9S6S | pdb_00009s6s

Ternary cryo-EM structure of human ALG9 with Dol25-PP-GlcNAc2Man6, Dol25-P-Man and Fab


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.89 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9S6S

This is version 2.0 of the entry. See complete history

Literature

Structures of ALG3/9/12 reveal the assembly logic of the N-glycan oligomannose core.

Alexander, J.A.N.Chen, S.Y.Mukherjee, S.de Capitani, M.Irobalieva, R.N.Rossi, L.Agrawal, P.Kowal, J.Meirelles, M.A.Aebi, M.Reymond, J.L.Kossiakoff, A.A.Riniker, S.Locher, K.P.

(2026) Nat Chem Biol 

  • DOI: https://doi.org/10.1038/s41589-026-02164-7
  • Primary Citation Related Structures: 
    9S6R, 9S6S, 9S6T, 9S6U

  • PubMed Abstract: 

    Asparagine-linked glycans are essential for the maturation and function of most eukaryotic secretory proteins. The biosynthesis and transfer of dolichylpyrophosphate-anchored GlcNAc 2 Man 9 Glc 3 glycan is a highly conserved process occurring in the endoplasmic reticulum (ER) membrane and involving over a dozen membrane proteins whose dysfunction is linked to congenital disorders of glycosylation (CDGs). Three membrane-integral mannosyltransferases, ALG3, ALG9 and ALG12, mediate four consecutive mannosylation reactions that convert GlcNAc 2 Man 5 to GlcNAc 2 Man 9 . Here, using chemoenzymatically synthesized lipid-linked glycan donor and acceptor analogs, we recapitulated this biosynthetic pathway in vitro. High-resolution cryo-electron microscopy structures of pseudo-Michaelis complexes of each step revealed how the branched glycan is accurately synthesized and unwanted side products are averted. Molecular dynamics simulations and mutagenesis studies uncovered a subtle but precise mechanism selecting the dolichylphosphomannose donor substrate over dolichylphosphoglucose, which is also present in the ER membrane. Our results also provide mechanistic explanations for enzyme dysfunction in CDGs and offer opportunities for N-glycan engineering.


  • Organizational Affiliation
    • Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH) Zürich, Zurich, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 122.64 kDa 
  • Atom Count: 6,456 
  • Modeled Residue Count: 773 
  • Deposited Residue Count: 1,072 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Alpha-1,2-mannosyltransferase ALG9617Homo sapiensMutation(s): 1 
Gene Names: ALG9DIBD1
EC: 2.4.1.259 (PDB Primary Data), 2.4.1.261 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H6U8 (Homo sapiens)
Explore Q9H6U8 
Go to UniProtKB:  Q9H6U8
PHAROS:  Q9H6U8
GTEx:  ENSG00000086848 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H6U8
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q9H6U8-1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Hs9-8 Fab heavy chainB [auth H]240synthetic constructMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Hs9-8 Fab light chainC [auth L]215synthetic constructMutation(s): 0 

Oligosaccharides

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Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-1-O-phosphono-alpha-D-glucopyranoseD [auth B]7N/A

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.89 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland310030_196862
Swiss National Science FoundationSwitzerland315230_220007

Revision History  (Full details and data files)

  • Version 1.0: 2026-03-18
    Type: Initial release
  • Version 1.1: 2026-03-25
    Changes: Data collection, Database references
  • Version 2.0: 2026-04-08
    Changes: Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Structure summary