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- EMDB-64000: Structure of glycosylphosphatidylinositol transamidase,state 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-64000
TitleStructure of glycosylphosphatidylinositol transamidase,state 1
Map data
Sample
  • Complex: monomeric glycosylphosphatidylinositol (GPI) transamidase
    • Protein or peptide: x 5 types
  • Ligand: x 7 types
KeywordsGPI transamidase / GPI biosynthesis / Membrane protein
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
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 (brewer's yeast) / Saccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.61 Å
AuthorsHua ZK / Ding XY / Zhang M / Liu XT / Zhang MJ / Yu HJ
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of glycosylphosphatidylinositol transamidase,state 1
Authors: Hua ZK / Ding XY / Zhang M / Liu XT / Zhang MJ / Yu HJ
History
DepositionApr 2, 2025-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64000.png

Downloads & links

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Map

FileDownload / File: emd_64000.map.gz / Format: CCP4 / Size: 70.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 264 pix.
= 242.88 Å		0.92 Å/pix.
x 264 pix.
= 242.88 Å		0.92 Å/pix.
x 264 pix.
= 242.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0136
Minimum - Maximum-0.060632184 - 0.099983044
Average (Standard dev.)0.00002793697 (±0.0036816548)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions264264264
Spacing264264264
CellA=B=C: 242.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_64000_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_64000_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 : monomeric glycosylphosphatidylinositol (GPI) transamidase

EntireName: monomeric glycosylphosphatidylinositol (GPI) transamidase
Components
  • Complex: monomeric glycosylphosphatidylinositol (GPI) transamidase
    • Protein or peptide: GPI transamidase component GAA1
    • Protein or peptide: GPI transamidase component GAB1
    • Protein or peptide: GPI-anchor transamidase
    • Protein or peptide: GPI transamidase component GPI17
    • Protein or peptide: GPI transamidase component GPI16
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: (11R,14S)-17-amino-14-hydroxy-8,14-dioxo-9,13,15-trioxa-14lambda~5~-phosphaheptadecan-11-yl decanoate
  • Ligand: TETRADECANE
  • Ligand: DODECANE
  • Ligand: DECANE
  • Ligand: [(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
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: monomeric glycosylphosphatidylinositol (GPI) transamidase

SupramoleculeName: monomeric glycosylphosphatidylinositol (GPI) transamidase
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: GPI transamidase component GAA1

MacromoleculeName: GPI transamidase component GAA1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 69.279828 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MALLEKLHRR IVDMGLVPRI IALLPVISML CALFGFISIA ILPMDGQYRR TYISENALMP SQAYSYFRES EWNILRGYRS QIKEMVNMT SMERNNLMGS WLQEFGTKTA IYENEQYGET LYGVMHAPRG DGTEAMVLAV PWFNSDDEFN IGGAALGVSL A RFFSRWPV ...String:
MALLEKLHRR IVDMGLVPRI IALLPVISML CALFGFISIA ILPMDGQYRR TYISENALMP SQAYSYFRES EWNILRGYRS QIKEMVNMT SMERNNLMGS WLQEFGTKTA IYENEQYGET LYGVMHAPRG DGTEAMVLAV PWFNSDDEFN IGGAALGVSL A RFFSRWPV WSKNIIVVFS ENPRAALRSW VEAYHTSLDL TGGSIEAAVV LDYSSTEDFF EYVEISYDGL NGELPNLDLV NI AISITEH EGMKVSLHGL PSDQLTNNNF WSRLKILCLG IRDWALSGVK KPHGNEAFSG WRIQSVTLKA HGNSGHDITT FGR IPEAMF RSINNLLEKF HQSFFFYLLL APRQFVSISS YLPSAVALSI AFAISSLNAF INNAYANISL FSEYNLVALL VWFV SLVIS FVVSQAFLLI PSSGLLMTIS MASCFLPLIL SRKIHISEPL SYRLKNVAFL YFSLVSTSLL MINFAMALLI GTLAF PMTF VKTIVESSSE HEVTTQSSNP IKTEPKDEIE LVENHMDTTP ATPQQQKQKL KNLVLLILTN PFISITLFGL FFDDEF HGF DIINKLVSAW LDLKCWSWFV LCIGWLPCWL LILASSFESK SVVVRSKEKQ S

UniProtKB: GPI transamidase component GAA1

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Macromolecule #2: GPI transamidase component GAB1

