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 29DS | pdb_000029ds

Cryo-EM structure of dimeric human UGGT1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.55 Å
  • Resolution: 4.55 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 29DS

This is version 1.0 of the entry. See complete history. 

Literature

Structural basis of glycoprotein recognition by the human folding sensor UDP-glucose:glycoprotein glucosyltransferase.

Aparicio, D., Ortigosa, J.R., Guay, K.P., Williams, R.V., Lannot, J.O., Zong, G., Comino, N., Rodriguez, J.F., Wang, L.X., Marti, M.A., Roversi, P., Hebert, D.N., Gierasch, L.M., Modenutti, C.P., Guerin, M.E.

(2026) Proc Natl Acad Sci U S A 123: e2621329123-e2621329123

  • DOI: https://doi.org/10.1073/pnas.2621329123
  • Primary Citation Related Structures: 
    29DS, 9TV4

  • PubMed Abstract: 

    UDP-glucose:glycoprotein glucosyltransferase 1 (UGGT1) plays a central role in quality control of glycoprotein folding within the early secretory pathway, yet the molecular basis of UGGT1 substrate recognition remains poorly understood. Here, we report cryo-EM structures of human full-length multidomain UGGT1. Monomeric UGGT1 structures reveal two conformational states corresponding to "open" and "closed" architectures. Three-dimensional variability and molecular dynamics simulations suggest the existence of intermediate conformations, leading to a model in which a continuum of structural transitions underlies UGGT1 function. Notably, in the open state, the EM-maps reveal at the top of the U-shaped protein a density that bridges the sensory TRXL2 and the glucosyltransferase catalytic domains, consistent with substrate association. This observation supports a mode of binding that places the substrate near the catalytic domain. A dimeric form of UGGT1 was observed in which the glycoprotein substrate binding sites are occluded, suggesting that dimerization may regulate UGGT1 activity. To better understand the spatial relationship between the site of misfolding and that of UGGT-mediated N-glycan reglucosylation, we identified N-glycosylation sites on endogenous glycoprotein substrates by glycoproteomics. No consensus sequence was found flanking modified sites, indicating that substrate recognition relies on mechanisms beyond primary sequence. Mutations in the UGGT1 gene cause a novel congenital disorder of glycosylation characterized by developmental delay and intellectual disability, and the human UGGT1 structure helps explain how disease-associated missense and deletion variants disrupt function. Together, our data provide insight into the relationship between UGGT1 structure and function, integrating enzyme conformational states with client glycoprotein interaction and processing.


  • Organizational Affiliation: 
    • Structural Glycobiology Laboratory, Department of Structural and Molecular Biology, Institute of Molecular Biology of Barcelona, Spanish National Research Council, Barcelona Science Park, Barcelona, Catalonia 08028, Spain.

Macromolecule Content 

  • Total Structure Weight: 354.78 kDa 
  • Atom Count: 13,649 
  • Modeled Residue Count: 2,752 
  • Deposited Residue Count: 3,110 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
UDP-glucose:glycoprotein glucosyltransferase 1
A, B
1,555Homo sapiensMutation(s): 0 
Gene Names: UGGT1, GT, UGCGL1, UGGT, UGT1, UGTR
EC: 2.4.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NYU2 (Homo sapiens)
Explore Q9NYU2 
Go to UniProtKB:  Q9NYU2
PHAROS:  Q9NYU2
GTEx:  ENSG00000136731 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NYU2
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.55 Å
  • Resolution: 4.55 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21_5207
RECONSTRUCTIONcryoSPARC4.6.0
RECONSTRUCTIONcryoSPARC4.6.0

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Economy and Competitiveness (MINECO)Spain--

Revision History  (Full details and data files)

  • Version 1.0: 2026-11-11
    Type: Initial release