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- PDB-9ub7: Structure of glycosylphosphatidylinositol transamidase,state 1 -

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Basic information

Entry
Database: PDB / ID: 9ub7
TitleStructure of glycosylphosphatidylinositol transamidase,state 1
Components
  • (GPI transamidase component ...) x 4
  • GPI-anchor transamidase
KeywordsMEMBRANE PROTEIN / GPI transamidase / GPI biosynthesis
Function / homology
Function and homology information


GPI-anchor transamidase activity / attachment of GPI anchor to protein / GPI-anchor transamidase complex / GPI anchor biosynthetic process / fungal-type cell wall organization / Hydrolases / nuclear inner membrane / cell division / endoplasmic reticulum membrane / endoplasmic reticulum ...GPI-anchor transamidase activity / attachment of GPI anchor to protein / GPI-anchor transamidase complex / GPI anchor biosynthetic process / fungal-type cell wall organization / Hydrolases / nuclear inner membrane / cell division / endoplasmic reticulum membrane / endoplasmic reticulum / proteolysis / membrane
Similarity search - Function
GPI-anchor transamidase / GPI transamidase component PIG-T / GPI transamidase component Gaa1 / GPI transamidase subunit PIG-U / Phosphatidylinositol-glycan biosynthesis class S protein / Gpi16 subunit, GPI transamidase component / Gaa1-like, GPI transamidase component / GPI transamidase subunit PIG-U / Phosphatidylinositol-glycan biosynthesis class S protein / Peptidase C13, legumain / Peptidase C13 family
Similarity search - Domain/homology
: / TETRADECANE / DECANE / DODECANE / Chem-XKP / CHOLESTEROL HEMISUCCINATE / GPI transamidase component GPI16 / GPI transamidase component GAA1 / GPI transamidase component GAB1 / GPI-anchor transamidase / GPI transamidase component GPI17
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.61 Å
AuthorsHua, Z.K. / Ding, X.Y. / Zhang, M. / Liu, X.T. / Zhang, M.J. / Yu, H.J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of glycosylphosphatidylinositol transamidase,state 1
Authors: Hua, Z.K. / Ding, X.Y. / Zhang, M. / Liu, X.T. / Zhang, M.J. / Yu, H.J.
History
DepositionApr 2, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GPI transamidase component GAA1
B: GPI transamidase component GAB1
C: GPI-anchor transamidase
D: GPI transamidase component GPI17
E: GPI transamidase component GPI16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)297,11921
Polymers291,2005
Non-polymers5,92016
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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GPI transamidase component ... , 4 types, 4 molecules ABDE

#1: Protein GPI transamidase component GAA1


Mass: 69279.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: GAA1, END2, YLR088W, L9449.4 / Production host: Homo sapiens (human) / References: UniProt: P39012
#2: Protein GPI transamidase component GAB1 / Cell division control protein 91


Mass: 44768.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: GAB1, CDC91, YLR459W, L9122.2 / Production host: Homo sapiens (human) / References: UniProt: P41733
#4: Protein GPI transamidase component GPI17


Mass: 60862.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: GPI17, YDR434W, D9461.20 / Production host: Homo sapiens (human) / References: UniProt: Q04080
#5: Protein GPI transamidase component GPI16


Mass: 68836.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: GPI16, YHR188C / Production host: Homo sapiens (human) / References: UniProt: P38875

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Protein , 1 types, 1 molecules C

#3: Protein GPI-anchor transamidase / GPI transamidase


Mass: 47452.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: GPI8, YDR331W, D9798.2 / Production host: Homo sapiens (human) / References: UniProt: P49018, Hydrolases

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Sugars , 3 types, 4 molecules

#6: 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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#7: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#14: 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
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 , 6 types, 12 molecules

#8: Chemical ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H50O4
#9: Chemical ChemComp-XKP / (11R,14S)-17-amino-14-hydroxy-8,14-dioxo-9,13,15-trioxa-14lambda~5~-phosphaheptadecan-11-yl decanoate


Mass: 495.587 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H46NO8P
#10: Chemical ChemComp-C14 / TETRADECANE


Mass: 198.388 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H30
#11: Chemical ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H26
#12: Chemical ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22
#13: Chemical ChemComp-A1EOT / [(2~{R})-1-[[(1~{S},2~{R},3~{S},4~{S},5~{R},6~{R})-2-[(2~{R},3~{R},4~{R},5~{S},6~{R})-3-azanyl-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]oxy-6-heptanoyloxy-3,4,5-tris(oxidanyl)cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-3-decoxy-propan-2-yl] nonanoate


Mass: 888.028 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H78NO17P / 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: monomeric glycosylphosphatidylinositol (GPI) transamidase
Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
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: 3000 nm / Nominal defocus min: 1100 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.61 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 55376 / Symmetry type: POINT

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