9LGG | pdb_00009lgg

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

• PDB DOI: https://doi.org/10.2210/pdb9LGG/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2025-01-10 Released: 2025-12-03 
• Deposition Author(s): Matoba, K., Mizutani, F., Arimori, T., Takagi, J.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED)

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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

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.

(null) Structure 

• DOI: https://doi.org/10.1016/j.str.2025.10.018

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

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

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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Muscle, skeletal receptor tyrosine-protein kinase,Ig3-Fz domains of hMuSK:L1 peptide	A, B, C, D	279	Homo sapiens, synthetic 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
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: O15146-1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F, G, H	2		N-Glycosylation

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	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 = 103.644	α = 90
b = 103.644	β = 90
c = 305.216	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-03 
Deposition Author(s): Matoba, K., Mizutani, F., Arimori, T., Takagi, J.

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Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	--

Revision History  

• Version 1.0: 2025-12-03
  Type: Initial release