Cryo-EM structure of GPI-T with a chimeric GPI-anchored protein

2025-07-23 REL PDBc INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin em_software _em_admin.last_update _em_software.name STRUCTURE_SUMMARY em_admin pdbx_entry_details pdbx_modification_feature _em_admin.last_update _pdbx_entry_details.has_protein_modification DATA_COLLECTION em_admin em_software _em_admin.last_update _em_software.name PDBj PDBc 2023-03-07 2023-08-16 2023-08-16 2025-07-23 National Natural Science Foundation of China (NSFC) 82151215 China Cryo-EM structure of GPI-T with a chimeric GPI-anchored protein Xu Y Li T Qu Q Li D cryo-EM, glycosylphosphatidylinositol, GPI, GPI anchored protein, GPI-AP, membrane protein complex, MEMBRANE PROTEIN Xu Y Li T Zhou Z Hong J Chao Y Zhu Z Zhang Y Qu Q Li D Structures of liganded glycosylphosphatidylinositol transamidase illuminate GPI-AP biogenesis. Nat Commun UK 14 5520 5520 2023 37684232 doi:10.1038/s41467-023-41281-y 2041-1723 EMD-32582 other EM volume

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8imx FULLOVERLAP Complex of GPI-T with a chimeric GPI-anchored protein Complex of GPI-T with a chimeric GPI-anchored protein 0 1 2 3 4 5 6 Homo sapiens 469 UL16-binding protein 2,GFP-like fluorescent chromoprotein cFP484 Homo sapiens 0.035573316

A chimera proprotein containing the N- and C-terminal signal peptide of ULBP2, and a thermostable green fluorescence protein replacing the main part of ULBP2.

1 Homo sapiens LEVO MAAAAATKILLCLPLLLLLSGWSRAGGSGGSASVIKPEMKIKLRMEGAVNGHKFVIEGEGIGKPYEGTQTLDLTVEEGAP LPFSYDILTPAFQYGNRAFTKYPEDIPDYFKQAFPEGYSWERSMTYEDQGICIATSDITMEGDCFFYEIRFDGTNFPPNG PVMQKKTLKWEPSTEKMYVEDGVLKGDVEMALLLEGGGHYRCDFKTTYKAKKDVRLPDAHEVDHRIEILSHDKDYNKVRL YEHAEARYSGGGSGGGSAWSHPQFEKGGGSGGGSGGSAWSHPQFEKGSSAGAPLAMSSGTTQLRATATTLILCCLLIILP CFILPGI Q9BZM5 Q9U6Y3 Q9BZM5 Glycosylphosphatidylinositol anchor attachment 1 protein,GFP-like fluorescent chromoprotein cFP484 Clavularia sp. 0.09699035199999999 1 Homo sapiens LEVO MGSGLLSDPVRRRALARLVLRLNAPLCVLSYVAGIAWFLALVFPPLTQRTYMSENAMGSTMVEEQFAGGDRARAFARDFA AHRKKSGALPVAWLERTMRSVGLEVYTQSFSRKLPFPDETHERYMVSGTNVYGILRAPRAASTESLVLTVPCGSDSTNSQ AVGLLLALAAHFRGQIYWAKDIVFLVTEHDLLGTEAWLEAYHDVNVTGMQSSPLQGRAGAIQAAVALELSSDVVTSLDVA VEGLNGQLPNLDLLNLFQTFCQKGGLLCTLQGKLQPEDWTSLDGPLQGLQTLLLMVLRQASGRPHGSHGLFLRYRVEALT