2024-06-05 REL RCSB RCSB RCSB 2021-07-08 2021-12-15 2021-12-15 2024-06-05 National Science Foundation (NSF, United States) 1531991 United States The Capsid Structure of the ChAdOx1 viral vector/chimpanzee adenovirus Y25 Baker AT Boyd RJ Adenovirus, simian adenovirus, chimpanzee adenovirus, vaccine vector, DNA virus, AdV, ChAdV-Y25, adenovirus Y25, Y25, viral vector, ChAdOx1, chimp Ad, dsDNA virus, icosahedral, chimpanzee adenovirus Y25, Y-25, Y 25, ChAdV, VIRUS Baker AT Boyd RJ Sarkar D Teijeira-Crespo A Chan CK Bates E Waraich K Vant J Wilson E Truong CD Lipka-Lloyd M Fromme P Vermaas J Williams D Machiesky L Heurich M Nagalo BM Coughlan L Umlauf S Chiu PL Rizkallah PJ Cohen TS Parker AL Singharoy A Borad MJ ChAdOx1 interacts with CAR and PF4 with implications for thrombosis with thrombocytopenia syndrome. Sci Adv US 7 eabl8213 eabl8213 2021 34851659 doi:10.1126/sciadv.abl8213 2375-2548 Baker AT Boyd RJ Sarkar D Vant J Crespo AT Waraich K Truong CD Bates E Wilson E Chan CK Lipka-Lloyd M Fromme P Nagalo MB Heurich M Williams D Chiu PL Rizkallah PJ Parker AL Singharoy A Borad MJ The Structure of ChAdOx1/AZD-1222 Reveals Interactions with CAR and PF4 with Implications for Vaccine-induced Immune Thrombotic Thrombocytopenia Biorxiv US 2021 doi:10.1101/2021.05.19.444882 2692-8205 7rd1 FULLOVERLAP Chimpanzee adenovirus Y25 Chimpanzee adenovirus Y25 0 1 2 3 4 5 6
Rescued from a bacterial artificial chromosome containing the ChAdOx1 genome and propagated in HEK293 T-Rex cells.
Chimpanzee adenovirus Y25 ChAdOx1 Pan troglodytes Icosahedral Capsid 500.0 25 VIRION SPECIES false false Pre-protein VI Chimpanzee adenovirus Y25 0.026299688999999998 12 Homo sapiens LEVO MEDINFSSLAPRHGTRPFMGTWSDIGTSQLNGGAFNWSSLWSGLKNFGSTLKTYGSKAWNSTTGQALRDKLKEQNFQQKV VDGLASGINGVVDLANQAVQRQINSRLDPVPPAGSVEMPQVEEELPPLDKRGEKRPRPDAEETLLTHTDEPPPYEEAVKL GLPTTRPIAPLATGVLKPESNKPATLDLPPPASRPSTVAKPLPPVAVARARPGGSARPHANWQSTLNSIVGLGVQSVKRR RCY G9G853 Hexon protein Chimpanzee adenovirus Y25 0.106121141 12 Homo sapiens LEVO MATPSMLPQWAYMHIAGQDASEYLSPGLVQFARATDTYFSLGNKFRNPTVAPTHDVTTDRSQRLTLRFVPVDREDNTYSY KVRYTLAVGDNRVLDMASTYFDIRGVLDRGPSFKPYSGTAYNSLAPKGAPNSSQWEQKKAGNGDTMETHTFGVAPMGGEN ITIDGLQIGTDATADQDKPIYADKTFQPEPQVGEENWQETESFYGGRALKKDTSMKPCYGSYARPTNVKGGQAKLKVGAD GVPTKEFDIDLAFFDTPGGTVNGQDEYKADIVMYTENTYLETPDTHVVYKPGKDDASSEINLVQQSMPNRPNYIGFRDNF IGLMYYNSTGNMGVLAGQASQLNAVVDLQDRNTELSYQLLLDSLGDRTRYFSMWNQAVDSYDPDVRIIENHGVEDELPNY