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- EMDB-32582: Cryo-EM structure of the human glycosylphosphatidylinositol trans... -

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Basic information

Entry
Database: EMDB / ID: EMD-32582
TitleCryo-EM structure of the human glycosylphosphatidylinositol transamidase complex at 2.53 Angstrom resolution
Map data
Sample
  • Complex: GPI transamidase complex
    • Protein or peptide: x 5 types
  • Ligand: x 13 types
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: 2.53 Å
AuthorsXu Y / Li T / Luo Y / Chao Y / Jia G / Zhou Z / Su Z / Qu Q / Li D
Funding support China, 5 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82151215 China
National Natural Science Foundation of China (NSFC)31870726 China
National Natural Science Foundation of China (NSFC)82041016 China
National Natural Science Foundation of China (NSFC)32070049 China
Ministry of Science and Technology (MoST, China)2021YFA1301900 China
CitationJournal: Nat Commun / Year: 2022
Title: Molecular insights into biogenesis of glycosylphosphatidylinositol anchor proteins.
Authors: Yidan Xu / Guowen Jia / Tingting Li / Zixuan Zhou / Yitian Luo / Yulin Chao / Juan Bao / Zhaoming Su / Qianhui Qu / Dianfan Li /
Abstract: Eukaryotic cells are coated with an abundance of glycosylphosphatidylinositol anchor proteins (GPI-APs) that play crucial roles in fertilization, neurogenesis, and immunity. The removal of a ...Eukaryotic cells are coated with an abundance of glycosylphosphatidylinositol anchor proteins (GPI-APs) that play crucial roles in fertilization, neurogenesis, and immunity. The removal of a hydrophobic signal peptide and covalent attachment of GPI at the new carboxyl terminus are catalyzed by an endoplasmic reticulum membrane GPI transamidase complex (GPI-T) conserved among all eukaryotes. Here, we report the cryo-electron microscopy (cryo-EM) structure of the human GPI-T at a global 2.53-Å resolution, revealing an equimolar heteropentameric assembly. Structure-based mutagenesis suggests a legumain-like mechanism for the recognition and cleavage of proprotein substrates, and an endogenous GPI in the structure defines a composite cavity for the lipid substrate. This elongated active site, stemming from the membrane and spanning an additional ~22-Å space toward the catalytic dyad, is structurally suited for both substrates which feature an amphipathic pattern that matches this geometry. Our work presents an important step towards the mechanistic understanding of GPI-AP biosynthesis.
History
DepositionJan 13, 2022-
Header (metadata) releaseApr 27, 2022-
Map releaseApr 27, 2022-
UpdateJun 1, 2022-
Current statusJun 1, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32582.png

Downloads & links

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Map

FileDownload / File: emd_32582.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 280 pix.
= 238. Å		0.85 Å/pix.
x 280 pix.
= 238. Å		0.85 Å/pix.
x 280 pix.
= 238. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-3.0894268 - 5.014552
Average (Standard dev.)0.012849043 (±0.18239129)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 238.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unshapened map

Fileemd_32582_additional_1.map
Annotationunshapened 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 : GPI transamidase complex

EntireName: GPI transamidase complex
Components
  • Complex: GPI transamidase complex
    • Protein or peptide: Glycosylphosphatidylinositol anchor attachment 1 protein
    • Protein or peptide: GPI-anchor transamidase
    • Protein or peptide: GPI transamidase component PIG-S
    • Protein or peptide: GPI transamidase component PIG-T
    • Protein or peptide: Phosphatidylinositol glycan anchor biosynthesis class U protein
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: Digitonin
  • Ligand: (4S,7R)-7-[(hexadecanoyloxy)methyl]-4-hydroxy-N,N,N-trimethyl-4,9-dioxo-3,5,8-trioxa-4lambda~5~-phosphahexacosan-1-aminium
  • Ligand: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
  • Ligand: CALCIUM ION
  • Ligand: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CHOLESTEROL
  • Ligand: 2-azanylethyl [(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl] hydrogen phosphate
  • Ligand: 2-amino-2-deoxy-alpha-D-glucopyranose
  • Ligand: CARDIOLIPIN
  • Ligand: [(2R)-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] octadecanoate
  • Ligand: [(2~{R})-1-hexadecanoyloxy-3-[[(1~{S},2~{R},3~{R},4~{S},5~{S},6~{R})-2-hexadecanoyloxy-3,4,5,6-tetrakis(oxidanyl)cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-propan-2-yl] (9~{Z},11~{Z})-octadeca-9,11-dienoate

