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Neuronal pentraxin-1
A, B
205Homo sapiensMutation(s): 0 
Gene Names: NPTX1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15818 (Homo sapiens)
Explore Q15818 
Go to UniProtKB:  Q15818
PHAROS:  Q15818
GTEx:  ENSG00000171246 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15818
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.45 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.22α = 90
b = 36.06β = 97.47
c = 92.17γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Human Frontier Science Program (HFSP)RGP0065/2014
Medical Research Council (MRC, United Kingdom)L009609
Medical Research Council (MRC, United Kingdom)MC_UP_1201/15

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-03
    Type: Initial release
  • Version 1.1: 2020-09-16
    Changes: Database references, Derived calculations
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description