CFPLDGSGTNAAYQGVKVKNGNDGDVESEWENDDTVAARNQLCKGNIFAMEINLQANLWRSFLYSNVALYLPDSYKYTPA NITLPTNTNTYDYMNGRVVPPSLVDAYINIGARWSLDPMDNVNPFNHHRNAGLRYRSMLLGNGRYVPFHIQVPQKFFAIK SLLLLPGSYTYEWNFRKDVNMILQSSLGNDLRTDGASISFTSINLYATFFPMAHNTASTLEAMLRNDTNDQSFNDYLSAA NMLYPIPANATNVPISIPSRNWAAFRGWSFTRLKTKETPSLGSGFDPYFVYSGSIPYLDGTFYLNHTFKKVSITFDSSVS WPGNDRLLTPNEFEIKRTVDGEGYNVAQCNMTKDWFLVQMLAHYNIGYQGFYVPEGYKDRMYSFFRNFQPMSRQVVDEVN YKDYQAVTLAYQHNNSGFVGYLAPTMRQGQPYPANYPYPLIGKSAVTSVTQKKFLCDRVMWRIPFSSNFMSMGALTDLGQ NMLYANSAHALDMNFEVDPMDESTLLYVVFEVFDVVRVHQPHRGVIEAVYLRTPFSAGNATT G9G854 Penton protein Chimpanzee adenovirus Y25 0.059533656 1 Homo sapiens LEVO MMRRAYPEGPPPSYESVMQQAMAAAAAMQPPLEAPYVPPRYLAPTEGRNSIRYSELAPLYDTTRLYLVDNKSADIASLNY QNDHSNFLTTVVQNNDFTPTEASTQTINFDERSRWGGQLKTIMHTNMPNVNEFMYSNKFKARVMVSRKTPNGVTVTDGSQ DILEYEWVEFELPEGNFSVTMTIDLMNNAIIDNYLAVGRQNGVLESDIGVKFDTRNFRLGWDPVTELVMPGVYTNEAFHP DIVLLPGCGVDFTESRLSNLLGIRKRQPFQEGFQIMYEDLEGGNIPALLDVDAYEKSKEESAAAATAAVATASTEVRGDN FASPAAVAAAEAAETESKIVIQPVEKDSKDRSYNVLPDKINTAYRSWYLAYNYGDPEKGVRSWTLLTTSDVTCGVEQVYW SLPDMMQDPVTFRSTRQVSNYPVVGAELLPVYSKSFFNEQAVYSQQLRAFTSLTHVFNRFPENQILVRPPAPTITTVSEN VPALTDHGTLPLRSSIRGVQRVTVTDARRRTCPYVYKALGIVAPRVLSSRTF G9G849 Hexon-interlacing protein Chimpanzee adenovirus Y25 0.014468118 4 Homo sapiens LEVO MSGSGSFEGGVFSPYLTGRLPSWAGVRQNVMGSTVDGRPVQPANSSTLTYATLSSSSVDAAAAAAAASAASAVRGMAMGA GYYGTLVANSSSTNNPASLNEEKLLLLMAQLEALTQRLGELTQQVAQLQEQTRAAVATVKSK G9G843 Pre-hexon-linking protein IIIa Chimpanzee adenovirus Y25 0.0659545 1 Homo sapiens LEVO MQQQPPPDPAMRAALQSQPSGINSSDDWTQAMQRIMALTTRNPEAFRQQPQANRLSAILEAVVPSRSNPTHEKVLAIVNA LVENKAIRGDEAGLVYNALLERVARYNSTNVQTNLDRMVTDVREAVAQRERFHRESNLGSMVALNAFLSTQPANVPRGQE DYTNFISALRLMVTEVPQSEVYQSGPDYFFQTSRQGLQTVNLSQAFKNLQGLWGVQAPVGDRATVSSLLTPNSRLLLLLV APFTDSGSINRNSYLGYLINLYREAIGQAHVDEQTYQEITHVSRALGQDDPGNLEATLNFLLTNRSQKIPPQYTLSAEEE RILRYVQQSVGLFLMQEGATPSAALDMTARNMEPSMYASNRPFINKLMDYLHRAAAMNSDYFTNAILNPHWLPPPGFYTG EYDMPDPNDGFLWDDVDSSVFSPRPGANERPLWKKEGSDRRPSSALSGREGAAAAVPEAASPFPSLPFSLNSIRSSELGR ITRPRLLGEEEYLNDSLLRPEREKNFPNNGIESLVDKMSRWKTYAQEHRDDPSQGATSRGSAARKRRWHDRQRGLMWDDE DSADDSSVLDLGGSGNPFAHLRPRIGRMM G9G848 Pre-hexon-linking protein VIII Chimpanzee adenovirus Y25 0.024779684 2 Homo sapiens LEVO MSKEIPTPYMWSYQPQMGLAAGAAQDYSTRMNWLSAGPAMISRVNDIRAHRNQILLEQSALTATPRNHLNPRNWPAALVY QEIPQPTTVLLPRDAQAEVQLTNSGVQLAGGATLCRHRPAQGIKRLVIRGRGTQLNDEVVSSSLGLRPDGVFQLAGSGRS SFTPRQAVLTLESSSSQPRSGGIGTLQFVEEFTPSVYFNPFSGSPGHYPDEFIPNFDAISESVDGYD G9G860 singleParticle particle 7.4 150.0 NaCl Salt 1.0 MgCl2 Magnesium Chloride 20.0 C4H11NO3 Tris UltrAuFoil R2/2 GOLD GLOW DISCHARGE ETHANE 100 298 FEI VITROBOT MARK IV