LRGINSFRQYKYDLVAVGKALEGMFRKLNHLLERLHQSFFLYLLPGLSRFVSIGLYMPAVGFLLLVLGLKALELWMQLHE AGMGLEEPGGAPGPSVPLPPSQGVGLASLVAPLLISQAMGLALYVLPVLGQHVATQHFPVAEAEAVVLTLLAIYAAGLAL PHNTHRVVSTQAPDRGWMALKLVALIYLALQLGCIALTNFSLGFLLATTMVPTAALAKPHGPRTLYAALLVLTSPAATLL GSLFLWRELQEAPLSLAEGWQLFLAALAQGVLEHHTYGALLFPLLSLGLYPCWLLFWNVLFWKGTLEVLFQGPGGSGGSA SVIKPEMKIKLRMEGAVNGHKFVIEGEGIGKPYEGTQTLDLTVEEGAPLPFSYDILTPAFQYGNRAFTKYPEDIPDYFKQ AFPEGYSWERSMTYEDQGICIATSDITMEGDCFFYEIRFDGTNFPPNGPVMQKKTLKWEPSTEKMYVEDGVLKGDVEMAL LLEGGGHYRCDFKTTYKAKKDVRLPDAHEVDHRIEILSHDKDYNKVRLYEHAEARYSGGGSGGGGSGGGGDYKDDDDADY KDDDDA O43292 Q9U6Y3 GPI-anchor transamidase,GFP-like fluorescent chromoprotein cFP484 Clavularia sp. 0.073443062 1 Homo sapiens LEVO MGSAVTDSLSRAATVLATVLLLSFGSVAASHIEDQAEQFFRSGHTNNWAVLVCTSRFWFNYRHVANTLSVYRSVKRLGIP DSHIVLMLADDMACNPRNPKPATVFSHKNMELNVYGDDVEVDYRSYEVTVENFLRVLTGRIPPSTPRSKRLLSDDRSNIL IYMTGHGGNGFLKFQDSEEITNIELADAFEQMWQKRRYNELLFIIDTCQGASMYERFYSPNIMALASSQVGEDSLSHQPD PAIGVHLMDRYTFYVLEFLEEINPASQTNMNDLFQVCPKSLCVSTPGHRTDLFQRDPKNVLITDFFGSVRKVEITTETIK LQQDSEIMESSYKEDQMDEKLMEPLKYAEQLPVAQIIHQKPKLKDWHPPGGFILGLWALIIMVFFKTYGIKHMKFIFGTL EVLFQGPGGSGGSASVIKPEMKIKLRMEGAVNGHKFVIEGEGIGKPYEGTQTLDLTVEEGAPLPFSYDILTPAFQYGNRA FTKYPEDIPDYFKQAFPEGYSWERSMTYEDQGICIATSDITMEGDCFFYEIRFDGTNFPPNGPVMQKKTLKWEPSTEKMY VEDGVLKGDVEMALLLEGGGHYRCDFKTTYKAKKDVRLPDAHEVDHRIEILSHDKDYNKVRLYEHAEARYSGGGSGGGYP YDVPDYA Q92643 Q9U6Y3 3.-.-.- GPI transamidase component PIG-S,GFP-like fluorescent chromoprotein cFP484 Clavularia sp. 0.090421062 1 Homo sapiens LEVO MGSAAAGAAATHLEVARGKRAALFFAAVAIVLGLPLWWKTTETYRASLPYSQISGLNALQLRLMVPVTVVFTRESVPLDD QEKLPFTVVHEREIPLKYKMKIKCRFQKAYRRALDHEEEALSSGSVQEAEAMLDEPQEQAEGSLTVYVISEHSSLLPQDM MSYIGPKRTAVVRGIMHREAFNIIGRRIVQVAQAMSLTEDVLAAALADHLPEDKWSAEKRRPLKSSLGYEITFSLLNPDP KSHDVYWDIEGAVRRYVQPFLNALGAAGNFSVDSQILYYAMLGVNPRFDSASSSYYLDMHSLPHVINPVESRLGSSAASL YPVLNFLLYVPELAHSPLYIQDKDGAPVATNAFHSPRWGGIMVYNVDSKTYNASVLPVRVEVDMVRVMEVFLAQLRLLFG IAQPQLPPKCLLSGPTSEGLMTWELDRLLWARSVENLATATTTLTSLAQLLGKISNIVIKDDVASEVYKAVAAVQKSAEE LASGHLASAFVASQEAVTSSELAFFDPSLLHLLYFPDDQKFAIYIPLFLPMAVPILLSLVKIFLETRKSWRKPEKTDGTL EVLFQGPGGSGGSASVIKPEMKIKLRMEGAVNGHKFVIEGEGIGKPYEGTQTLDLTVEEGAPLPFSYDILTPAFQYGNRA FTKYPEDIPDYFKQAFPEGYSWERSMTYEDQGICIATSDITMEGDCFFYEIRFDGTNFPPNGPVMQKKTLKWEPSTEKMY