9S6U | pdb_00009s6u

Ternary cryo-EM structure of human ALG9 with Dol25-PP-GlcNAc2Man8, Dol25-P-Man and Fab

PDB DOI: https://doi.org/10.2210/pdb9S6U/pdb
EM Map EMD-54632: EMDB EMDataResource

Classification: TRANSFERASE
Organism(s): Homo sapiens, synthetic construct
Expression System: Homo sapiens, Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): Yes

Deposited: 2025-08-01 Released: 2026-03-18
Deposition Author(s): 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.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.95 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 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

PubMed: 41807832 Search on PubMed Search on PubMed Central
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 ₂Man ₉Glc 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 ₂Man ₅ to GlcNAc ₂Man 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: 123.43 kDa
Atom Count: 6,528
Modeled Residue Count: 775
Deposited Residue Count: 1,072
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-1,2-mannosyltransferase ALG9	A	617	Homo sapiens	Mutation(s): 1 Gene Names: ALG9, DIBD1 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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9H6U8
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A	Go to GlyGen: Q9H6U8-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hs9-8 Fab heavy chain	B [auth H]	240	synthetic construct	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Hs9-8 Fab light chain	C [auth L]	215	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1JMB (Subject of Investigation/LOI) Query on A1JMB Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	[(2~{R},3~{R},4~{R},5~{S},6~{R})-3-acetamido-5-[(2~{S},3~{R},4~{R},5~{S},6~{R})-3-acetamido-6-(hydroxymethyl)-5-[(2~{S},3~{S},4~{S},5~{R},6~{R})-4-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3-[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-4,5-bis(oxidanyl)oxan-2-yl]oxy-6-[[(2~{S},3~{S},4~{S},5~{R},6~{R})-4-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3-[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-4,5-bis(oxidanyl)oxan-2-yl]oxy-6-[[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]-3,5-bis(oxidanyl)oxan-2-yl]oxymethyl]-3,5-bis(oxidanyl)oxan-2-yl]oxy-4-oxidanyl-oxan-2-yl]oxy-6-(hydroxymethyl)-4-oxidanyl-oxan-2-yl] [oxidanyl-[(3~{S},6~{Z},10~{E},14~{E})-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraenoxy]phosphoryl] hydrogen phosphate C₈₃ H₁₄₂ N₂ O₅₂ P₂ NXZQPIZBBWUWAA-ZUFSPYJNSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
Y01 Query on Y01 Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A], I [auth A]	CHOLESTEROL HEMISUCCINATE C₃₁ H₅₀ O₄ WLNARFZDISHUGS-MIXBDBMTSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]
A1JMT (Subject of Investigation/LOI) Query on A1JMT Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	[(3S,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraenyl] dihydrogen phosphate C₂₅ H₄₅ O₄ P GYBNOAFGEKAZTA-YGRYZZMUSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]