Grid was R2/2 UltrAUFoil. Sample was applied and blotted twice before plunging..
Concentrated by centrifugation
 FEI TITAN KRIOS OTHER BRIGHT FIELD FIELD EMISSION GUN 300 GATAN K2 SUMMIT (4k x 4k) SUPER-RESOLUTION 1 2875 0.2 1.1802 1 8375 3.07 FSC 0.143 CUT-OFF RELION 3.1.1 5748 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD 1 emd_24408.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 1260 1260 1260 0 0 0 1260 1260 1260 1929.6006 1929.6006 1929.6006 90.0 90.0 90.0 X Y Z -0.05644682 0.0945594 0.0001226028 0.0024764268 1.531429 1.531429 1.531429 0.005 EMDB Relion-generated, post-processed map AB INITIO MODEL REAL emd_24408_msk_1.map emd_24408_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 1260 1260 1260 0 0 0 1260 1260 1260 1929.6006 1929.6006 1929.6006 90.0 90.0 90.0 X Y Z -0.012369449 3.19817 0.0029376952 0.04244461 1.531429 1.531429 1.531429 EMDB DeepEMhancer-sharpened using highRes model emd_24408_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 1260 1260 1260 0 0 0 1260 1260 1260 1929.6006 1929.6006 1929.6006 90.0 90.0 90.0 X Y Z -0.0718572 2.1227164 0.0019700092 0.03380048 1.531429 1.531429 1.531429 EMDB DeepEMhancer-sharpened using wideTarget model emd_24408_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 1260 1260 1260 0 0 0 1260 1260 1260 1929.6006 1929.6006 1929.6006 90.0 90.0 90.0 X Y Z -0.07767624 0.24288863 0.0019700092 0.015069088 1.531429 1.531429 1.531429 EMDB DeepEMhancer-sharpened using wideTarget model and low pass-filtered emd_24408_additional_4.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 1260 1260 1260 0 0 0 1260 1260 1260 1929.6006 1929.6006 1929.6006 90.0 90.0 90.0 X Y Z -0.05644682 0.0945594 0.00010006207 0.0024164915 1.531429 1.531429 1.531429 EMDB Hollowed to remove noise generated by nonstructured genome emd_24408_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 1260 1260 1260 0 0 0 1260 1260 1260 1929.6006 1929.6006 1929.6006 90.0 90.0 90.0 X Y Z -0.024679083 0.054995622 -0.000039578885 0.0019992893 1.531429 1.531429 1.531429 EMDB Random half map emd_24408_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 1260 1260 1260 0 0 0 1260 1260 1260 1929.6006 1929.6006 1929.6006 90.0 90.0 90.0 X Y Z -0.026412308 0.054745976 -0.000040946343 0.002009298 1.531429 1.531429 1.531429 EMDB Random half map