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Supramolecule #1: GPI transamidase complex

SupramoleculeName: GPI transamidase complex / type: complex / Chimera: Yes / 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: Glycosylphosphatidylinositol anchor attachment 1 protein

MacromoleculeName: Glycosylphosphatidylinositol anchor attachment 1 protein
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 96.990352 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGSGLLSDPV RRRALARLVL RLNAPLCVLS YVAGIAWFLA LVFPPLTQRT YMSENAMGST MVEEQFAGGD RARAFARDFA AHRKKSGAL PVAWLERTMR SVGLEVYTQS FSRKLPFPDE THERYMVSGT NVYGILRAPR AASTESLVLT VPCGSDSTNS Q AVGLLLAL ...String:
MGSGLLSDPV RRRALARLVL RLNAPLCVLS YVAGIAWFLA LVFPPLTQRT YMSENAMGST MVEEQFAGGD RARAFARDFA AHRKKSGAL PVAWLERTMR SVGLEVYTQS FSRKLPFPDE THERYMVSGT NVYGILRAPR AASTESLVLT VPCGSDSTNS Q AVGLLLAL AAHFRGQIYW AKDIVFLVTE HDLLGTEAWL EAYHDVNVTG MQSSPLQGRA GAIQAAVALE LSSDVVTSLD VA VEGLNGQ LPNLDLLNLF QTFCQKGGLL CTLQGKLQPE DWTSLDGPLQ GLQTLLLMVL RQASGRPHGS HGLFLRYRVE ALT LRGINS FRQYKYDLVA VGKALEGMFR KLNHLLERLH QSFFLYLLPG LSRFVSIGLY MPAVGFLLLV LGLKALELWM QLHE AGMGL EEPGGAPGPS VPLPPSQGVG LASLVAPLLI SQAMGLALYV LPVLGQHVAT QHFPVAEAEA VVLTLLAIYA AGLAL PHNT HRVVSTQAPD RGWMALKLVA LIYLALQLGC IALTNFSLGF LLATTMVPTA ALAKPHGPRT LYAALLVLTS PAATLL GSL FLWRELQEAP LSLAEGWQLF LAALAQGVLE HHTYGALLFP LLSLGLYPCW LLFWNVLFWK GTLEVLFQGP GGSGGSA SV IKPEMKIKLR MEGAVNGHKF VIEGEGIGKP YEGTQTLDLT VEEGAPLPFS YDILTPAFQY GNRAFTKYPE DIPDYFKQ A FPEGYSWERS MTYEDQGICI ATSDITMEGD CFFYEIRFDG TNFPPNGPVM QKKTLKWEPS TEKMYVEDGV LKGDVEMAL LLEGGGHYRC DFKTTYKAKK DVRLPDAHEV DHRIEILSHD KDYNKVRLYE HAEARYSGGG SGGGGSGGGG DYKDDDDADY KDDDDA

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Macromolecule #2: GPI-anchor transamidase

MacromoleculeName: GPI-anchor transamidase / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 73.443062 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGSAVTDSLS RAATVLATVL LLSFGSVAAS HIEDQAEQFF RSGHTNNWAV LVCTSRFWFN YRHVANTLSV YRSVKRLGIP DSHIVLMLA DDMACNPRNP KPATVFSHKN MELNVYGDDV EVDYRSYEVT VENFLRVLTG RIPPSTPRSK RLLSDDRSNI L IYMTGHGG ...String:
MGSAVTDSLS RAATVLATVL LLSFGSVAAS HIEDQAEQFF RSGHTNNWAV LVCTSRFWFN YRHVANTLSV YRSVKRLGIP DSHIVLMLA DDMACNPRNP KPATVFSHKN MELNVYGDDV EVDYRSYEVT VENFLRVLTG RIPPSTPRSK RLLSDDRSNI L IYMTGHGG NGFLKFQDSE EITNIELADA FEQMWQKRRY NELLFIIDTC QGASMYERFY SPNIMALASS QVGEDSLSHQ PD PAIGVHL MDRYTFYVLE FLEEINPASQ TNMNDLFQVC PKSLCVSTPG HRTDLFQRDP KNVLITDFFG SVRKVEITTE TIK LQQDSE IMESSYKEDQ MDEKLMEPLK YAEQLPVAQI IHQKPKLKDW HPPGGFILGL WALIIMVFFK TYGIKHMKFI FGTL EVLFQ GPGGSGGSAS VIKPEMKIKL RMEGAVNGHK FVIEGEGIGK PYEGTQTLDL TVEEGAPLPF SYDILTPAFQ YGNRA FTKY PEDIPDYFKQ AFPEGYSWER SMTYEDQGIC IATSDITMEG DCFFYEIRFD GTNFPPNGPV MQKKTLKWEP STEKMY VED GVLKGDVEMA LLLEGGGHYR CDFKTTYKAK KDVRLPDAHE VDHRIEILSH DKDYNKVRLY EHAEARYSGG GSGGGYP YD VPDYA