MacromoleculeName: GPI transamidase component GAB1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 44.768891 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDSTALKVAL GCIAIRLAVN SLFPSLQQQL DQSVEFSTPV TSFRSLQEGI YLLRNNIQVY NHGVVHHPPI LIFFLSLFNS DRLISLIYA LIDGLIAYQL TEVTKAFKNL KLKVWLPGLL YAVNPLTLLS CISRSSIIFT NFAISSSLYC ILAEGNVLLS S VMISISGY ...String:
MDSTALKVAL GCIAIRLAVN SLFPSLQQQL DQSVEFSTPV TSFRSLQEGI YLLRNNIQVY NHGVVHHPPI LIFFLSLFNS DRLISLIYA LIDGLIAYQL TEVTKAFKNL KLKVWLPGLL YAVNPLTLLS CISRSSIIFT NFAISSSLYC ILAEGNVLLS S VMISISGY LSVYPILLLI PLLGMLKSWR QRILSAIVSI LSLLILLLFS YSILGSQSWS FLTQVYGSII TFEKVFPNLG LW WYFFIEM FDTFIPFFKA VFNIFIAVFI TPFTLRYHKQ PFYAFILCIG WIVLTKPYPS LGDAGFFFSF LPFFTPLFGY LRY PIISAL LFLHAIVLAP IFYHLWVVLG SGNSNFFYAI SLVYALAIAS ILVDLNWAML RIEYDNGIPN FKLKVTQI

UniProtKB: GPI transamidase component GAB1

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Macromolecule #3: GPI-anchor transamidase

MacromoleculeName: GPI-anchor transamidase / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 47.45216 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRIAMHLPLL LLYIFLLPLS GANNTDAAHE VIATNTNNWA VLVSTSRFWF NYRHMANVLS MYRTVKRLGI PDSQIILMLS DDVACNSRN LFPGSVFNNK DHAIDLYGDS VEVDYRGYEV TVENFIRLLT DRWTEDHPKS KRLLTDENSN IFIYMTGHGG D DFLKFQDA ...String:
MRIAMHLPLL LLYIFLLPLS GANNTDAAHE VIATNTNNWA VLVSTSRFWF NYRHMANVLS MYRTVKRLGI PDSQIILMLS DDVACNSRN LFPGSVFNNK DHAIDLYGDS VEVDYRGYEV TVENFIRLLT DRWTEDHPKS KRLLTDENSN IFIYMTGHGG D DFLKFQDA EEIASEDIAD AFQQMYEKKR YNEIFFMIDT CQANTMYSKF YSPNILAVGS SEMDESSYSH HSDVEIGVAV ID RFTYYCL DFLEQIDKNS TLTLQDLFDS FTFEKIHSHV GVRTDLFDRN PSEVLITDFF ANVQNVIPDD SKPLSVSHYH HYK DHIDTA QYELNNNVLD LALETYRKNN QSSKIEKKIK DIKSTSVLDV DIDSNECFFT SFKQSATIIL ALIVTILWFM LRGN TAKAT YDLYTN

UniProtKB: GPI-anchor transamidase

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Macromolecule #4: GPI transamidase component GPI17

MacromoleculeName: GPI transamidase component GPI17 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 60.862703 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSNANLRKWV GFCFVAIYLF LGVPLWYKLT TVYRASLPIN YIESLQNNKF QDIHLVIPVY VKSDTYRFPD VHDAIQVQVN HLLNSQEQR VPWSLQVLPY NETIEQMESE GNQFHVVTLK LDEFIGYSSA YDTKETLVYY DDAAVLSNDL PFFVAQTLVE H TFQLEWTH ...String:
MSNANLRKWV GFCFVAIYLF LGVPLWYKLT TVYRASLPIN YIESLQNNKF QDIHLVIPVY VKSDTYRFPD VHDAIQVQVN HLLNSQEQR VPWSLQVLPY NETIEQMESE GNQFHVVTLK LDEFIGYSSA YDTKETLVYY DDAAVLSNDL PFFVAQTLVE H TFQLEWTH LNKTCEGVST NNDVAISYDP NIHLSVTLLS GDGNPVAWEI EPTLTDYFSP FRKFLSPLVN FTVDSSIVYH ND LNLHSLN GSCTSVTWFD LSHTIDLSEL SSMAYYPEDS ALNLAIVFPS ASSSPDGLAF INGTRISDEI TTLDWNSYLV PQW GVIIIN KMPLKPNSVI SEDYLEPMMY RFATDIFQLL GLTEGSQDLL SPYITIDSFK RLTILQNLDK ATETLWSLVK LTQQ FQGMS IPREVSDNVI EALDLRLQII DLLNDPGKGG DIVWNNALHL SNELVKLCEK AFFNGEMVQQ NFFPQEHMIA VYLPL LGPI SAVMFFGFYN VMKEKNQKSK KNGTEREVAK EKLELKEAQK LHAIDGEDEL

