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- PDB-9ub8: Structure of glycosylphosphatidylinositol transamidase,state 2 -

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Basic information

Entry
Database: PDB / ID: 9ub8
TitleStructure of glycosylphosphatidylinositol transamidase,state 2
Components
  • GPI transamidase component GAA1
  • GPI transamidase component GAB1
  • GPI transamidase component GPI16
  • GPI transamidase component GPI17
KeywordsMEMBRANE PROTEIN / GPI achoring / Transamidase
Function / homology
Function and homology information


attachment of GPI anchor to protein / GPI-anchor transamidase complex / GPI anchor biosynthetic process / fungal-type cell wall organization / nuclear inner membrane / cell division / endoplasmic reticulum membrane / endoplasmic reticulum / membrane
Similarity search - Function
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
Similarity search - Domain/homology
GPI transamidase component GPI16 / GPI transamidase component GAA1 / GPI transamidase component GAB1 / GPI transamidase component GPI17
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.41 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 2
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
E: GPI transamidase component GAA1
D: GPI transamidase component GPI17
C: GPI transamidase component GPI16
F: GPI transamidase component GAB1
G: GPI transamidase component GPI17
H: GPI transamidase component GPI16


Theoretical massNumber of molelcules
Total (without water)487,4958
Polymers487,4958
Non-polymers00
Water00
1


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

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Components

#1: Protein GPI transamidase component GAA1


Mass: 69279.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / 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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: GAB1, CDC91, YLR459W, L9122.2 / Production host: Homo sapiens (human) / References: UniProt: P41733
#3: Protein GPI transamidase component GPI17


Mass: 60862.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: GPI17, YDR434W, D9461.20 / Production host: Homo sapiens (human) / References: UniProt: Q04080
#4: Protein GPI transamidase component GPI16


Mass: 68836.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: GPI16, YHR188C / Production host: Homo sapiens (human) / References: UniProt: P38875
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: dimeric glycosylphosphatidylinositol (GPI) transamidase
Type: COMPLEX / Entity ID: all / 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: 4.41 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 29585 / Symmetry type: POINT

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