VEDGVLKGDVEMALLLEGGGHYRCDFKTTYKAKKDVRLPDAHEVDHRIEILSHDKDYNKVRLYEHAEARYSGGGSGGGGG GGGGGGEQKLISEEDL Q96S52 Q9U6Y3 GPI transamidase component PIG-T,GFP-like fluorescent chromoprotein cFP484 Clavularia sp. 0.09420724999999999 1 Homo sapiens LEVO MGSAAAMPLALLVLLLLGPGGWCLAEPPRDSLREELVITPLPSGDVAATFQFRTRWDSELQREGVSHYRLFPKALGQLIS KYSLRELHLSFTQGFWRTRYWGPPFLQAPSGAELWVWFQDTVTDVDKSWKELSNVLSGIFCASLNFIDSTNTVTPTASFK PLGLANDTDHYFLRYAVLPREVVCTENLTPWKKLLPCSSKAGLSVLLKADRLFHTSYHSQAVHIRPVCRNARCTSISWEL RQTLSVVFDAFITGQGKKDWSLFRMFSRTLTEPCPLASESRVYVDITTYNQDNETLEVHPPPTTTYQDVILGTRKTYAIY DLLDTAMINNSRNLNIQLKWKRPPENEAPPVPFLHAQRYVSGYGLQKGELSTLLYNTHPYRAFPVLLLDTVPWYLRLYVH TLTITSKGKENKPSYIHYQPAQDRLQPHLLEMLIQLPANSVTKVSIQFERALLKWTEYTPDPNHGFYVSPSVLSALVPSM VAAKPVDWEESPLFNSLFPVSDGSNYFVRLYTEPLLVNLPTPDFSMPYNVICLTCTVVAVCYGSFYNLLTRTFHIEEPRT GGLAKRLANLIRRARGVPPLGTLEVLFQGPGGSGGSASVIKPEMKIKLRMEGAVNGHKFVIEGEGIGKPYEGTQTLDLTV EEGAPLPFSYDILTPAFQYGNRAFTKYPEDIPDYFKQAFPEGYSWERSMTYEDQGICIATSDITMEGDCFFYEIRFDGTN FPPNGPVMQKKTLKWEPSTEKMYVEDGVLKGDVEMALLLEGGGHYRCDFKTTYKAKKDVRLPDAHEVDHRIEILSHDKDY NKVRLYEHAEARYSGGGSGGGHHHHHHHHHH Q969N2 Q9U6Y3 Phosphatidylinositol glycan anchor biosynthesis class U protein,GFP-like fluorescent chromoprotein cFP484 Clavularia sp. 0.07714169500000001 1 Homo sapiens LEVO MGSAAPLVLVLVVAVTVRAALFRSSLAEFISERVEVVSPLSSWKRVVEGLSLLDLGVSPYSGAVFHETPLIIYLFHFLID YAELVFMITDALTAIALYFAIQDFNKVVFKKQKLLLELDQYAPDVAELIRTPMEMRYIPLKVALFYLLNPYTILSCVAKS TCAINNTLIAFFILTTIKGSAFLSAIFLALATYQSLYPLTLFVPGLLYLLQRQYIPVKMKSKAFWIFSWEYAMMYVGSLV VIICLSFFLLSSWDFIPAVYGFILSVPDLTPNIGLFWYFFAEMFEHFSLFFVCVFQINVFFYTIPLAIKLKEHPIFFMFI QIAVIAIFKSYPTVGDVALYMAFFPVWNHLYRFLRNIFVLTCIIIVCSLLFPVLWHLWIYAGSANSNFFYAITLTFNVGQ ILLISDYFYAFLRREYYLTHGLYLTAKDGTEAMLVLKGTLEVLFQGPGGSGGSASVIKPEMKIKLRMEGAVNGHKFVIEG EGIGKPYEGTQTLDLTVEEGAPLPFSYDILTPAFQYGNRAFTKYPEDIPDYFKQAFPEGYSWERSMTYEDQGICIATSDI TMEGDCFFYEIRFDGTNFPPNGPVMQKKTLKWEPSTEKMYVEDGVLKGDVEMALLLEGGGHYRCDFKTTYKAKKDVRLPD AHEVDHRIEILSHDKDYNKVRLYEHAEARYSGGGSGGG Q9H490 Q9U6Y3 Met-Ser-Ser peptide synthetic construct 0.000323367 1 LEVO MSS CHOLESTEROL HEMISUCCINATE 0.000486726 13 Y01 MAGNESIUM ION 2.4305e-05 1 MG [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate 0.0007179959999999999 4 6OU Digitonin 0.0012293119999999998 1 AJP CALCIUM ION 4.0078e-05 1 CA 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 