UniProtKB: GPI transamidase component GPI17

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Macromolecule #5: GPI transamidase component GPI16

MacromoleculeName: GPI transamidase component GPI16 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 68.836031 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MILTLAYFML GTLLLGVFAE DTVSQIGIND SLWYPYDEAL VLKPLPNNDL LLSFAFQLQS EPFDPAVSSM SYDAYEHYTT FPRAIPPLL ESTATRQFHL RFTRGFWDAL SWGQLPHAGK EAGASGVELW SQVQAMDQEQ AFHNWKKLSN SLSGLFCSSL N FIDESRTT ...String:
MILTLAYFML GTLLLGVFAE DTVSQIGIND SLWYPYDEAL VLKPLPNNDL LLSFAFQLQS EPFDPAVSSM SYDAYEHYTT FPRAIPPLL ESTATRQFHL RFTRGFWDAL SWGQLPHAGK EAGASGVELW SQVQAMDQEQ AFHNWKKLSN SLSGLFCSSL N FIDESRTT FPRRSYASDI GAPLFNSTEK LYLMRASLPN EPICTENLTP FIKLLPTRGK SGLTSLLDGH KLFDSLWNSI SL DIATICS EDEDALCHYE MDARIEMVTH VPSALARGER PIPKPLDGNT LRCDTDKPFD SYQCFPLPEP SQTHFKLSQL FAR PINNGN LFANRPTRIC AEVDRSTWTA FLSVDDTIFS THDNCFDLSN DQNEGGSGYD FILESTDTTK VTPIVPVPIH VSRS LTGNG QDRGGMRIVF HNDNDTPVKL IYFESLPWFM RVYLSSLQIT STTSPQLQEN DIILDKYYLQ AADRKRPGHL EFTML IPAN TDIVMTYQFD KALLQFAEYP PDANHGFEID AAVITVLSLE SSSSLYEMRT STLLLSLSTP DFSMPYNVII LTSTIM GLI FGMLYNLMVK RMVTVEEADK ITLQSGLKYK LLKLKEKFLG KKKTKTD

UniProtKB: GPI transamidase component GPI16

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Macromolecule #8: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 8 / Number of copies: 2 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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Macromolecule #9: (11R,14S)-17-amino-14-hydroxy-8,14-dioxo-9,13,15-trioxa-14lambda~...

MacromoleculeName: (11R,14S)-17-amino-14-hydroxy-8,14-dioxo-9,13,15-trioxa-14lambda~5~-phosphaheptadecan-11-yl decanoate
type: ligand / ID: 9 / Number of copies: 2 / Formula: XKP
Molecular weightTheoretical: 495.587 Da
Chemical component information

ChemComp-XKP:
(11R,14S)-17-amino-14-hydroxy-8,14-dioxo-9,13,15-trioxa-14lambda~5~-phosphaheptadecan-11-yl decanoate

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Macromolecule #10: TETRADECANE

MacromoleculeName: TETRADECANE / type: ligand / ID: 10 / Number of copies: 3 / Formula: C14
Molecular weightTheoretical: 198.388 Da
Chemical component information

ChemComp-C14:
TETRADECANE

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Macromolecule #11: DODECANE

MacromoleculeName: DODECANE / type: ligand / ID: 11 / Number of copies: 3 / Formula: D12
Molecular weightTheoretical: 170.335 Da
Chemical component information

ChemComp-D12:
DODECANE

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Macromolecule #12: DECANE

MacromoleculeName: DECANE / type: ligand / ID: 12 / Number of copies: 1 / Formula: D10
Molecular weightTheoretical: 142.282 Da
Chemical component information

ChemComp-D10:
DECANE

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Macromolecule #13: [(2~{R})-1-[[(1~{S},2~{R},3~{S},4~{S},5~{R},6~{R})-2-[(2~{R},3~{R...

MacromoleculeName: [(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- ...Name: [(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
type: ligand / ID: 13 / Number of copies: 1 / Formula: A1EOT
Molecular weightTheoretical: 888.028 Da

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Macromolecule #14: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 14 / 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k 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: 3.0 µm / Nominal defocus min: 1.1 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: 3.61 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 55376
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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