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- EMDB-54631: Ternary cryo-EM structure of chicken ALG12 with Dol25-PP-GlcNAc2M... -

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Entry
Database: EMDB / ID: EMD-54631
TitleTernary cryo-EM structure of chicken ALG12 with Dol25-PP-GlcNAc2Man7, Dol25-P-Man, and Fab
Map data
Sample
  • Complex: Ternary complex of chicken ALG12 with Gg12-11 Fab, anti-kappa light chain nanobody as well as Dol25-P-Man and Dol25-PP-GlcNAc2Man7 substrates
    • Complex: Anti-kapp light chain nanobody
    • Complex: Gg12-11 Fab
      • Protein or peptide: Gg12-11 Fab heavy chain
      • Protein or peptide: Gg12-11 Fab light chain
    • Complex: ALG12
      • Protein or peptide: Mannosyltransferase
  • Ligand: [(3S,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraenyl] dihydrogen phosphate
  • Ligand: [(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~{R},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3-[(2~{R},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-4,5-bis(oxidanyl)oxan-2-yl]oxy-6-[[(2~{S},3~{S},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-4-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3-[(2~{R},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-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
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: Lauryl Maltose Neopentyl Glycol
  • Ligand: water
KeywordsMannosyltransferase / ternary complex / N-linked glycosylation / TRANSFERASE
Function / homology
Function and homology information


dol-P-Man:Man(7)GlcNAc(2)-PP-Dol alpha-1,6-mannosyltransferase activity / Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein / alpha-1,6-mannosyltransferase activity / dolichol-linked oligosaccharide biosynthetic process / protein N-linked glycosylation / Transferases; Glycosyltransferases; Hexosyltransferases / endoplasmic reticulum membrane
Similarity search - Function
GPI mannosyltransferase / Alg9-like mannosyltransferase family
Similarity search - Domain/homology
Biological speciesLama glama (llama) / synthetic construct (others) / Gallus gallus (chicken)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.42 Å
AuthorsAlexander JAN / Chen SY / Mukherjee S / de Capitani M / Irobalieva RN / Rossi L / Agrawal P / Kowal J / Meirelles MA / Aebi M ...Alexander JAN / Chen SY / Mukherjee S / de Capitani M / Irobalieva RN / Rossi L / Agrawal P / Kowal J / Meirelles MA / Aebi M / Reymond JL / Kossiakoff AA / Riniker S / Locher KP
Funding support Switzerland, 2 items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_196862 Switzerland
Swiss National Science Foundation315230_220007 Switzerland
CitationJournal: Nat Chem Biol / Year: 2026
Title: Structures of ALG3/9/12 reveal the assembly logic of the N-glycan oligomannose core.
Authors: J Andrew N Alexander / Shu-Yu Chen / Somnath Mukherjee / Mario de Capitani / Rossitza N Irobalieva / Lorenzo Rossi / Parth Agrawal / Julia Kowal / Matheus A Meirelles / Markus Aebi / Jean- ...Authors: J Andrew N Alexander / Shu-Yu Chen / Somnath Mukherjee / Mario de Capitani / Rossitza N Irobalieva / Lorenzo Rossi / Parth Agrawal / Julia Kowal / Matheus A Meirelles / Markus Aebi / Jean-Louis Reymond / Anthony A Kossiakoff / Sereina Riniker / Kaspar P Locher /
Abstract: Asparagine-linked glycans are essential for the maturation and function of most eukaryotic secretory proteins. The biosynthesis and transfer of dolichylpyrophosphate-anchored GlcNAcManGlc glycan is a ...Asparagine-linked glycans are essential for the maturation and function of most eukaryotic secretory proteins. The biosynthesis and transfer of dolichylpyrophosphate-anchored GlcNAcManGlc 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 GlcNAcMan to GlcNAcMan. 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.
History
DepositionAug 1, 2025-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateMar 25, 2026-
Current statusMar 25, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54631.png

Downloads & links

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Map

FileDownload / File: emd_54631.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 512 pix.
= 332.8 Å		0.65 Å/pix.
x 512 pix.
= 332.8 Å		0.65 Å/pix.
x 512 pix.
= 332.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.34
Minimum - Maximum-1.4673973 - 2.3104947
Average (Standard dev.)-0.00003855409 (±0.034168508)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 332.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_54631_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

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Half map: #1

Fileemd_54631_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Ternary complex of chicken ALG12 with Gg12-11 Fab, anti-kappa lig...

EntireName: Ternary complex of chicken ALG12 with Gg12-11 Fab, anti-kappa light chain nanobody as well as Dol25-P-Man and Dol25-PP-GlcNAc2Man7 substrates
Components
  • Complex: Ternary complex of chicken ALG12 with Gg12-11 Fab, anti-kappa light chain nanobody as well as Dol25-P-Man and Dol25-PP-GlcNAc2Man7 substrates
    • Complex: Anti-kapp light chain nanobody
    • Complex: Gg12-11 Fab
      • Protein or peptide: Gg12-11 Fab heavy chain
      • Protein or peptide: Gg12-11 Fab light chain
    • Complex: ALG12
      • Protein or peptide: Mannosyltransferase
  • Ligand: [(3S,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraenyl] dihydrogen phosphate
  • Ligand: [(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~{R},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3-[(2~{R},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-4,5-bis(oxidanyl)oxan-2-yl]oxy-6-[[(2~{S},3~{S},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-4-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3-[(2~{R},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-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
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: Lauryl Maltose Neopentyl Glycol
  • Ligand: water

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Supramolecule #1: Ternary complex of chicken ALG12 with Gg12-11 Fab, anti-kappa lig...

