[English] 日本語
Yorodumi
- EMDB-68941: The cryo-EM map of GPI-MT-I complex with Gpi14 D38A mutation -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-68941
TitleThe cryo-EM map of GPI-MT-I complex with Gpi14 D38A mutation
Map data
Sample
  • Complex: membrane-bound glycosyltransferase
    • Protein or peptide: Protein PBN1
    • Protein or peptide: GPI mannosyltransferase 1
  • Ligand: [(2~{R})-3-[[(1~{S},2~{R},3~{R},4~{S},5~{S},6~{R})-2-decanoyloxy-3,4,5,6-tetrakis(oxidanyl)cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-2-undecanoyloxy-propyl] dodecanoate
  • Ligand: dolichyl phosphate mannose
Keywordsmembrane protein / glycosyltransferase / TRANSFERASE
Function / homology
Function and homology information


GPI mannosyltransferase activity / alpha-1,4-mannosyltransferase activity / glycosylphosphatidylinositol-mannosyltransferase I complex / mannosyltransferase activity / GPI anchor biosynthetic process / fungal-type cell wall organization / Transferases; Glycosyltransferases; Hexosyltransferases / ERAD pathway / protein processing / endoplasmic reticulum membrane / endoplasmic reticulum
Similarity search - Function
GPI mannosyltransferase 1 / Glycosylphosphatidylinositol-mannosyltransferase I, PIG-X/PBN1 / Protein Pbn1 / Mannosyltransferase (PIG-M) / PIG-X / PBN1 / PIG-X / PBN1
Similarity search - Domain/homology
Protein PBN1 / GPI mannosyltransferase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsLiu J / Yang YZ / Zhang M / Yu HJ
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of a membrane-bound glycosyltransferase
Authors: Liu J / Yang YZ / Zhang M / Yu HJ
History
DepositionFeb 5, 2026-
Header (metadata) releaseSep 9, 2026-
Map releaseSep 9, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_68941.png

Downloads & links

-
Map

FileDownload / File: emd_68941.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 224 pix.
= 208.32 Å		0.93 Å/pix.
x 224 pix.
= 208.32 Å		0.93 Å/pix.
x 224 pix.
= 208.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.176
Minimum - Maximum-1.0549312 - 1.6891327
Average (Standard dev.)0.0018943024 (±0.040530827)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 208.32 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_68941_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_68941_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : membrane-bound glycosyltransferase

EntireName: membrane-bound glycosyltransferase
Components
  • Complex: membrane-bound glycosyltransferase
    • Protein or peptide: Protein PBN1
    • Protein or peptide: GPI mannosyltransferase 1
  • Ligand: [(2~{R})-3-[[(1~{S},2~{R},3~{R},4~{S},5~{S},6~{R})-2-decanoyloxy-3,4,5,6-tetrakis(oxidanyl)cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-2-undecanoyloxy-propyl] dodecanoate
  • Ligand: dolichyl phosphate mannose

-
Supramolecule #1: membrane-bound glycosyltransferase

SupramoleculeName: membrane-bound glycosyltransferase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: strain ATCC 204508 / S288c
Molecular weightTheoretical: 99 KDa

-
Macromolecule #1: Protein PBN1

MacromoleculeName: Protein PBN1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 46.591445 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: VTRHRVTVLY NAPEDIGNHM RQNDTHLTVR GGSGVVLQQR WLLERTGSLD KSFTRITWRP RADLARSLSV IENELSAGFS VYSNSSDVP ERFITNPVYN SFHSEKFDIE QYLPPEVDLN LSWNPEDFTY DISVEPTQIQ IVEYRLLKQG EEFTIARVKD E KLEVGVFF ...String:
VTRHRVTVLY NAPEDIGNHM RQNDTHLTVR GGSGVVLQQR WLLERTGSLD KSFTRITWRP RADLARSLSV IENELSAGFS VYSNSSDVP ERFITNPVYN SFHSEKFDIE QYLPPEVDLN LSWNPEDFTY DISVEPTQIQ IVEYRLLKQG EEFTIARVKD E KLEVGVFF VDASDESDVD IGGIRCNWRM DDGKMERCQK TSLLYKQGHI AYNHSTTTTS LYLNEPIGLH PKIMIDLTDF EE RPKCMYL MHLQLPLELF IDKFQSSPLL LFGEDDLELP EYSLRDKAWG SESIFELKAG TMNEVTLHTR YIEPSNNKGD KLE VSFDPE VILACDTGDN KVSRNPFYKK GLGYESLFTD DTTFRHLNST TLLVPIPRPD TKDYSKIKNG TLLCLLISII YIFS KVFGN

UniProtKB: Protein PBN1

-
Macromolecule #2: GPI mannosyltransferase 1

MacromoleculeName: GPI mannosyltransferase 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
EC number: Transferases; Glycosyltransferases; Hexosyltransferases
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 45.720371 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: TGEEWGLTVL SFLVRVGFFL FGIYQDANFK VRYTDIAYFV FHDAAKYVYE GKSPYARDTY RYTPLLSWLL VPNHYFGWFH LGKVIFVIF DLVTGLIIMK LLNQAISRKR ALILESIWLL NPMVITISTR GNAESVLCCL IMFTLFFLQK SRYTLAGILY G LSIHFKIY ...String:
TGEEWGLTVL SFLVRVGFFL FGIYQDANFK VRYTDIAYFV FHDAAKYVYE GKSPYARDTY RYTPLLSWLL VPNHYFGWFH LGKVIFVIF DLVTGLIIMK LLNQAISRKR ALILESIWLL NPMVITISTR GNAESVLCCL IMFTLFFLQK SRYTLAGILY G LSIHFKIY PIIYCIPIAI FIYYNKRNQG PRTQLTSLLN IGLSTLTTLL GCGWAMYKIY GYEFLDQAYL YHLYRTDHRH NF SVWNMLL YLDSANKENG ESNLSRYAFV PQLLLVLVTG CLEWWNPTFD NLLRVLFVQT FAFVTYNKVC TSQYFVWYLI FLP FYLSRT HIGWKKGLLM ATLWVGTQGI WLSQGYYLEF EGKNVFYPGL FIASVLFFVT NVWLLGQFIT DIKI

UniProtKB: GPI mannosyltransferase 1

-
Macromolecule #4: [(2~{R})-3-[[(1~{S},2~{R},3~{R},4~{S},5~{S},6~{R})-2-decanoyloxy-...

MacromoleculeName: [(2~{R})-3-[[(1~{S},2~{R},3~{R},4~{S},5~{S},6~{R})-2-decanoyloxy-3,4,5,6-tetrakis(oxidanyl)cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-2-undecanoyloxy-propyl] dodecanoate
type: ligand / ID: 4 / Number of copies: 1 / Formula: A1E5V
Molecular weightTheoretical: 839.042 Da

-
Macromolecule #5: dolichyl phosphate mannose

MacromoleculeName: dolichyl phosphate mannose / type: ligand / ID: 5 / Number of copies: 1 / Formula: MJC
Molecular weightTheoretical: 1.011439 KDa
Chemical component information

ChemComp-MJC:
dolichyl phosphate mannose

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 201962
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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