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- EMDB-32336: Structure of a human glycosylphosphatidylinositol (GPI) transamidase -

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Basic information

Entry
Database: EMDB / ID: EMD-32336
TitleStructure of a human glycosylphosphatidylinositol (GPI) transamidase
Map data
Sample
  • Complex: Human glycosylphosphatidylinositol transamidase
    • Protein or peptide: Phosphatidylinositol glycan anchor biosynthesis class U protein
    • Protein or peptide: GPI transamidase component PIG-S
    • Protein or peptide: GPI transamidase component PIG-T
    • Protein or peptide: GPI-anchor transamidase
    • Protein or peptide: Glycosylphosphatidylinositol anchor attachment 1 protein
  • Ligand: [2-[[(2~{R})-2-hexanoyloxy-3-[(~{E})-hex-3-enoxy]propoxy]-oxidanyl-phosphoryl]oxy-3,4,5,6-tetrakis(oxidanyl)phenyl] (2~{E},4~{E})-hepta-2,4-dienoate
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION
Function / homology
Function and homology information


GPI-anchor transamidase activity / attachment of GPI anchor to protein / GPI-anchor transamidase complex / GPI anchor biosynthetic process / protein retention in ER lumen / Attachment of GPI anchor to uPAR / Hydrolases / regulation of receptor signaling pathway via JAK-STAT / protein disulfide isomerase activity / tubulin binding ...GPI-anchor transamidase activity / attachment of GPI anchor to protein / GPI-anchor transamidase complex / GPI anchor biosynthetic process / protein retention in ER lumen / Attachment of GPI anchor to uPAR / Hydrolases / regulation of receptor signaling pathway via JAK-STAT / protein disulfide isomerase activity / tubulin binding / neuron differentiation / cytoplasmic vesicle / protein-containing complex assembly / neuron apoptotic process / centrosome / endoplasmic reticulum membrane / endoplasmic reticulum / mitochondrion / proteolysis / membrane / plasma membrane / cytosol
Similarity search - Function
GPI transamidase component PIG-T / GPI transamidase component Gaa1 / GPI transamidase subunit PIG-U / Phosphatidylinositol-glycan biosynthesis class S protein / GPI-anchor transamidase / 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
Glycosylphosphatidylinositol anchor attachment 1 protein / GPI-anchor transamidase / GPI transamidase component PIG-T / GPI transamidase component PIG-S / Phosphatidylinositol glycan anchor biosynthesis class U protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsZhang H / Su J / Li B / Gao Y / Zhang XC / Zhao Y
Funding support China, 2 items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB37030304 China
Chinese Academy of SciencesXDB37030301 China
CitationJournal: Nat Struct Mol Biol / Year: 2022
Title: Structure of human glycosylphosphatidylinositol transamidase.
Authors: Hongwei Zhang / Jiawei Su / Bin Li / Yiwei Gao / Mengran Liu / Lingli He / Hao Xu / Yanli Dong / Xuejun Cai Zhang / Yan Zhao /
Abstract: Glycosylphosphatidylinositol (GPI) molecules are complex glycophospholipids and serve as membrane anchors for tethering many proteins to the cell surface. Attaching GPI to the protein in the ...Glycosylphosphatidylinositol (GPI) molecules are complex glycophospholipids and serve as membrane anchors for tethering many proteins to the cell surface. Attaching GPI to the protein in the endoplasmic reticulum (ER) is catalyzed by the transmembrane GPI transamidase (GPIT) complex, which is essential for maturation of the GPI-anchored proteins. The GPIT complex is known to be composed of five subunits: PIGK, PIGU, PIGT, PIGS and GPAA1. Here, we determined the structure of the human GPIT complex at a resolution of 3.1 Å using single-particle cryo-EM, elucidating its overall assembly. The PIGK subunit functions as the catalytic component, in which we identified a C206-H164-N58 triad that is critical for the transamination reaction. Transmembrane helices constitute a widely opened cleft, which is located underneath PIGK, serving as a GPI substrate-binding site. The ubiquitin E3 ligase RNF121 is visualized at the back of the complex and probably serves as a quality control factor for the GPIT complex.
History
DepositionDec 2, 2021-
Header (metadata) releaseFeb 16, 2022-
Map releaseFeb 16, 2022-
UpdateMar 30, 2022-
Current statusMar 30, 2022Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7w72
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_32336.png

