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- PDB-9rqm: GT-C O-Mannosyltransferase TMEM260 co-purified with natural donor... -

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Basic information

Entry
Database: PDB / ID: 9rqm
TitleGT-C O-Mannosyltransferase TMEM260 co-purified with natural donor and in complex with acceptor peptide
Components
  • Plexin-B2
  • Protein 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 / excitatory synapse assembly / semaphorin receptor complex / semaphorin receptor activity / regulation of neuron migration / negative regulation of cell adhesion / regulation of GTPase activity / positive regulation of axonogenesis / regulation of protein phosphorylation ...dolichyl-phosphate-mannose-protein mannosyltransferase / dolichyl-phosphate-mannose-protein mannosyltransferase activity / excitatory synapse assembly / semaphorin receptor complex / semaphorin receptor activity / regulation of neuron migration / negative regulation of cell adhesion / regulation of GTPase activity / positive regulation of axonogenesis / regulation of protein phosphorylation / homophilic cell-cell adhesion / semaphorin-plexin signaling pathway / neuroblast proliferation / synapse assembly / regulation of cell migration / receptor-mediated endocytosis / positive regulation of translation / neural tube closure / protein maturation / positive regulation of neuron projection development / brain development / transmembrane signaling receptor activity / regulation of cell shape / signaling receptor activity / endoplasmic reticulum membrane / cell surface / extracellular exosome / plasma membrane
Similarity search - Function
Protein of unknown function DUF2723 / : / : / Protein O-mannosyl-transferase TMEM260 N-terminal domain / TMEM260-associated domain 2 / : / Plexin-B, PSI domain / Plexin A/B, PSI domain / Plexin, TIG domain 1 / TIG domain ...Protein of unknown function DUF2723 / : / : / Protein O-mannosyl-transferase TMEM260 N-terminal domain / TMEM260-associated domain 2 / : / Plexin-B, PSI domain / Plexin A/B, PSI domain / Plexin, TIG domain 1 / TIG domain / Plexin, cytoplasmic RasGAP domain / Plexin, cytoplasmic RhoGTPase-binding domain / Plexin cytoplasmic RasGAP domain / Plexin cytoplasmic RhoGTPase-binding domain / Plexin family / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / Plexin repeat / Plexin repeat / IPT/TIG domain / ig-like, plexins, transcription factors / Rho GTPase activation protein / IPT domain / PSI domain / domain found in Plexins, Semaphorins and Integrins / Immunoglobulin E-set / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Chem-IZY / Plexin-B2 / Protein O-mannosyl-transferase TMEM260
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsCifuente, J.O. / Ubarretxena-Belandia, I.
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
Citation
Journal: To Be Published
Title: Structure of O-Mannosyltransferase TMEM260
Authors: Cifuente, J.O. / Povolo, L. / Halim, A. / Ubarretxena-Belandia, I.
#1: Journal: To Be Published
Title: Real-space refinement in PHENIX for cryo-EM and crystallography
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
Revision 1.0Jul 8, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
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

Downloads & links

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Assembly

Deposited unit
A: Protein O-mannosyl-transferase TMEM260
B: Plexin-B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,6244
Polymers84,8002
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: TMEM260 / 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: Protein/peptide Plexin-B2 / MM1


Mass: 2462.845 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Synthetic peptide N-terminal Dansylated with GSGA linker and sequence PVITRIQPETGPLGGGIRITI from PLXNB2 IPT1 domain
Source: (synth.) Homo sapiens (human) / References: UniProt: O15031
#3: 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
#4: 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) incubated with Synthetic peptide derived from PLXNB2 IPT1 domain
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
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.: 1.2 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 magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: OTHER
Image recordingElectron dose: 49.8 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 21886

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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: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 271859 / 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: 98.93 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00675685
ELECTRON MICROSCOPYf_angle_d0.90457748
ELECTRON MICROSCOPYf_chiral_restr0.0885875
ELECTRON MICROSCOPYf_plane_restr0.0121971
ELECTRON MICROSCOPYf_dihedral_angle_d10.32381986

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