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Macromolecule #3: GPI transamidase component PIG-S

MacromoleculeName: GPI transamidase component PIG-S / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 90.421062 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGSAAAGAAA THLEVARGKR AALFFAAVAI VLGLPLWWKT TETYRASLPY SQISGLNALQ LRLMVPVTVV FTRESVPLDD QEKLPFTVV HEREIPLKYK MKIKCRFQKA YRRALDHEEE ALSSGSVQEA EAMLDEPQEQ AEGSLTVYVI SEHSSLLPQD M MSYIGPKR ...String:
MGSAAAGAAA THLEVARGKR AALFFAAVAI VLGLPLWWKT TETYRASLPY SQISGLNALQ LRLMVPVTVV FTRESVPLDD QEKLPFTVV HEREIPLKYK MKIKCRFQKA YRRALDHEEE ALSSGSVQEA EAMLDEPQEQ AEGSLTVYVI SEHSSLLPQD M MSYIGPKR TAVVRGIMHR EAFNIIGRRI VQVAQAMSLT EDVLAAALAD HLPEDKWSAE KRRPLKSSLG YEITFSLLNP DP KSHDVYW DIEGAVRRYV QPFLNALGAA GNFSVDSQIL YYAMLGVNPR FDSASSSYYL DMHSLPHVIN PVESRLGSSA ASL YPVLNF LLYVPELAHS PLYIQDKDGA PVATNAFHSP RWGGIMVYNV DSKTYNASVL PVRVEVDMVR VMEVFLAQLR LLFG IAQPQ LPPKCLLSGP TSEGLMTWEL DRLLWARSVE NLATATTTLT SLAQLLGKIS NIVIKDDVAS EVYKAVAAVQ KSAEE LASG HLASAFVASQ EAVTSSELAF FDPSLLHLLY FPDDQKFAIY IPLFLPMAVP ILLSLVKIFL ETRKSWRKPE KTDGTL EVL FQGPGGSGGS ASVIKPEMKI KLRMEGAVNG HKFVIEGEGI GKPYEGTQTL DLTVEEGAPL PFSYDILTPA FQYGNRA FT KYPEDIPDYF KQAFPEGYSW ERSMTYEDQG ICIATSDITM EGDCFFYEIR FDGTNFPPNG PVMQKKTLKW EPSTEKMY V EDGVLKGDVE MALLLEGGGH YRCDFKTTYK AKKDVRLPDA HEVDHRIEIL SHDKDYNKVR LYEHAEARYS GGGSGGGGG GGGGGGEQKL ISEEDL

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Macromolecule #4: GPI transamidase component PIG-T

