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- EMDB-66120: Cryo-EM structure of Candida glabrata GPI mannosyltransferase I b... -

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Basic information

Entry
Database: EMDB / ID: EMD-66120
TitleCryo-EM structure of Candida glabrata GPI mannosyltransferase I bound to Dol-P-Man
Map data
Sample
  • Complex: GPI mannosyltransferase I
    • Protein or peptide: GPI mannosyltransferase 1
    • Protein or peptide: Protein PBN1
  • Ligand: dolichyl phosphate mannose
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsGT-C / GPI / Mannosyltransferase / MEMBRANE PROTEIN
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
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 speciesNakaseomyces glabratus (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.48 Å
AuthorsSun H / Wu WH / Yan ZF
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Fungi / Year: 2025
Title: Structural Insights into the Glycosylphosphatidylinositol Mannosyltransferase I Complex from Candida glabrata
Authors: Sun H / Wu W / Li X / Deng Y / Huang J / Yin M / Yan Z
History
DepositionSep 5, 2025-
Header (metadata) releaseDec 3, 2025-
Map releaseDec 3, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66120.png

Downloads & links

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Map

FileDownload / File: emd_66120.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 220 pix.
= 239.36 Å		1.09 Å/pix.
x 220 pix.
= 239.36 Å		1.09 Å/pix.
x 220 pix.
= 239.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.088 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-1.898059 - 3.1673372
Average (Standard dev.)0.0040624323 (±0.08804717)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 239.36002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_66120_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_66120_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_66120_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : GPI mannosyltransferase I

EntireName: GPI mannosyltransferase I
Components
  • Complex: GPI mannosyltransferase I
    • Protein or peptide: GPI mannosyltransferase 1
    • Protein or peptide: Protein PBN1
  • Ligand: dolichyl phosphate mannose
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: GPI mannosyltransferase I

SupramoleculeName: GPI mannosyltransferase I / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Nakaseomyces glabratus (fungus)

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Macromolecule #1: GPI mannosyltransferase 1

MacromoleculeName: GPI mannosyltransferase 1 / type: protein_or_peptide / ID: 1
Details: Sequence reference for strain 'Nakaseomyces glabratus' is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id Q6FXQ5.
Number of copies: 1 / Enantiomer: LEVO
EC number: Transferases; Glycosyltransferases; Hexosyltransferases
Source (natural)Organism: Nakaseomyces glabratus (fungus)
Molecular weightTheoretical: 50.289254 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MFKLGTIGLL SLAVLLRIAF FLFGVYQDEH FTVKYTDIDY QVFNDAAWFV AHRKSPYNRD TYRYTPLLSW LLLPNHMIPW FHFGKLIFV LCDLATGVLI LQMLKKLKSK YRYGTDRMTI MAAIWLLNPM VITISTRGNA ESVLCFLILS FLYCFLCEQY L LGGLLFGL ...String:
MFKLGTIGLL SLAVLLRIAF FLFGVYQDEH FTVKYTDIDY QVFNDAAWFV AHRKSPYNRD TYRYTPLLSW LLLPNHMIPW FHFGKLIFV LCDLATGVLI LQMLKKLKSK YRYGTDRMTI MAAIWLLNPM VITISTRGNA ESVLCFLILS FLYCFLCEQY L LGGLLFGL SIHFKIYPII YALPIAIYVA AAHYNKTQSV FKSSFKLFLV GFSTLIVLIL LTVFMYMLYG DKFIDQTYLY HI YRTDHRH NFSVWNMLLY FNSALPKTSE LSKFVFLPQM IIVLAISLTQ LRRPSSFPLL CNVLFLETFA FVTFNKVCTS QYF IWYLIF LPFVLYNTRI SMRRGIVMLV VWVATQALWL RQGYLLEFEG QNVFYPGLFC ASVGFFVSNA WILGQFIEDT IIQN DYVYR IEPSESRSKD SAVIDKPAIA KTEKAE

UniProtKB: GPI mannosyltransferase 1

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Macromolecule #2: Protein PBN1

MacromoleculeName: Protein PBN1 / type: protein_or_peptide / ID: 2
Details: Sequence reference for strain 'Nakaseomyces glabratus' is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id Q6FX62.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Nakaseomyces glabratus (fungus)
Molecular weightTheoretical: 47.799812 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MESVRHRIAL LFANEADIQD VETVEDGVIV FPNSNITIQD RWTYAIDYEL DSIRRISWRN PSSTRQFSVI ESRLAPGFNI YSNDKEARL NLFGIQPVYS PMYKSLHSET WKSINEILPG GKNLNIPWNP ELCDYDILIT ANTVQVFSYC SLVEKKKFVK D AGKVEIGL ...String:
MESVRHRIAL LFANEADIQD VETVEDGVIV FPNSNITIQD RWTYAIDYEL DSIRRISWRN PSSTRQFSVI ESRLAPGFNI YSNDKEARL NLFGIQPVYS PMYKSLHSET WKSINEILPG GKNLNIPWNP ELCDYDILIT ANTVQVFSYC SLVEKKKFVK D AGKVEIGL FHVDTEDEED INLSGLRCTW EDTSNNIGKC EKTTLFYKPF HLYVDDSSDI APITIENTNG LHPKMKIDLS GI RKDKDCR HFVFSQLPSE IFVDKFQSPG SIVFGLDDLE LPDYKVNSLS WGSESIVTLK EGQINEITYF SRYLEPKERA SNK TVGFEP ILFKACQVGK EEDLSNPFYS RSLGYEAYFS ENTKFYHINS TSVHVNIPYP NKNDIGNIEY TTFGIVVLAI CYLI YKLLR PSRKLSTVKR D

UniProtKB: Protein PBN1

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Macromolecule #4: dolichyl phosphate mannose

MacromoleculeName: dolichyl phosphate mannose / type: ligand / ID: 4 / Number of copies: 1 / Formula: MJC
Molecular weightTheoretical: 1.011439 KDa
Chemical component information

ChemComp-MJC:
dolichyl phosphate mannose

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Macromolecule #5: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / 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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 56.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 1.7 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: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.48 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 80856
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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