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- PDB-9s6t: Ternary cryo-EM structure of chicken ALG12 with Dol25-PP-GlcNAc2M... -

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Basic information

Entry
Database: PDB / ID: 9s6t
TitleTernary cryo-EM structure of chicken ALG12 with Dol25-PP-GlcNAc2Man7, Dol25-P-Man, and Fab
Components
  • Gg12-11 Fab heavy chain
  • Gg12-11 Fab light chain
  • Mannosyltransferase
KeywordsTRANSFERASE / Mannosyltransferase / ternary complex / N-linked glycosylation
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
: / : / Lauryl Maltose Neopentyl Glycol / CHOLESTEROL HEMISUCCINATE / Mannosyltransferase
Similarity search - Component
Biological speciesGallus gallus (chicken)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.42 Å
AuthorsAlexander, 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. ...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 support Switzerland, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_196862 Switzerland
Swiss National Science Foundation315230_220007 Switzerland
CitationJournal: Nat.Chem.Biol. / Year: 2026
Title: Structural basis for oligomannose N-glycan synthesis in the endoplasmic reticulum
Authors: 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. / ...Authors: 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.
History
DepositionAug 1, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mannosyltransferase
H: Gg12-11 Fab heavy chain
L: Gg12-11 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,7567
Polymers104,7623
Non-polymers3,9944
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Mannosyltransferase


Mass: 56295.227 Da / Num. of mol.: 1 / Mutation: E35Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: ALG12 / Production host: Homo sapiens (human)
References: UniProt: F1P077, Transferases; Glycosyltransferases; Hexosyltransferases

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Antibody , 2 types, 2 molecules HL

#2: Antibody Gg12-11 Fab heavy chain


Mass: 25119.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#3: Antibody Gg12-11 Fab light chain


Mass: 23346.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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Non-polymers , 5 types, 89 molecules

#4: Chemical ChemComp-A1JMT / [(3S,6Z,10E,14E)-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraenyl] dihydrogen phosphate


Mass: 440.596 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H45O4P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-A1JMC / [(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 / 4'-DEOXY-4'-IODOADRIAMYCIN


Mass: 2061.945 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C83H142N2O52P2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H50O4
#7: Chemical ChemComp-AV0 / Lauryl Maltose Neopentyl Glycol / 2,2-didecylpropane-1,3-bis-b-D-maltopyranoside / 2-decyl-2-{[(4-O-alpha-D-glucopyranosyl-beta-D-glucopyranosyl)oxy]methyl}dodecyl4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside


Mass: 1005.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C47H88O22
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Ternary complex of chicken ALG12 with Gg12-11 Fab, anti-kappa light chain nanobody as well as Dol25-P-Man and Dol25-PP-GlcNAc2Man7 substratesCOMPLEX#1-#30MULTIPLE SOURCES
2Anti-kapp light chain nanobodyCOMPLEX1RECOMBINANT
3Gg12-11 FabCOMPLEX#2-#31RECOMBINANT
4ALG12COMPLEX#11RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.12 MDaNO
21NO
31NO
43
54
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
32Lama glama (llama)9844
43synthetic construct (others)32630
54Gallus gallus (chicken)9031
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
32Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)866768
43Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)866768
54Homo sapiens (human)9606
Buffer solutionpH: 7.5
SpecimenConc.: 3.9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2800 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 43 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.42 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 580115 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 30.85 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00166102
ELECTRON MICROSCOPYf_angle_d0.52238329
ELECTRON MICROSCOPYf_chiral_restr0.041975
ELECTRON MICROSCOPYf_plane_restr0.0039983
ELECTRON MICROSCOPYf_dihedral_angle_d10.26881157

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