MacromoleculeName: GPI transamidase component PIG-T / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 94.20725 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGSAAAMPLA LLVLLLLGPG GWCLAEPPRD SLREELVITP LPSGDVAATF QFRTRWDSEL QREGVSHYRL FPKALGQLIS KYSLRELHL SFTQGFWRTR YWGPPFLQAP SGAELWVWFQ DTVTDVDKSW KELSNVLSGI FCASLNFIDS TNTVTPTASF K PLGLANDT ...String:
MGSAAAMPLA LLVLLLLGPG GWCLAEPPRD SLREELVITP LPSGDVAATF QFRTRWDSEL QREGVSHYRL FPKALGQLIS KYSLRELHL SFTQGFWRTR YWGPPFLQAP SGAELWVWFQ DTVTDVDKSW KELSNVLSGI FCASLNFIDS TNTVTPTASF K PLGLANDT DHYFLRYAVL PREVVCTENL TPWKKLLPCS SKAGLSVLLK ADRLFHTSYH SQAVHIRPVC RNARCTSISW EL RQTLSVV FDAFITGQGK KDWSLFRMFS RTLTEPCPLA SESRVYVDIT TYNQDNETLE VHPPPTTTYQ DVILGTRKTY AIY DLLDTA MINNSRNLNI QLKWKRPPEN EAPPVPFLHA QRYVSGYGLQ KGELSTLLYN THPYRAFPVL LLDTVPWYLR LYVH TLTIT SKGKENKPSY IHYQPAQDRL QPHLLEMLIQ LPANSVTKVS IQFERALLKW TEYTPDPNHG FYVSPSVLSA LVPSM VAAK PVDWEESPLF NSLFPVSDGS NYFVRLYTEP LLVNLPTPDF SMPYNVICLT CTVVAVCYGS FYNLLTRTFH IEEPRT GGL AKRLANLIRR ARGVPPLGTL EVLFQGPGGS GGSASVIKPE MKIKLRMEGA VNGHKFVIEG EGIGKPYEGT QTLDLTV EE GAPLPFSYDI LTPAFQYGNR AFTKYPEDIP DYFKQAFPEG YSWERSMTYE DQGICIATSD ITMEGDCFFY EIRFDGTN F PPNGPVMQKK TLKWEPSTEK MYVEDGVLKG DVEMALLLEG GGHYRCDFKT TYKAKKDVRL PDAHEVDHRI EILSHDKDY NKVRLYEHAE ARYSGGGSGG GHHHHHHHHH H

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Macromolecule #5: Phosphatidylinositol glycan anchor biosynthesis class U protein

MacromoleculeName: Phosphatidylinositol glycan anchor biosynthesis class U protein
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 80.691539 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGSAAPLVLV LVVAVTVRAA LFRSSLAEFI SERVEVVSPL SSWKRVVEGL SLLDLGVSPY SGAVFHETPL IIYLFHFLID YAELVFMIT DALTAIALYF AIQDFNKVVF KKQKLLLELD QYAPDVAELI RTPMEMRYIP LKVALFYLLN PYTILSCVAK S TCAINNTL ...String:
MGSAAPLVLV LVVAVTVRAA LFRSSLAEFI SERVEVVSPL SSWKRVVEGL SLLDLGVSPY SGAVFHETPL IIYLFHFLID YAELVFMIT DALTAIALYF AIQDFNKVVF KKQKLLLELD QYAPDVAELI RTPMEMRYIP LKVALFYLLN PYTILSCVAK S TCAINNTL IAFFILTTIK GSAFLSAIFL ALATYQSLYP LTLFVPGLLY LLQRQYIPVK MKSKAFWIFS WEYAMMYVGS LV VIICLSF FLLSSWDFIP AVYGFILSVP DLTPNIGLFW YFFAEMFEHF SLFFVCVFQI NVFFYTIPLA IKLKEHPIFF MFI QIAVIA IFKSYPTVGD VALYMAFFPV WNHLYRFLRN IFVLTCIIIV CSLLFPVLWH LWIYAGSANS NFFYAITLTF NVGQ ILLIS DYFYAFLRRE YYLTHGLYLT AKDGTEAMLV LKGTLEVLFQ GPGGSGGSAS VIKPEMKIKL RMEGAVNGHK FVIEG EGIG KPYEGTQTLD LTVEEGAPLP FSYDILTPAF QYGNRAFTKY PEDIPDYFKQ AFPEGYSWER SMTYEDQGIC IATSDI TME GDCFFYEIRF DGTNFPPNGP VMQKKTLKWE PSTEKMYVED GVLKGDVEMA LLLEGGGHYR CDFKTTYKAK KDVRLPD AH EVDHRIEILS HDKDYNKVRL YEHAEARYSG GGSGGGKLEF SAWSHPQFEK GGGSGGGSGG SAWSHPQFEK

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Macromolecule #7: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 7 / Number of copies: 9 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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Macromolecule #8: Digitonin

MacromoleculeName: Digitonin / type: ligand / ID: 8 / Number of copies: 1 / Formula: AJP
Molecular weightTheoretical: 1.229312 KDa
Chemical component information

ChemComp-AJP:
Digitonin / detergent*YM

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Macromolecule #9: (4S,7R)-7-[(hexadecanoyloxy)methyl]-4-hydroxy-N,N,N-trimethyl-4,9...

