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- EMDB-54179: GT-C O-Mannosyltransferase TMEM260 co-purified with natural donor... -

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Basic information

Entry
Database: EMDB / ID: EMD-54179
TitleGT-C O-Mannosyltransferase TMEM260 co-purified with natural donor and in complex with acceptor peptide
Map data
Sample
  • Complex: protein-specific O-mannosyl-transferase (TMEM260) incubated with Synthetic peptide derived from PLXNB2 IPT1 domain
    • Protein or peptide: Protein O-mannosyl-transferase TMEM260
    • Protein or peptide: Plexin-B2
  • Ligand: Dolichol monophosphate beta-D-Mannose
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsGlycosyltransferase / ER integral membrane protein / TRANSFERASE
Function / homology
Function and homology information


dolichyl-phosphate-mannose-protein mannosyltransferase / dolichyl-phosphate-mannose-protein mannosyltransferase activity / excitatory synapse assembly / neuroblast proliferation / regulation of neuron migration / semaphorin receptor complex / positive regulation of axonogenesis / negative regulation of cell adhesion / semaphorin receptor activity / regulation of GTPase activity ...dolichyl-phosphate-mannose-protein mannosyltransferase / dolichyl-phosphate-mannose-protein mannosyltransferase activity / excitatory synapse assembly / neuroblast proliferation / regulation of neuron migration / semaphorin receptor complex / positive regulation of axonogenesis / negative regulation of cell adhesion / semaphorin receptor activity / regulation of GTPase activity / neural tube closure / homophilic cell-cell adhesion / semaphorin-plexin signaling pathway / regulation of protein phosphorylation / regulation of cell migration / synapse assembly / receptor-mediated endocytosis / positive regulation of translation / brain development / positive regulation of neuron projection development / protein maturation / regulation of cell shape / transmembrane signaling receptor activity / 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
Plexin-B2 / Protein O-mannosyl-transferase TMEM260
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsCifuente JO / Ubarretxena-Belandia I
Funding support Spain, Denmark, 4 items
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 JO / 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 JO / Povolo L / Halim A / Ubarretxena-Belandia I
History
DepositionJun 26, 2025-
Header (metadata) releaseJul 8, 2026-
Map releaseJul 8, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54179.png

Downloads & links

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Map

FileDownload / File: emd_54179.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 320 pix.
= 263.616 Å		0.82 Å/pix.
x 320 pix.
= 263.616 Å		0.82 Å/pix.
x 320 pix.
= 263.616 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8238 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.026
Minimum - Maximum-0.095338315 - 0.20138758
Average (Standard dev.)0.00030682018 (±0.0042025466)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 263.616 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54179_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: sharpened map

Fileemd_54179_additional_1.map
Annotationsharpened map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_54179_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_54179_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : protein-specific O-mannosyl-transferase (TMEM260) incubated with ...

EntireName: protein-specific O-mannosyl-transferase (TMEM260) incubated with Synthetic peptide derived from PLXNB2 IPT1 domain
Components
  • Complex: protein-specific O-mannosyl-transferase (TMEM260) incubated with Synthetic peptide derived from PLXNB2 IPT1 domain
    • Protein or peptide: Protein O-mannosyl-transferase TMEM260
    • Protein or peptide: Plexin-B2
  • Ligand: Dolichol monophosphate beta-D-Mannose
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: protein-specific O-mannosyl-transferase (TMEM260) incubated with ...

SupramoleculeName: protein-specific O-mannosyl-transferase (TMEM260) incubated with Synthetic peptide derived from PLXNB2 IPT1 domain
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Protein O-mannosyl-transferase TMEM260

MacromoleculeName: Protein O-mannosyl-transferase TMEM260 / type: protein_or_peptide / ID: 1 / Details: TMEM260 / Number of copies: 1 / Enantiomer: LEVO
EC number: dolichyl-phosphate-mannose-protein mannosyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 82.336734 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSPHGDGRGQ AQGRAVRVGL RRSGGIRGGV AVFAAVAAVF TFTLPPSVPG GDSGELITAA HELGVAHPPG YPLFTLVAKL AITLFPFGS IAYRVNLLCG LFGAVAASLL FFTVFRLSGS SAGGILAAGV FSFSRLTWQW SIAAEVFSLN NLFVGLLMAL T VHFEEAAT ...String:
MSPHGDGRGQ AQGRAVRVGL RRSGGIRGGV AVFAAVAAVF TFTLPPSVPG GDSGELITAA HELGVAHPPG YPLFTLVAKL AITLFPFGS IAYRVNLLCG LFGAVAASLL FFTVFRLSGS SAGGILAAGV FSFSRLTWQW SIAAEVFSLN NLFVGLLMAL T VHFEEAAT AKERSKVAKI GAFCCGLSLC NQHTIILYVL CIIPWILFQL LKKKELSLGS LLKLSLYFSA GLLPYVHLPI SS YLNHARW TWGDQTTLQG FLTHFLREEY GTFSLAKSEI GSSMSEILLS QVTNMRTELS FNIQALAVCA NICLATKDRQ NPS LVWLFT GMFCIYSLFF AWRANLDISK PLFMGVVERF WMQSNAVVAV LAGIGLAAVV SETNRVLNSN GLQCLEWLSA TLFV VYQIY SNYSVCDQRT NYVIDKFAKN LLTSMPHDAI ILLRGDLPGN SLRYMHYCEG LRPDISLVDQ EMMTYEWYLP KMAKH LPGV NFPGNRWNPV EGILPSGMVT FNLYHFLEVN KQKETFVCIG IHEGDPTWKK NYSLWPWGSC DKLVPLEIVF NPEEWI KLT KSIYNWTEEY GRFDPSSWES VANEEMWQAR MKTPFFIFNL AETAHMPSKV KAQLYAQAYD LYKEIVYLQK EHPVNWH KN YAIACERMLR LQARDADPEV LLSETIRHFR LYSQKAPNDP QQADILGALK HLRKELQSLR NRKNVDYKDH DGDYKDHD I DYKDDDDK

UniProtKB: Protein O-mannosyl-transferase TMEM260

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Macromolecule #2: Plexin-B2

MacromoleculeName: Plexin-B2 / type: protein_or_peptide / ID: 2
Details: Synthetic peptide N-terminal Dansylated with GSGA linker and sequence PVITRIQPETGPLGGGIRITI from PLXNB2 IPT1 domain
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 2.462845 KDa
SequenceString:
GSGAPVITRI QPETGPLGGG IRITI

UniProtKB: Plexin-B2

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Macromolecule #3: Dolichol monophosphate beta-D-Mannose

MacromoleculeName: Dolichol monophosphate beta-D-Mannose / type: ligand / ID: 3 / Number of copies: 1 / Formula: IZY
Molecular weightTheoretical: 602.737 Da

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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

Concentration1.2 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
50.0 mMTristris(hydroxymethyl)aminomethane
0.025 g%DDMn-dodecyl -D-maltoside
2.0 mMMgCl2magnesium chloride
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 180 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.0005 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 4 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 21886 / Average electron dose: 49.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. v4.7.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: Ab initio reconstruction in cryoSPARC
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.7.0) / Number images used: 271859
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.7.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.7.0)
Final 3D classificationSoftware - Name: cryoSPARC (ver. v4.7.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

nx78


Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9rqm:
GT-C O-Mannosyltransferase TMEM260 co-purified with natural donor and in complex with acceptor peptide

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