SupramoleculeName: Ternary complex of chicken ALG12 with Gg12-11 Fab, anti-kappa light chain nanobody as well as Dol25-P-Man and Dol25-PP-GlcNAc2Man7 substrates
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: Anti-kapp light chain nanobody

SupramoleculeName: Anti-kapp light chain nanobody / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Lama glama (llama)

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Supramolecule #3: Gg12-11 Fab

SupramoleculeName: Gg12-11 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: synthetic construct (others)

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Supramolecule #4: ALG12

SupramoleculeName: ALG12 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Gallus gallus (chicken)

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Macromolecule #1: Mannosyltransferase

MacromoleculeName: Mannosyltransferase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Transferases; Glycosyltransferases; Hexosyltransferases
Source (natural)Organism: Gallus gallus (chicken)
Molecular weightTheoretical: 56.295227 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPGGSTMAQK RSSSGRSFPL LLLIIVVAFV HLTVCPFTKV QESFNLQAIH DVVYHQLDLD KYDHHEFPGV VPRTFLGPIF IAALSSPAI YILSLLKMSK FYSQLIVRGS LGLSVIYTLW KLQKEVRKQF GATTSTVFCL ITVTQFHLMF YCTRTLPNVF A LPFVLLAL ...String:
GPGGSTMAQK RSSSGRSFPL LLLIIVVAFV HLTVCPFTKV QESFNLQAIH DVVYHQLDLD KYDHHEFPGV VPRTFLGPIF IAALSSPAI YILSLLKMSK FYSQLIVRGS LGLSVIYTLW KLQKEVRKQF GATTSTVFCL ITVTQFHLMF YCTRTLPNVF A LPFVLLAL TFWIQQKQRP FIWFSALAII VFRSELAIFL GLMLLVTFLT KRISVLKILS HAVPAGFFWL GLTVAVDSLF WR QLVWPEG KVLWYNTILN KSSNWGTSPF FWYFYSALPR ALGCSIVFVP LGAAEKRTRI LLLPALGFIF LYSFLPHKEL RFI IYTFPV FNIVAAKVCS RILNNYRKSW LYKLGSLFVV MHLLVNAAYS GTSLYVSHFN YPGGVAIQKL HELVPSTAEV SVHI DVAAA QTGVSRFLEI NSDWRYDKRE DVKPGDQLMF SYTHILMETN PLQISHYKTT HRPLANIPGI SKIGLNLTAL PPFTL NLKP KLVLLEKLPL SS

UniProtKB: Mannosyltransferase

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Macromolecule #2: Gg12-11 Fab heavy chain

MacromoleculeName: Gg12-11 Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 25.119914 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: EISEVQLVES GGGLVQPGGS LRLSCAASGF NVSYSSIHWV RQAPGKGLEW VASISSYYGY TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARYYWDWWRG GWAFDYWGQG TLVTVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF P EPVTVSWN ...String:
EISEVQLVES GGGLVQPGGS LRLSCAASGF NVSYSSIHWV RQAPGKGLEW VASISSYYGY TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARYYWDWWRG GWAFDYWGQG TLVTVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF P EPVTVSWN SGALTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTQTYI CNVNHKPSNT KVDKKVEPKS CDKTHT

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Macromolecule #3: Gg12-11 Fab light chain

MacromoleculeName: Gg12-11 Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 23.346848 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQSSYDPITF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQSSYDPITF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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Macromolecule #4: [(3S,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraen...

MacromoleculeName: [(3S,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraenyl] dihydrogen phosphate
type: ligand / ID: 4 / Number of copies: 1 / Formula: A1JMT
Molecular weightTheoretical: 440.596 Da

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Macromolecule #5: [(2~{R},3~{R},4~{R},5~{S},6~{R})-3-acetamido-5-[(2~{S},3~{R},4~{R...

MacromoleculeName: [(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- ...Name: [(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~{R},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3-[(2~{R},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-4,5-bis(oxidanyl)oxan-2-yl]oxy-6-[[(2~{S},3~{S},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-4-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3-[(2~{R},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-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
type: ligand / ID: 5 / Number of copies: 1 / Formula: A1JMC
Molecular weightTheoretical: 2.061945 KDa

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Macromolecule #6: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 6 / Number of copies: 1 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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Macromolecule #7: Lauryl Maltose Neopentyl Glycol

MacromoleculeName: Lauryl Maltose Neopentyl Glycol / type: ligand / ID: 7 / Number of copies: 1 / Formula: AV0
Molecular weightTheoretical: 1.005188 KDa
Chemical component information

ChemComp-AV0:
Lauryl Maltose Neopentyl Glycol

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Macromolecule #8: water

MacromoleculeName: water / type: ligand / ID: 8 / Number of copies: 85 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3.9 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 43.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.42 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 580115
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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