MacromoleculeName: (4S,7R)-7-[(hexadecanoyloxy)methyl]-4-hydroxy-N,N,N-trimethyl-4,9-dioxo-3,5,8-trioxa-4lambda~5~-phosphahexacosan-1-aminium
type: ligand / ID: 9 / Number of copies: 2 / Formula: BJR
Molecular weightTheoretical: 763.1 Da
Chemical component information

ChemComp-BJR:
(4S,7R)-7-[(hexadecanoyloxy)methyl]-4-hydroxy-N,N,N-trimethyl-4,9-dioxo-3,5,8-trioxa-4lambda~5~-phosphahexacosan-1-aminium

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Macromolecule #10: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine

MacromoleculeName: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / type: ligand / ID: 10 / Number of copies: 1 / Formula: PEE
Molecular weightTheoretical: 744.034 Da
Chemical component information

ChemComp-PEE:
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE, phospholipid*YM

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Macromolecule #11: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 11 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #12: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phospho...

MacromoleculeName: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
type: ligand / ID: 12 / Number of copies: 1 / Formula: P5S
Molecular weightTheoretical: 792.075 Da
Chemical component information

ChemComp-P5S:
O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine

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Macromolecule #13: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 13 / 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 #14: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 14 / Number of copies: 5 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #15: 2-azanylethyl [(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-...

MacromoleculeName: 2-azanylethyl [(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl] hydrogen phosphate
type: ligand / ID: 15 / Number of copies: 1 / Formula: 05E
Molecular weightTheoretical: 303.204 Da
Chemical component information

ChemComp-05E:
2-azanylethyl [(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl] hydrogen phosphate

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Macromolecule #16: 2-amino-2-deoxy-alpha-D-glucopyranose

MacromoleculeName: 2-amino-2-deoxy-alpha-D-glucopyranose / type: ligand / ID: 16 / Number of copies: 1 / Formula: PA1
Molecular weightTheoretical: 179.171 Da
Chemical component information

ChemComp-PA1:
2-amino-2-deoxy-alpha-D-glucopyranose

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Macromolecule #17: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 17 / Number of copies: 1 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

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Macromolecule #18: [(2R)-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy...

MacromoleculeName: [(2R)-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] octadecanoate
type: ligand / ID: 18 / Number of copies: 1 / Formula: DKB
Molecular weightTheoretical: 720.012 Da
Chemical component information

ChemComp-DKB:
[(2R)-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] octadecanoate

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Macromolecule #19: [(2~{R})-1-hexadecanoyloxy-3-[[(1~{S},2~{R},3~{R},4~{S},5~{S},6~{...

MacromoleculeName: [(2~{R})-1-hexadecanoyloxy-3-[[(1~{S},2~{R},3~{R},4~{S},5~{S},6~{R})-2-hexadecanoyloxy-3,4,5,6-tetrakis(oxidanyl)cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-propan-2-yl] (9~{Z},11~{Z})-octadeca-9,11-dienoate
type: ligand / ID: 19 / Number of copies: 1 / Formula: 06O
Molecular weightTheoretical: 1.073462 KDa
Chemical component information

ChemComp-06O:
[(2~{R})-1-hexadecanoyloxy-3-[[(1~{S},2~{R},3~{R},4~{S},5~{S},6~{R})-2-hexadecanoyloxy-3,4,5,6-tetrakis(oxidanyl)cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-propan-2-yl] (9~{Z},11~{Z})-octadeca-9,11-dienoate

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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

Concentration20 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
20.0 mMTris-HClTris(hydroxymethyl)aminomethane hydrochloride
0.1 %Digitonin
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.026000000000000002 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 53.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2959791
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.53 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.1) / Number images used: 151590
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.1)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 3.1)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7wld:
Cryo-EM structure of the human glycosylphosphatidylinositol transamidase complex at 2.53 Angstrom resolution

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