Downloads & links

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Map

FileDownload / File: emd_32336.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 320 pix.
= 332.8 Å		1.04 Å/pix.
x 320 pix.
= 332.8 Å		1.04 Å/pix.
x 320 pix.
= 332.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.018
Minimum - Maximum-0.050868012 - 0.111189045
Average (Standard dev.)0.00016682458 (±0.0025670088)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 332.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z332.800332.800332.800
α/β/γ90.00090.00090.000
start NX/NY/NZ535455
NX/NY/NZ134138134
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0510.1110.000

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Supplemental data

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Sample components

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Entire : Human glycosylphosphatidylinositol transamidase

EntireName: Human glycosylphosphatidylinositol transamidase
Components
  • Complex: Human glycosylphosphatidylinositol transamidase
    • Protein or peptide: Phosphatidylinositol glycan anchor biosynthesis class U protein
    • Protein or peptide: GPI transamidase component PIG-S
    • Protein or peptide: GPI transamidase component PIG-T
    • Protein or peptide: GPI-anchor transamidase
    • Protein or peptide: Glycosylphosphatidylinositol anchor attachment 1 protein
  • Ligand: [2-[[(2~{R})-2-hexanoyloxy-3-[(~{E})-hex-3-enoxy]propoxy]-oxidanyl-phosphoryl]oxy-3,4,5,6-tetrakis(oxidanyl)phenyl] (2~{E},4~{E})-hepta-2,4-dienoate
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION

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Supramolecule #1: Human glycosylphosphatidylinositol transamidase

SupramoleculeName: Human glycosylphosphatidylinositol transamidase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293

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Macromolecule #1: Phosphatidylinositol glycan anchor biosynthesis class U protein

MacromoleculeName: Phosphatidylinositol glycan anchor biosynthesis class U protein
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 48.448422 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAAPLVLVLV VAVTVRAALF RSSLAEFISE RVEVVSPLSS WKRVVEGLSL LDLGVSPYSG AVFHETPLII YLFHFLIDYA ELVFMITDA LTAIALYFAI QDFNKVVFKK QKLLLELDQY APDVAELIRT PMEMRYIPLK VALFYLLNPY TILSCVAKST C AINNTLIA ...String:
MAAPLVLVLV VAVTVRAALF RSSLAEFISE RVEVVSPLSS WKRVVEGLSL LDLGVSPYSG AVFHETPLII YLFHFLIDYA ELVFMITDA LTAIALYFAI QDFNKVVFKK QKLLLELDQY APDVAELIRT PMEMRYIPLK VALFYLLNPY TILSCVAKST C AINNTLIA FFILTTIKGS AFLSAIFLAL ATYQSLYPLT LFVPGLLYLL QRQYIPVKMK SKAFWIFSWE YAMMYVGSLV VI ICLSFFL LSSWDFIPAV YGFILSVPDL TPNIGLFWYF FAEMFEHFSL FFVCVFQINV FFYTIPLAIK LKEHPIFFMF IQI AVIAIF KSYPTVGDVA LYMAFFPVWN HLYRFLRNIF VLTCIIIVCS LLFPVLWHLW IYAGSANSNF FYAITLTFNV GQIL LISDY FYAFLRREYY LTHGL

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Macromolecule #2: GPI transamidase component PIG-S

