9LGG | pdb_00009lgg

Crystal structure of the human MuSK(Ig3_Fz)/L1 peptide complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 
    0.242 (Depositor), 0.242 (DCC) 
  • R-Value Work: 
    0.204 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 
    0.206 (Depositor) 

Starting Model: in silico
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This is version 1.2 of the entry. See complete history

Literature

Muscle-specific tyrosine kinase activation by a peptide-based dimerizer is orientation dependent.

Mizutani, F.Matoba, K.Peacock, H.Yamada, M.Mihara, E.Higuchi, O.Suga, H.Arimori, T.Takagi, J.

(2026) Structure 34: 284

  • DOI: https://doi.org/10.1016/j.str.2025.10.018
  • Primary Citation Related Structures: 
    9LGG

  • PubMed Abstract: 

    Muscle-specific receptor tyrosine kinase (MuSK) is a single-pass transmembrane protein expressed on skeletal muscle. MuSK is activated by binding of nerve-derived agrin with the help of muscle coreceptor LRP4, leading to the clustering of acetylcholine receptors (AChR), which is required for the formation and maintenance of functional neuromuscular junctions. The structural mechanism of MuSK activation by physiological and artificial agonistic agents has remained elusive. In this study, we isolated a 27-residue linear peptide (L1) that binds human MuSK with high affinity. Genetic fusion of L1 to either the N or C termini of the human IgG Fc resulted in two different versions of MuSK dimerizers, denoted as L1-Fc and Fc-L1. Only Fc-L1 activated MuSK on myotubes and induced AChR clustering. Crystallographic analysis of MuSK-L1 interactions revealed that MuSK activation requires a particular dimeric conformation, pointing toward the importance of the lateral size of the receptor complex at the muscle cell surface.


  • Organizational Affiliation
    • Laboratory for Protein Synthesis and Expression, Institute for Protein Research, The University of Osaka, Suita 565-0871, Japan.

Macromolecule Content 

  • Total Structure Weight: 126.67 kDa 
  • Atom Count: 8,049 
  • Modeled Residue Count: 1,012 
  • Deposited Residue Count: 1,116 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Muscle, skeletal receptor tyrosine-protein kinase,Ig3-Fz domains of hMuSK:L1 peptide
A, B, C, D
279Homo sapienssynthetic construct
This entity is chimeric
Mutation(s): 0 
Gene Names: MUSK
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for O15146 (Homo sapiens)
Explore O15146 
Go to UniProtKB:  O15146
PHAROS:  O15146
GTEx:  ENSG00000030304 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15146
Glycosylation
Glycosylation Sites: 2Go to GlyGen: O15146-1
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, F, G, H
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
I [auth D]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free:  0.242 (Depositor), 0.242 (DCC) 
  • R-Value Work:  0.204 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 0.206 (Depositor) 
Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.644α = 90
b = 103.644β = 90
c = 305.216γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Agency for Medical Research and Development (AMED)Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-03
    Type: Initial release
  • Version 1.1: 2025-12-10
    Changes: Database references
  • Version 1.2: 2026-02-25
    Changes: Database references