9S6R | pdb_00009s6r

Ternary cryo-EM structure of yeast ALG3 with Dol25-PP-GlcNAc2Man5, Dol25-P-Man, and Fab

PDB DOI: https://doi.org/10.2210/pdb9S6R/pdb
EM Map EMD-54629: EMDB EMDataResource

Classification: TRANSFERASE
Organism(s): synthetic construct, Saccharomyces cerevisiae
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG, Homo sapiens
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: 3.08 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: 105.56 kDa
Atom Count: 5,114
Modeled Residue Count: 618
Deposited Residue Count: 922
Unique protein chains: 3

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sc-16 Fab heavy chain	A [auth H]	240	synthetic construct	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Sc-16 Fab light chain	B [auth L]	215	synthetic construct	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase	C [auth A]	467	Saccharomyces cerevisiae	Mutation(s): 1 Gene Names: ALG3, RHK1, YBL082C, YBL0720 EC: 2.4.1.258
UniProt
Find proteins for P38179 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38179 Go to UniProtKB: P38179
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P38179
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1JMA (Subject of Investigation/LOI) Query on A1JMA 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~{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~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(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 C₆₅ H₁₁₂ N₂ O₃₇ P₂ MDEDZFMSXUPMSK-WHWUJTIZSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
IZY (Subject of Investigation/LOI) Query on IZY 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]	Dolichol monophosphate beta-D-Mannose C₃₁ H₅₅ O₉ P AGLXCEGQRIYVRV-YNCWARPRSA-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 E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	CHOLESTEROL HEMISUCCINATE C₃₁ H₅₀ O₄ WLNARFZDISHUGS-MIXBDBMTSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]