MacromoleculeName: GPI transamidase component PIG-S / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 59.09782 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AATHLEVARG KRAALFFAAV AIVLGLPLWW KTTETYRASL PYSQISGLNA LQLRLMVPVT VVFTRESVPL DDQAKLPFTV VHEREIPLK YKMKIKCRFQ KAYRRALDHE EEALSSGSVQ EAEAMLDEPQ EQAEGSLTVY VISEHSSLLP QDMASYIGPK R TAVVRGIM ...String:
AATHLEVARG KRAALFFAAV AIVLGLPLWW KTTETYRASL PYSQISGLNA LQLRLMVPVT VVFTRESVPL DDQAKLPFTV VHEREIPLK YKMKIKCRFQ KAYRRALDHE EEALSSGSVQ EAEAMLDEPQ EQAEGSLTVY VISEHSSLLP QDMASYIGPK R TAVVRGIM HREAFNIIGR RIVQVAQAMS LTEDVLAAAL ADHLPEDKWS AEKRRPLKSS LGYEITFSLL NPDPKSHDVY WD IEGAVRR YVQPFLNALG AAGNFSVDSQ ILYYAMLGVN PRFDSASSSY YLDMHSLPHV INPVESRLGS SAASLYPVLN FLL YVPELA HSPLYIQDKD GAPVATNAFH SPRWGGIMVY NVDSKTYNAS VLPVRVEVDM VRVMEVFLAQ LRLLFGIAQP QLPP KCLLS GPTSEGLMTW ELDRLLWARS VENLATATTT LTSLAQLLGK ISNIVIKDDV ASEVYKAVAA VQKSAEELAS AHLAS AFVA SQEAVTSSEL AFFDASLLHL LYFPDDQKFA IYIPLFLPMA VPILLSLVK

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Macromolecule #3: GPI transamidase component PIG-T

MacromoleculeName: GPI transamidase component PIG-T / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 60.397691 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ARDSLREELV ITPLPSGDVA ATFQFRTRWD SELQREGVSH YRLFPKALGQ LISKYSLREL HLSFTQGFWR TRYWGPPFLQ APSGAELWV WFQDTVTDVD KSWKELSNVL SGIFCASLNF IDSTNTVTPT ASFKPLGLAN DTDHYFLRYA VLPREVVCTE N LTPWKKLL ...String:
ARDSLREELV ITPLPSGDVA ATFQFRTRWD SELQREGVSH YRLFPKALGQ LISKYSLREL HLSFTQGFWR TRYWGPPFLQ APSGAELWV WFQDTVTDVD KSWKELSNVL SGIFCASLNF IDSTNTVTPT ASFKPLGLAN DTDHYFLRYA VLPREVVCTE N LTPWKKLL PCSSKAGLSV LLKADRLFHT SYHSQAVHIR PVCRNARCTS ISWELRQTLS VVFDAFITGQ GKKDWSLFRM FS RTLTEPC PLASESRVYV DITTYNQDNE TLEVHPPPTT TYQDVILGTR KTYAIYDLLD TAMINNSRNL NIQLKWKRPP ENE APPVPF LHAQRYVSGY GLQKGELSTL LYNTHPYRAF PVLLLDTVPW YLRLYVHTLT ITSKGKENKP SYIHYQPAQD RLQP HLLEM LIQLPANSVT KVSIQFERAL LKWTEYTPDP NHGFYVSPSV LSALVPSMVA AKPVDWEESP LFNSLFPVSD GSNYF VRLY TEPLLVNLPT PDFSMPYNVI CLTCTVVAVC YGSFYNLLTR TFH

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Macromolecule #4: GPI-anchor transamidase

