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- PDB-9rqn: GT-C O-Mannosyltransferase TMEM260 with co-purified Dol-P-Man -

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Basic information

Entry
Database: PDB / ID: 9rqn
TitleGT-C O-Mannosyltransferase TMEM260 with co-purified Dol-P-Man
ComponentsProtein O-mannosyl-transferase TMEM260
KeywordsTRANSFERASE / Glycosyltransferase / ER integral membrane protein
Function / homology
Function and homology information


dolichyl-phosphate-mannose-protein mannosyltransferase / dolichyl-phosphate-mannose-protein mannosyltransferase activity / protein maturation / endoplasmic reticulum membrane
Similarity search - Function
Protein of unknown function DUF2723 / : / : / Protein O-mannosyl-transferase TMEM260 N-terminal domain / TMEM260-associated domain 2
Similarity search - Domain/homology
Chem-IZY / Protein O-mannosyl-transferase TMEM260
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.94 Å
AuthorsCifuente, J.O. / Ubarretxena-Belandia, I. / Povolo, L. / Halim, A.
Funding support Spain, Denmark, 4items
OrganizationGrant numberCountry
MCIN (Recovery, Transformation and Resilience Plan)PRTR-C17.I1; PRTR-C17.I01.P01.S13 Spain
The Carlsberg FoundationCF21-0655 Denmark
Villum Fonden00025438 Denmark
The Basque Government Biotechnology Complementary Plan Applied to HealthAAAA_ACG_AY_2539/22_05 Spain
CitationJournal: To Be Published
Title: Structure of O-Mannosyltransferase TMEM260
Authors: Cifuente, J.O. / Povolo, L. / Halim, A. / Ubarretxena-Belandia, I.
History
DepositionJun 26, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.0Jul 8, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.0Jul 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 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

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Assembly

Deposited unit
A: Protein O-mannosyl-transferase TMEM260
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,1613
Polymers82,3371
Non-polymers8242
Water00
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

#1: Protein Protein O-mannosyl-transferase TMEM260 / Transmembrane protein 260


Mass: 82336.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: contains C-Terminal 3xFLAG tag (DYKDDDDKDYKDDDDKDYKDDDDK).
Source: (gene. exp.) Homo sapiens (human) / Gene: TMEM260, C14orf101 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / Variant (production host): Expi293F
References: UniProt: Q9NX78, dolichyl-phosphate-mannose-protein mannosyltransferase
#2: Chemical ChemComp-IZY / Dolichol monophosphate beta-D-Mannose / [(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl] [(3~{S},6~{Z},10~{E},14~{E})-3,7,11,15,19-pentamethylicosa-6,10,14,18-tetraenyl] hydrogen phosphate


Mass: 602.737 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H55O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
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

ComponentName: protein-specific O-mannosyl-transferase (TMEM260) copurified with Dol-P-Man
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.08 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: Expi293F / Plasmid: pTMEM260-3xFLAG
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMsodium chlorideNaCl1
250 mMtris(hydroxymethyl)aminomethaneTris1
30.025 g%n-dodecyl -D-maltosideDDM1
42 mMmagnesium chlorideMgCl21
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 4 K

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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: 2000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 60.5 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 12967

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1cryoSPARCv4.7.0particle selection
2EPUimage acquisition
4cryoSPARCv4.7.0CTF correction
7UCSF Chimeramodel fittinginitial fitting
8PHENIXmodel fitting
9Cootmodel fitting
11cryoSPARCv4.7.0initial Euler assignment
12cryoSPARCv4.7.0final Euler assignment
13cryoSPARCv4.7.0classification
14cryoSPARCv4.7.03D reconstruction
15PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 635355 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingAccession code: Q9NX78 / Source name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 58.65 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00635480
ELECTRON MICROSCOPYf_angle_d0.87647462
ELECTRON MICROSCOPYf_chiral_restr0.0981832
ELECTRON MICROSCOPYf_plane_restr0.0111929
ELECTRON MICROSCOPYf_dihedral_angle_d11.41611921

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