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- PDB-9wno: Cryo-EM structure of Candida glabrata GPI mannosyltransferase I b... -

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Basic information

Entry
Database: PDB / ID: 9wno
TitleCryo-EM structure of Candida glabrata GPI mannosyltransferase I bound to Dol-P-Man
Components
  • GPI mannosyltransferase 1
  • Protein PBN1
KeywordsMEMBRANE PROTEIN / GT-C / GPI / Mannosyltransferase
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
dolichyl phosphate mannose / CHOLESTEROL HEMISUCCINATE / Protein PBN1 / GPI mannosyltransferase 1
Similarity search - Component
Biological speciesNakaseomyces glabratus (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.48 Å
AuthorsSun, H. / Wu, W.H. / Yan, Z.F.
Funding support1items
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, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GPI mannosyltransferase 1
B: Protein PBN1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,6577
Polymers98,0892
Non-polymers2,5685
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein GPI mannosyltransferase 1 / GPI mannosyltransferase I / GPI-MT-I / Glycosylphosphatidylinositol-anchor biosynthesis protein 14


Mass: 50289.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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.
Source: (gene. exp.) Nakaseomyces glabratus (fungus) / Gene: GPI14, CAGL0B03905g / Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: Q6FXQ5, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Protein Protein PBN1


Mass: 47799.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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.
Source: (gene. exp.) Nakaseomyces glabratus (fungus) / Gene: PBN1, CAGL0B00506g / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q6FX62

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Sugars , 2 types, 3 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 2 molecules

#4: Chemical ChemComp-MJC / dolichyl phosphate mannose


Mass: 1011.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C61H103O9P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H50O4 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: GPI mannosyltransferase I / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Nakaseomyces glabratus (fungus)
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2100 nm / Nominal defocus min: 1700 nm
Image recordingElectron dose: 56 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
12cryoSPARC3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.48 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 80856 / Symmetry type: POINT
RefinementHighest resolution: 3.48 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0037008
ELECTRON MICROSCOPYf_angle_d0.5749529
ELECTRON MICROSCOPYf_dihedral_angle_d4.701951
ELECTRON MICROSCOPYf_chiral_restr0.0431080
ELECTRON MICROSCOPYf_plane_restr0.0041169

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