MacromoleculeName: GPI-anchor transamidase / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.302629 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAVTDSLSRA ATVLATVLLL SFGSVAASHI EDQAEQFFRS GHTNNWAVLV CTSRFWFNYR HVANTLSVYR SVKRLGIPDS HIVLMLADD MACNPRNPKP ATVFSHKNME LNVYGDDVEV DYRSYEVTVE NFLRVLTGRI PPSTPRSKRL LSDDRSNILI Y MTGHGGNG ...String:
MAVTDSLSRA ATVLATVLLL SFGSVAASHI EDQAEQFFRS GHTNNWAVLV CTSRFWFNYR HVANTLSVYR SVKRLGIPDS HIVLMLADD MACNPRNPKP ATVFSHKNME LNVYGDDVEV DYRSYEVTVE NFLRVLTGRI PPSTPRSKRL LSDDRSNILI Y MTGHGGNG FLKFQDSEEI TNIELADAFE QMWQKRRYNE LLFIIDTCQG ASMYERFYSP NIMALASSQV GEDSLSHQPD PA IGVHLMD RYTFYVLEFL EEINPASQTN MNDLFQVCPK SLCVSTPGHR TDLFQRDPKN VLITDFFGSV RKVEITTETI KLQ QDSEIM ESSYKEDQMD EKLMEPLKYA EQLPVAQIIH QKPKLKDWHP PGGFILGLWA LIIMVFFKTY GIKHMKFIF

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Macromolecule #5: Glycosylphosphatidylinositol anchor attachment 1 protein

MacromoleculeName: Glycosylphosphatidylinositol anchor attachment 1 protein
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 67.683836 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGLLSDPVRR RALARLVLRL NAPLCVLSYV AGIAWFLALV FPPLTQRTYM SENAMGSTMV EEQFAGGDRA RAFARDFAAH RKKSGALPV AWLERTMRSV GLEVYTQSFS RKLPFPDETH ERYMVSGTNV YGILRAPRAA STESLVLTVP CGSDSTNSQA V GLLLALAA ...String:
MGLLSDPVRR RALARLVLRL NAPLCVLSYV AGIAWFLALV FPPLTQRTYM SENAMGSTMV EEQFAGGDRA RAFARDFAAH RKKSGALPV AWLERTMRSV GLEVYTQSFS RKLPFPDETH ERYMVSGTNV YGILRAPRAA STESLVLTVP CGSDSTNSQA V GLLLALAA HFRGQIYWAK DIVFLVTEHD LLGTEAWLEA YHDVNVTGMQ SSPLQGRAGA IQAAVALELS SDVVTSLDVA VE GLNGQLP NLDLLNLFQT FCQKGGLLCT LQGKLQPEDW TSLDGPLQGL QTLLLMVLRQ ASGRPHGSHG LFLRYRVEAL TLR GINSFR QYKYDLVAVG KALEGMFRKL NHLLERLHQS FFLYLLPGLS RFVSIGLYMP AVGFLLLVLG LKALELWMQL HEAG MGLEE PGGAPGPSVP LPPSQGVGLA SLVAPLLISQ AMGLALYVLP VLGQHVATQH FPVAEAEAVV LTLLAIYAAG LALPH NTHR VVSTQAPDRG WMALKLVALI YLALQLGCIA LTNFSLGFLL ATTMVPTAAL AKPHGPRTLY AALLVLTSPA ATLLGS LFL WRELQEAPLS LAEGWQLFLA ALAQGVLEHH TYGALLFPLL SLGLYPCWLL FWNVLFWK

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Macromolecule #7: [2-[[(2~{R})-2-hexanoyloxy-3-[(~{E})-hex-3-enoxy]propoxy]-oxidany...

MacromoleculeName: [2-[[(2~{R})-2-hexanoyloxy-3-[(~{E})-hex-3-enoxy]propoxy]-oxidanyl-phosphoryl]oxy-3,4,5,6-tetrakis(oxidanyl)phenyl] (2~{E},4~{E})-hepta-2,4-dienoate
type: ligand / ID: 7 / Number of copies: 1 / Formula: 8JY
Molecular weightTheoretical: 622.639 Da
Chemical component information

ChemComp-8JY:
[2-[[(2~{R})-2-hexanoyloxy-3-[(~{E})-hex-3-enoxy]propoxy]-oxidanyl-phosphoryl]oxy-3,4,5,6-tetrakis(oxidanyl)phenyl] (2~{E},4~{E})-hepta-2,4-dienoate

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Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #9: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 9 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 22.0 µm / Nominal defocus min: 12.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 61148
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: ANGULAR RECONSTITUTION

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