2024-11-06 REL RCSB RCSB RCSB 2020-06-08 2020-07-01 2020-07-01 2024-11-06 National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) P01-AI138398-S1 United States Structure of the SARS-CoV-2 spike glycoprotein in complex with the C105 neutralizing antibody Fab fragment (state 2) Barnes CO Bjorkman PJ SARS-CoV-2, Spike glycoprotein, COVID-19, monoclonal neutralizing antibody, Fabs, nsEMPEM, VIRAL PROTEIN-IMMUNE SYSTEM complex Barnes CO West Jr AP Huey-Tubman KE Hoffmann MAG Sharaf NG Hoffman PR Koranda N Gristick HB Gaebler C Muecksch F Lorenzi JCC Finkin S Hagglof T Hurley A Millard KG Weisblum Y Schmidt F Hatziioannou T Bieniasz PD Caskey M Robbiani DF Nussenzweig MC Bjorkman PJ Structures of Human Antibodies Bound to SARS-CoV-2 Spike Reveal Common Epitopes and Recurrent Features of Antibodies. Cell 182 828 2020 32645326 doi:10.1016/j.cell.2020.06.025 1097-4172 EMD-22127 other EM volume
Structure of the SARS-CoV-2 spike glycoprotein in complex with the C105 neutralizing antibody Fab fragment (state 1)
 6xcn FULLOVERLAP SARS-CoV-2 S 2P trimer complexed with monoclonal Fab fragments from neutralizing antibody C105 SARS-CoV-2 S 2P trimer complexed with monoclonal Fab fragments from neutralizing antibody C105 0 1 2 3 0.75 SARS-CoV-2 spike glycoprotein 2P trimer 1 1 Severe acute respiratory syndrome coronavirus 2 neutralizing antibody C105 Fab 1 2 3 Homo sapiens Spike glycoprotein Severe acute respiratory syndrome coronavirus 2 0.139788953 3 Homo sapiens LEVO MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFD NPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVY SSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQT LLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRV QPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSF VIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPC NGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFL PFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNEVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGS NVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTI SVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGF NFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAG TITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALN TLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRV DFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNT FVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDL QELGKYEQYIKWPSGRLVPRGSPGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGHHHHHH P0DTC2 C105 Fab Heavy Chain Homo sapiens 0.024662506 3 Homo sapiens LEVO QVQLVESGGGLIQPGGSLRLSCAASGFTVSSNYMSWVRQAPGKGLEWVSVIYSGGSTYYADSVKGRFTISRDNSKNTLYL QMNSLRAEDTAVYYCARGEGWELPYDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWN SGALTSGVHTFPAVLQSS(UNK)LYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTHHHHHH C105 Fab Light Chain Homo sapiens 0.022893227 3 Homo sapiens LEVO QSALTQPPSASGSPGQSVTISCTGTSSDVGGYKYVSWYQQHPGKAPKLMIYEVSKRPSGVPDRFSGSKSGNTASLTVSGL QAEDEADYYCSSYEGSNNFVVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPV KAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 24 NAG singleParticle particle 1.5 8.0 100.0 NaCl sodium chloride 20.0 Tris-HCl UltrAuFoil R1.2/1.3 GOLD 300 GOLD HOLEY ARRAY GLOW DISCHARGE AIR
60 s glow discharge in air at 0.20 mA current
 ETHANE 100 295 FEI VITROBOT MARK IV
3 microliters added, blotted for 3 s with 0 blot force.
Monodisperse sample taken after size-exclusion chromatography
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 1.0 2.5 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN
Collected with 3x3 pattern and beam image shift
GATAN K3 BIOQUANTUM (6k x 4k) 1 5940 1.89 60.0 1
Gain-normalized and collected in counting mode with 40 frames per movie
Ab initio volume generated in cryoSPARC
 1 C3 3.66 FSC 0.143 CUT-OFF cryoSPARC 2.14.2 14119 MAXIMUM LIKELIHOOD cryoSPARC 2.14.2 MAXIMUM LIKELIHOOD cryoSPARC 2.14.2 3 cryoSPARC 2.14.2 emd_22128.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 352 352 352 0 0 0 352 352 352 294.272 294.272 294.272 90.0 90.0 90.0 X Y Z -0.37918574 0.70283484 0.003918611 0.023558956 0.836 0.836 0.836 0.1 AUTHOR Dynamic mask used for non-uniform refinement of state 2 complex 6VYB B PDB experimental model RIGID BODY FIT Correlation coefficient REAL 90.0 emd_22128_msk_1.map emd_22128_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 352 352 352 0 0 0 352 352 352 294.272 294.272 294.272 90.0 90.0 90.0 X Y Z -0.12634714 0.36470464 0.0039840857 0.018394627 0.836 0.836 0.836 AUTHOR Unsharpened, non-uniform refined volume of C105-SARS-CoV-2 S 2P trimer complex (state 2)