2024-10-23 REL RCSB RCSB RCSB 2022-02-18 2023-03-01 2023-03-01 2024-10-23 National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB) 3U54EB027690-04S United States SARS-Cov2 S protein structure in complex with neutralizing monoclonal antibody 002-02 Patel A Ortlund E SARS-Cov2 6P spike protein, immune complex, VIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex Patel A Kumar S Lai L Chakravarthy C Valanparambil R Reddy ES Gottimukkala K Bajpai P Raju DR Edara VV Davis-Gardner ME Linderman S Dixit K Sharma P Mantus G Cheedarla N Verkerke HP Frank F Neish AS Roback JD Davis CW Wrammert J Ahmed R Suthar MS Sharma A Murali-Krishna K Chandele A Ortlund EA Molecular basis of SARS-CoV-2 Omicron variant evasion from shared neutralizing antibody response. Structure UK 31 801 811.e5 2023 37167972 doi:10.1016/j.str.2023.04.010 0969-2126 2005 STRUE6 7u0q FULLOVERLAP Cov2 Spike timer in complex with monoclonal antibody Cov2 Spike timer in complex with monoclonal antibody 0 1 2 3 Spike glycoprotein 1 1 Severe acute respiratory syndrome coronavirus 2 mAb 002-02 light chain, mAb 002-02 Heavy chain 1 2 3 Homo sapiens Spike glycoprotein Severe acute respiratory syndrome coronavirus 2 0.13378131199999999 3 Homo sapiens LEVO MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFD NPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVY SSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQT LLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRV QPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSF VIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPC NGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFL PFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGS NVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPGSASSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTI SVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGF NFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAG TITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAQALN TLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRV DFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNT FVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDL QELGKYEQ P0DTC2 mAb 002-02 light chain Homo sapiens 0.023414973000000002 2 Homo sapiens LEVO EIVLTQSPGTLSLSPGERATLSCRASQSISSYLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSETDFTLTISRLEP EDFAVYFCQQYGSSPRTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQ ESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC mAb 002-02 Heavy chain Homo sapiens 0.049124128999999996 2 Homo sapiens LEVO EVQLVESGGGLVQPGGSLRLSCAASEITVSRNYMSWVRQAPGKGLEWVSVIYSGGSTFYADSVKGRFTISRDNSRNTLYL QMNSLRADDTAVYYCARDYGDFYFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNS GALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTHTCPPCPAPELLGGPSV FLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYK CKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDS DGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 23 NAG singleParticle particle 0.7 7.4 137.0 NaCl Sodium Chloride 2.7 KCl potassium chloride 8.0 Na2HPO4 disodium hydrogen phosphate 2.0 KH2PO4 potassium di-hydrogen phosphate
PBS buffer
 C-flat-1.2/1.3 COPPER 400 CARBON HOLEY GLOW DISCHARGE AIR ETHANE 100 294 FEI VITROBOT MARK IV
20 second wait time and 3 seconds blot time.
FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 0.6 2.7 81000.0 NITROGEN 30 GATAN K3 (6k x 4k) 1 7815 63.81 1 4065022
used previous low resolution structure for this antibody as starting model
 1 C1 3.86 FSC 0.143 CUT-OFF cryoSPARC 3.2.0 452356 MAXIMUM LIKELIHOOD cryoSPARC 3.2.0 MAXIMUM LIKELIHOOD cryoSPARC 3.2.0 4 250000.0 cryoSPARC 3.2.0 emd_26263.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 416 416 416 0 0 0 416 416 416 444.7456 444.7456 444.7456 90.0 90.0 90.0 X Y Z -2.9589877 4.9675555 -0.003292063 0.060644124 1.0691 1.0691 1.0691 0.29 AUTHOR overall map RIGID BODY FIT correlation coefficient REAL emd_26263_msk_1.map emd_26263_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 416 416 416 0 0 0 416 416 416 444.7456 444.7456 444.7456 90.0 90.0 90.0 X Y Z -1.0262325 1.7259419 -0.008237422 0.021015411 1.0691 1.0691 1.0691 AUTHOR localrefine map RBD chainA emd_26263_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 416 416 416 0 0 0 416 416 416 444.7456 444.7456 444.7456 90.0 90.0 90.0 X Y Z -1.3204665 1.8725526 -0.00823303 0.024136279 1.0691 1.0691 1.0691 AUTHOR localrefine map RBD chainC emd_26263_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 416 416 416 0 0 0 416 416 416 444.7456 444.7456 444.7456 90.0 90.0 90.0 Z Y X -80.066140000000004 87.964590000000001 -0.000041046987 1.1955847 1.0691 1.0691 1.0691 AUTHOR combine focused map emd_26263_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 416 416 416 0 0 0 416 416 416 444.7456 444.7456 444.7456 90.0 90.0 90.0 X Y Z -0.7566974 1.7222916 -0.00047281437 0.05357331 1.0691 1.0691 1.0691 AUTHOR halfmap2 emd_26263_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 416 416 416 0 0 0 416 416 416 444.7456 444.7456 444.7456 90.0 90.0 90.0 X Y Z -0.674254 1.6426003 -0.000460516 0.053485688 1.0691 1.0691 1.0691 AUTHOR halfmap1