Structure of a nanoparticle for a COVID-19 vaccine candidate

2024-11-13 REL PDBe PDBe PDBe 2020-12-01 2021-01-13 2021-01-13 2024-11-13 Chinese Academy of Sciences 2018-I2M-2-002 United Kingdom Structure of a nanoparticle for a COVID-19 vaccine candidate Duyvesteyn HME Stuart DI SARS-CoV-2, SpyTag, VLP, Receptor-binding domain, vaccine, COVID-19, SpyCatcher, nanocage, icosahedral, nanoparticle, coronavirus, mi3, VIRUS LIKE PARTICLE Tan TK Rijal P Rahikainen R Keeble AH Schimanski L Hussain S Harvey R Hayes JWP Edwards JC McLean RK Martini V Pedrera M Thakur N Conceicao C Dietrich I Shelton H Ludi A Wilsden G Browning C Zagrajek AK Bialy D Bhat S Stevenson-Leggett P Hollinghurst P Tully M Moffat K Chiu C Waters R Gray A Azhar M Mioulet V Newman J Asfor AS Burman A Crossley S Hammond JA Tchilian E Charleston B Bailey D Tuthill TJ Graham SP Duyvesteyn HME Malinauskas T Huo J Tree JA Buttigieg KR Owens RJ Carroll MW Daniels RS McCauley JW Stuart DI Huang KA Howarth M Townsend AR A COVID-19 vaccine candidate using SpyCatcher multimerization of the SARS-CoV-2 spike protein receptor-binding domain induces potent neutralising antibody responses. Nat Commun UK 12 542 542 2021 33483491 doi:10.1038/s41467-020-20654-7 2041-1723 7b3y FULLOVERLAP RBD-Spycatcher-mi3 RBD-Spycatcher-mi3 0 1 Human immunodeficiency virus 1 Fibronectin binding protein,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 0.036000714999999996

Model just contains mi3 cage component of VLP. Note that the Spy and RBD (spy tag and RBD are omitted from the sequence) are are not included in the model. The spycatcher003-mi3 can be found on genbank with code MT945417 and that of the SpyTag-RBD at MT945427.,Model just contains mi3 cage component of VLP. Note that the Spy and RBD (spy tag and RBD are omitted from the sequence) are are not included in the model. The spycatcher003-mi3 can be found on genbank with code MT945417 and that of the SpyTag-RBD at MT945427.

1 Escherichia coli LEVO MGSSVTTLSGLSGEQGPSGDMTTEEDSATHIKFSKRDEDGRELAGATMELRDSSGKTISTWISDGHVKDFYLYPGKYTFV ETAAPDGYEVATPIEFTVNEDGQVTVDGEATEGDAHTGGSGGSGGSGGSMKMEELFKKHKIVAVLRANSVEEAKKKALAV FLGGVHLIEITFTVPDADTVIKELSFLKEMGAIIGAGTVTSVEQARKAVESGAEFIVSPHLDEEISQFAKEKGVFYMPGV MTPTELVKAMKLGHTILKLFPGEVVGPQFVKAMKGPFPNVKFVPTGGVNLDNVCEWFKAGVLAVGVGSALVKGTPVEVAE KAKAFVEKIRGCTEGSGEPEA A0A0H3BX48 Q9WXS1 singleParticle particle 0.9 7.5

PBS

Quantifoil COPPER 200 CARBON HOLEY GLOW DISCHARGE 30 ETHANE FEI VITROBOT MARK IV FEI TITAN KRIOS OTHER OTHER FIELD EMISSION GUN 300 50.0 2.7 165000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 30 GATAN K2 SUMMIT (4k x 4k) COUNTING 1-40 1 7393 48.1

SerialEM collection employing beam tilt for multishots per hole using custom script.

Ab initio model.

I 3.7 FSC 0.143 CUT-OFF cryoSPARC 150785 MAXIMUM LIKELIHOOD cryoSPARC MAXIMUM LIKELIHOOD cryoSPARC cryoSPARC emd_11997.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 -140 -140 -140 280 280 280 456.4 456.4 456.4 90.0 90.0 90.0 X Y Z -0.2755475 0.8551857 0.0011880954 0.039292116 1.63 1.63 1.63 0.193 AUTHOR ::::EMDATABANK.org::::EMD-11997:::: RBD Spy mi3 cage vlp 5KP9 PDB experimental model RIGID BODY FIT REAL 9.4