2024-11-20 REL PDBe PDBe PDBe 2022-12-21 2023-04-19 2023-04-19 2024-11-20 Academy of Finland 336492 Finland Academy of Finland 342988 Finland Cryo-EM map of SARS-CoV-2 S-trimer (3 RBDs up) in complex with neutralizing sherpabody TriSb92 Huiskonen JT Rissanen I Hannula L SARS-CoV-2 spike, sherpabody, viral protein, coronavirus Makela AR Ugurlu H Hannula L Kant R Salminen P Fagerlund R Maki S Haveri A Strandin T Kareinen L Hepojoki J Kuivanen S Levanov L Pasternack A Naves RA Ritvos O Osterlund P Sironen T Vapalahti O Kipar A Huiskonen JT Rissanen I Saksela K Intranasal trimeric sherpabody inhibits SARS-CoV-2 including recent immunoevasive Omicron subvariants. Nat Commun UK 14 1637 1637 2023 36964125 doi:10.1038/s41467-023-37290-6 2041-1723 8c1v FULLOVERLAP SARS-CoV-2 Spike in open conformation with bound sherpabody SARS-CoV-2 Spike in open conformation with bound sherpabody 0 1 2 Severe acute respiratory syndrome coronavirus 2 Spike glycoprotein Severe acute respiratory syndrome coronavirus 2 0.124497945 3 Homo sapiens LEVO PAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWI FGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGN FKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAY YVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNAT RFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKL PDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGY QPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEIL DITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIP IGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGD STECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNK VTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYR FNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLD PPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHV TYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPEL DSFK P0DTC2 Sb92 Homo sapiens 0.006644363999999999 3 Escherichia coli LEVO EEYIAVGDFFSTDPADLTFKKGEILLVIERGTSAGDGWWIAKDAKGNEGLVPRTYLEPYS 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 39 NAG singleParticle particle 0.3 8.0
10 mM Tris pH 8 + 150 mM NaCl
 Quantifoil R1.2/1.3 COPPER 200 GLOW DISCHARGE ETHANE FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.5 3.0 GATAN K2 QUANTUM (4k x 4k) COUNTING 1-40 5996 1.375 1 C1 FOURIER SPACE 2.9 FSC 0.143 CUT-OFF cryoSPARC 4.0.0 150665 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_16383.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 419.84 419.84 419.84 90.0 90.0 90.0 X Y Z -0.8595966 1.855372 0.0010489178 0.028650466 0.82 0.82 0.82 0.21 AUTHOR SARS-CoV-2 S-trimer in complex with Sb92 inhibitor, filtered to local resolution RIGID BODY FIT
Initial fitting of non-RBD regions of the S-trimer, RBDs and Sb92s was done in ChimeraX, and then Coot was used to adjust the linker regions between RBDs and S.
 emd_16383_msk_2.map emd_16383_msk_1.map emd_16383_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 419.84 419.84 419.84 90.0 90.0 90.0 X Y Z -2.3460014 2.4712584 0.001286708 0.27393273 0.82 0.82 0.82 AUTHOR Half map A emd_16383_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 419.84 419.84 419.84 90.0 90.0 90.0 X Y Z -2.4678226 2.466071 0.001281768 0.2741131 0.82 0.82 0.82 AUTHOR Half map B