[English] 日本語
Yorodumi
- EMDB-54178: GT-C O-Mannosyltransferase TMEM260 incubated with Far-P-Man -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-54178
TitleGT-C O-Mannosyltransferase TMEM260 incubated with Far-P-Man
Map data
Sample
  • Complex: protein-specific O-mannosyl-transferase (TMEM260) incubated with Far-P-Man
    • Protein or peptide: Protein O-mannosyl-transferase TMEM260
  • Ligand: Farmesyl 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 / 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
Protein O-mannosyl-transferase TMEM260
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.65 Å
AuthorsCifuente JO / Ubarretxena-Belandia I / Povolo L / Halim A
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

-
Structure visualization

Supplemental images

emd_54178.png

Downloads & links

-
Map

FileReleased
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)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8238 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035
Minimum - Maximum-0.08828092 - 0.21677853
Average (Standard dev.)0.00045549084 (±0.004932473)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Mask #1

Fileemd_54178_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Sharpened map

Fileemd_54178_additional_1.map
AnnotationSharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_54178_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_54178_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

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

EntireName: protein-specific O-mannosyl-transferase (TMEM260) incubated with Far-P-Man
Components
  • Complex: protein-specific O-mannosyl-transferase (TMEM260) incubated with Far-P-Man
    • Protein or peptide: Protein O-mannosyl-transferase TMEM260
  • Ligand: Farmesyl monophosphate beta-D-Mannose
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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

SupramoleculeName: protein-specific O-mannosyl-transferase (TMEM260) incubated with Far-P-Man
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 80 KDa

-
Macromolecule #1: Protein O-mannosyl-transferase TMEM260

MacromoleculeName: Protein O-mannosyl-transferase TMEM260 / type: protein_or_peptide / ID: 1
Details: contains C-Terminal 3xFLAG tag (DYKDDDDKDYKDDDDKDYKDDDDK).
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

-
Macromolecule #2: Farmesyl monophosphate beta-D-Mannose

MacromoleculeName: Farmesyl monophosphate beta-D-Mannose / type: ligand / ID: 2 / Number of copies: 1 / Formula: A1JKY
Molecular weightTheoretical: 464.487 Da

-
Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2 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

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 12964 / Average electron dose: 60.1 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 stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
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: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.7.0) / Number images used: 332040
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)

-
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-9rql:
GT-C O-Mannosyltransferase TMEM260 incubated with Far-P-Man

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more