2 NAG 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine 0.0007600759999999999 1 LBN [(2R)-1-hexadecanoyloxy-3-[[3-[[(2R)-3-hexadecanoyloxy-2-[(Z)-octadec-9-enoyl]oxy-propoxy]-oxidanyl-phosphoryl]oxy-2-oxidanyl-propoxy]-oxidanyl-phosphoryl]oxy-propan-2-yl] (Z)-octadec-9-enoate 0.00140592 1 80T 2-azanylethyl [(2R,3S,4S,5S,6S)-3,4,5,6-tetrakis(oxidanyl)oxan-2-yl]methyl hydrogen phosphate 0.000303204 2 80Y 2-amino-2-deoxy-alpha-D-glucopyranose 0.000179171 1 PA1 2-azanylethyl [(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl] hydrogen phosphate 0.000303204 1 05E [(2R)-1-[[(1S,2R,3R,4S,5S,6R)-2-hexadecanoyloxy-3,4,5,6-tetrakis(oxidanyl)cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-3-octadecoxy-propan-2-yl] (5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoate 0.0011115530000000002 1 81Q singleParticle particle 8 8.0 0.15 NaCl Sodium chloride 0.1 Digitonin Digitonin 0.05 Tris Tris(hydroxymethyl)aminomethane

0.1 % Digitonin, 150 mM NaCl, 50 mM Tris-HCl, pH 8.0

Quantifoil R1.2/1.3 GOLD 300 CARBON HOLEY GLOW DISCHARGE 35 AIR 0.026000000000000002 ETHANE 100 277 FEI VITROBOT MARK IV FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 1.0 2.0 FEI FALCON IV (4k x 4k) 50.0 1 3170202 CTFFIND v4.0 PHASE FLIPPING AND AMPLITUDE CORRECTION EMD-32582 C1 FOURIER SPACE 2.85 FSC 0.143 CUT-OFF 34261 ANGULAR RECONSTITUTION cryoSPARC v4.2.0 ANGULAR RECONSTITUTION cryoSPARC v4.2.0 emd_35575.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 260.96 260.96 260.96 90.0 90.0 90.0 X Y Z -1.8881043 3.0878632 0.0046553565 0.113127194 0.932 0.932 0.932 0.48 AUTHOR ::::EMDATABANK.org::::EMD-35575:::: emd_35575_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 260.96 260.96 260.96 90.0 90.0 90.0 X Y Z -0.71410793 1.4900658 0.004655356 0.055755027 0.932 0.932 0.932 AUTHOR ::::EMDATABANK.org::::EMD-35575:::: emd_35575_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 260.96 260.96 260.96 90.0 90.0 90.0 X Y Z -2.7504542 2.557622 0.00282085 0.33557165 0.932 0.932 0.932 AUTHOR ::::EMDATABANK.org::::EMD-35575:::: emd_35575_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 260.96 260.96 260.96 90.0 90.0 90.0 X Y Z -2.7026403 3.0947561 0.0028116524 0.3360728 0.932 0.932 0.932 AUTHOR ::::EMDATABANK.org::::EMD-35575::::