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- EMDB-68960: The cryo-EM map of GPI-MT-I complex -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-68960
TitleThe cryo-EM map of GPI-MT-I complex
Map data
Sample
  • Complex: membrane-bound glycosyltransferase
    • Protein or peptide: Protein PBN1
    • Protein or peptide: GPI mannosyltransferase 1
  • 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 cerevisae (yeast) / Saccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 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 6, 2026-
Header (metadata) releaseSep 9, 2026-
Map releaseSep 9, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_68960.png

Downloads & links

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Map

FileDownload / File: emd_68960.map.gz / Format: CCP4 / Size: 52.7 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 240 pix.
= 223.2 Å		0.93 Å/pix.
x 240 pix.
= 223.2 Å		0.93 Å/pix.
x 240 pix.
= 223.2 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: 0.409
Minimum - Maximum-1.2993287 - 1.8880581
Average (Standard dev.)0.0029944463 (±0.053081017)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 223.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_68960_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_68960_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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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: dolichyl phosphate mannose

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Supramolecule #1: membrane-bound glycosyltransferase

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

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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

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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: 45.764379 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: TGEEWGLTVL SFLVRVGFFL FGIYQDANFK VRYTDIDYFV FHDAAKYVYE GKSPYARDTY RYTPLLSWLL VPNHYFGWFH LGKVIFVIF DLVTGLIIMK LLNQAISRKR ALILESIWLL NPMVITISTR GNAESVLCCL IMFTLFFLQK SRYTLAGILY G LSIHFKIY ...String:
TGEEWGLTVL SFLVRVGFFL FGIYQDANFK VRYTDIDYFV 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

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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

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 50.0 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

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 184449
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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