9E1T | pdb_00009e1t

CryoEM structure of LARGE1 bound to UDP-GlcA

• PDB DOI: https://doi.org/10.2210/pdb9E1T/pdb
• EM Map EMD-47420: EMDB EMDataResource

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2024-10-21 Released: 2025-02-12 
• Deposition Author(s): Joseph, S., Spellmon, N., Campbell, K.P.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI), National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

LARGE1 processively polymerizes length-controlled matriglycan on prodystroglycan.

Joseph, S., Schnicker, N.J., Spellmon, N., Xu, Z., Yan, R., Yu, Z., Davulcu, O., Yang, T., Hopkins, J., Anderson, M.E., Venzke, D., Campbell, K.P.

(2025) Nat Commun 16: 9028-9028

• PubMed: 41073435 
• DOI: https://doi.org/10.1038/s41467-025-64080-z
• Primary Citation Related Structures: 
  9E1T


• PubMed Abstract: 
  

  Matriglycan is a linear glycan (xylose-β1,3-glucuronate) _n , which binds proteins in the extracellular matrix that contain laminin-globular domains and Lassa Fever Virus. It is indispensable for neuromuscular function. Matriglycan of insufficient length can cause muscular dystrophy with abnormal brain and eye development. LARGE1 (Like-acetylglucosaminyltransferase-1) uniquely synthesizes matriglycan on dystroglycan. The mechanism of matriglycan synthesis is not obvious from cryo-EM reconstructions of LARGE1. However, by reconstituting activity in vitro on recombinant prodystroglycan we show that the presence of the dystroglycan N-terminal domain (DGN), phosphorylated core M3, and a xylose-glucuronate primer are necessary for matriglycan polymerization by LARGE1. By introducing active site mutations, we demonstrate that LARGE1 processively polymerizes matriglycan on prodystroglycan, with its length regulated by the dystroglycan prodomain, DGN. Our enzymatic analysis of LARGE1 uncovers the mechanism of matriglycan synthesis on dystroglycan, which can form the basis for therapeutic strategies to treat matriglycan-deficient neuromuscular disorders and arenaviral infections.

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Organizational Affiliation: 
• Senator Paul D. Wellstone Muscular Dystrophy Specialized Research Center, University of Iowa Roy J. and Lucille A. Carver College of Medicine, Iowa City, IA, USA.
Department of Molecular Physiology and Biophysics, University of Iowa Roy J. and Lucille A. Carver College of Medicine, Iowa City, IA, USA.
Department of Neurology, University of Iowa Roy J. and Lucille A. Carver College of Medicine, Iowa City, IA, USA.
Protein and Crystallography Facility, University of Iowa, Iowa City, IA, USA.
Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
Pacific Northwest National Laboratory, Environmental Molecular Sciences Laboratory, Richland, WA, USA.
BioCAT Beamline 18-ID-D, Advanced Photon Source, Argonne National Laboratory, Lemont, IL, USA.
Senator Paul D. Wellstone Muscular Dystrophy Specialized Research Center, University of Iowa Roy J. and Lucille A. Carver College of Medicine, Iowa City, IA, USA. [e-mail].
Department of Molecular Physiology and Biophysics, University of Iowa Roy J. and Lucille A. Carver College of Medicine, Iowa City, IA, USA. [e-mail].
Department of Neurology, University of Iowa Roy J. and Lucille A. Carver College of Medicine, Iowa City, IA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 180.88 kDa 
• Atom Count: 10,056 
• Modeled Residue Count: 1,204 
• Deposited Residue Count: 1,540 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xylosyl- and glucuronyltransferase LARGE1	A, B	770	Homo sapiens	Mutation(s): 0  Gene Names: LARGE1, KIAA0609, LARGE EC: 2.4 (PDB Primary Data), 2.4.2 (PDB Primary Data), 2.4.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O95461 (Homo sapiens) Explore O95461  Go to UniProtKB:  O95461
PHAROS:  O95461 GTEx:  ENSG00000133424

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UGA (Subject of Investigation/LOI)	D [auth A], F [auth B]	URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID C15 H22 N2 O18 P2 HDYANYHVCAPMJV-LXQIFKJMSA-N
MN	C [auth A], E [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION
RECONSTRUCTION	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-02-12 
Deposition Author(s): Joseph, S., Spellmon, N., Campbell, K.P.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)	United States	U54 NS053672
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)	United States	U24 GM129547

Revision History  

• Version 1.0: 2025-02-12
  Type: Initial release
  
• Version 1.1: 2025-05-21
  Changes: Data collection
• Version 2.0: 2025-10-22
  Type: Coordinate replacement
  Reason: Ligand geometry
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Structure summary