2024-11-20 REL RCSB RCSB RCSB 2022-06-01 2023-01-25 2023-01-25 2024-11-20 Howard Hughes Medical Institute (HHMI) GT15335 United States sd1.040 Fab in complex with SARS-CoV-2 Spike 2P glycoprotein Abernathy ME Barnes CO antibody, SD1, SARS-CoV-2, complex, ANTIVIRAL PROTEIN Bianchini F Crivelli V Abernathy ME Guerra C Palus M Muri J Marcotte H Piralla A Pedotti M De Gasparo R Simonelli L Matkovic M Toscano C Biggiogero M Calvaruso V Svoboda P Cervantes Rincon T Fava T Podesvova L Shanbhag AA Celoria A Sgrignani J Stefanik M Honig V Pranclova V Michalcikova T Prochazka J Guerrini G Mehn D Ciabattini A Abolhassani H Jarrossay D Uguccioni M Medaglini D Pan-Hammarstrom Q Calzolai L Fernandez D Baldanti F Franzetti-Pellanda A Garzoni C Sedlacek R Ruzek D Varani L Cavalli A Barnes CO Robbiani DF Human neutralizing antibodies to cold linear epitopes and subdomain 1 of the SARS-CoV-2 spike glycoprotein. Sci Immunol US 8 eade0958 eade0958 2023 36701425 doi:10.1126/sciimmunol.ade0958 2470-9468 Bianchini F Crivelli V Abernathy ME Guerra C Palus M Muri J Marcotte H Piralla A Pedotti M Gasparo R Simonelli L Matkovic M Toscano C Biggiogero M Calvaruso V Svoboda P Rincon TC Fava T Podesvova L Shanbhag AA Celoria A Sgrignani J Stefanik M Honig V Pranclova V Michalcikova T Prochazka J Guerrini G Mehn D Ciabattini A Abolhassani H Jarrossay D Uguccioni M Medaglini D Pan-Hammarstrom Q Calzolai L Fernandez D Baldanti F Franzetti-Pellanda A Garzoni C Sedlacek R Ruzek D Varani L Cavalli A Barnes CO Robbiani DF Human neutralizing antibodies to cold linear epitopes and to subdomain 1 of SARS-CoV-2. Biorxiv US 2022 36482967 doi:10.1101/2022.11.24.515932 2692-8205 8d48 FULLOVERLAP sd1.040 Fab in complex with SARS-CoV-2 Spike 2P sd1.040 Fab in complex with SARS-CoV-2 Spike 2P 0 1 2 3 0.079 Spike glycoprotein 1 1 Severe acute respiratory syndrome coronavirus 2 sd1.040 Fab heavy chain, sd1.040 Fab light chain 1 2 3 Homo sapiens Spike glycoprotein Severe acute respiratory syndrome coronavirus 2 0.139787969 1 Homo sapiens LEVO MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFD NPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVY SSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQT LLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRV QPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSF VIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPC NGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFL PFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGS NVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTI SVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGF NFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAG TITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALN TLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRV DFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNT FVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDL QELGKYEQYIKWPSGRLVPRGSPGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGHHHHHH P0DTC2 sd1.040 Fab heavy chain Homo sapiens 0.024945761999999996 1 Homo sapiens LEVO QVQLVQSGAEVKKPGASVKVSCKASGYTFTSFYIHWVRQAPGQGLEWMGIIDPSGGSTSYPQKFQGRVTMTRDTSTSTVY MDLSSLRSEDTAVYYCTRDGSAGDNSWFDPWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTV SWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTHHHHHH sd1.040 Fab light chain Homo sapiens 0.024346984 1 Homo sapiens LEVO DIVMTQSPDSLAVSLGERATINCKSSRNVLYSSNNKNYLAWYQQKPGQPPKLLIYWASARESGVPDRFSGSGSGTDFTLT ISSLQAEDVAVYYCQQYYNTPYTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNAL QSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC singleParticle particle 3 8.0 20.0 (HOCH2)3CNH2 Tris 150.0 NaCl sodium chloride Quantifoil R1.2/1.3 COPPER 300 GLOW DISCHARGE ETHANE 100 295 FEI VITROBOT MARK IV TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.0 2.5 GIF Bioquantum 20 GATAN K3 BIOQUANTUM (6k x 4k) 1 9894 2.88 59.3 1 4343219 C1 3.7 FSC 0.143 CUT-OFF cryoSPARC 277530 MAXIMUM LIKELIHOOD cryoSPARC MAXIMUM LIKELIHOOD cryoSPARC emd_27177.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 432 432 432 0 0 0 432 432 432 368.1072 368.1072 368.1072 90.0 90.0 90.0 X Y Z -1.0883248 1.5007387 -0.000049515864 0.014740729 0.8521 0.8521 0.8521 0.187 AUTHOR sd1.040 Fab in complex with SARS-CoV-2 Spike 2P glycoprotein 6VXX A PDB experimental model 5AZE H PDB experimental model 7D0D L PDB experimental model RIGID BODY FIT REAL emd_27177_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 432 432 432 0 0 0 432 432 432 368.1072 368.1072 368.1072 90.0 90.0 90.0 X Y Z -0.14109875 0.41419837 -0.000049515864 0.007221243 0.8521 0.8521 0.8521 AUTHOR sd1.040 Fab in complex with SARS-CoV-2 Spike 2P glycoprotein emd_27177_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 432 432 432 0 0 0 432 432 432 368.1072 368.1072 368.1072 90.0 90.0 90.0 X Y Z -0.24345164 0.50309247 0.000098362056 0.01705391 0.8521 0.8521 0.8521 AUTHOR sd1.040 Fab in complex with SARS-CoV-2 Spike 2P glycoprotein emd_27177_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 432 432 432 0 0 0 432 432 432 368.1072 368.1072 368.1072 90.0 90.0 90.0 X Y Z -0.1998791 0.51290256 0.00009935233 0.017081384 0.8521 0.8521 0.8521 AUTHOR sd1.040 Fab in complex with SARS-CoV-2 Spike 2P glycoprotein