2024-10-16 REL PDBe PDBe PDBe 2022-03-24 2022-08-17 2022-08-17 2024-10-16 The Francis Crick Institute FC001061 United Kingdom Wellcome Trust FC001061 United Kingdom Medical Research Council (MRC, United Kingdom) FC001061 United Kingdom Cancer Research UK FC001061 United Kingdom Wellcome Trust 206175/Z/17/Z United Kingdom CryoEM structure of SARS-CoV-2 spike monomer in complex with neutralising antibody P008_60 Rosa A Pye VE Cronin N Cherepanov P covid-19, SARS-CoV-2, spike, neutralizing antibody, immunity, VIRAL PROTEIN Seow J Khan H Rosa A Calvaresi V Graham C Pickering S Pye VE Cronin NB Huettner I Malim MH Politis A Cherepanov P Doores KJ A neutralizing epitope on the SD1 domain of SARS-CoV-2 spike targeted following infection and vaccination. Cell Rep US 40 111276 111276 2022 35981534 doi:10.1016/j.celrep.2022.111276 2211-1247 7zbu FULLOVERLAP Monomeric Spike glycoprotein ectodomain from SARS-CoV-2 in complex with a neutralising antibody P008_60 Monomeric Spike glycoprotein ectodomain from SARS-CoV-2 in complex with a neutralising antibody P008_60 0 1 2 3 Homo sapiens 0.125 Spike glycoprotein Severe acute respiratory syndrome coronavirus 2 0.142269859 1 Homo sapiens LEVO MGILPSPGMPALLSLVSLLSVLLMGCVAETGMFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLH STQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIK VCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTP INLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAV DCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLY NSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNY NYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKK STNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVA VLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPSRASSVAS QSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTG IAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDL ICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNS AIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVT QQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHF PREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDI SGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQSGRENLYFQGGGGSGYIPEAPRDGQAYVRKDGEWVLLSTFL GHHHHHH P0DTC2 P008_60 antibody, Heavy chain Homo sapiens 0.025954071999999998 1 Homo sapiens LEVO EVQLVESGGGVVQPGRSLRLTCAASGFIFSSYGMHWVRQAPGKGLEWVAVISYDGSYKYYADSVKGRFTISRDNSKNTLY LQMNSLRAEDTAVYYCTKADYYDFWSGYQKTYYYYMDVWGKGTTVTISSASTKGPSVFPLAPSSKSTSGGTAALGCLVKD YFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVGRTKHHHHHH P008_60 antibody, Light chain Homo sapiens 0.023589067999999998 1 Homo sapiens LEVO DIQLTQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGTSSRATGIPDRFSGSGSGTDFTLTISRLE PEDFAVYYCQQYGSSPQITFGQGTRLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGN SQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 8 NAG 3-[5-[(4-ethyl-3-methyl-5-oxidanylidene-pyrrol-2-yl)methyl]-2-[[5-[(3-ethyl-4-methyl-5-oxidanylidene-pyrrol-2-yl)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1H-pyrrol-2-yl]methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid 0.000588694 1 3Q9 singleParticle particle 0.5 8.0
0.1% n-octyl glucoside in 150 mM NaCl, 20 mM Tris-HCl, pH8.0
 Quantifoil R2/2 COPPER 200 GLOW DISCHARGE ETHANE 100 FEI VITROBOT MARK IV
blotted for 3 to 4 sec before plunging.
SARS-CoV-2 spike ectodomain (0.5 mg/ml), supplemented 0.2 mg/ml P008_60 Fab and 0.1% n-octyl glucoside in 150 mM NaCl, 20 mM Tris-HCl, pH8.0
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 0.7000000000000001 3.6 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 20 GATAN K3 (6k x 4k) 5760 4092 1 16624 4.1 50.0 1
The micrograph stacks were aligned, binned to the physical pixel size of 1.1 A and summed, with dose weighting applied, as implemented in MotionCor2
1740430
Initially, particles were picked with Gautomatch-v0.53 using 2D class averages of the trimeric spike, low-pass filtered to 20 A resolution, as templates. The resulting 1,740,430 particles, extracted in Relion-3.1 and binned to a pixel size of 4.4 A, were subjected to two rounds of reference-free 2D classification in cryoSPARC-2. 283,956 particles belonging to well-defined 2D classes were subjected to classification into twelve 3D classes in Relion-3.1. Neither the 2D nor 3D class averages of the trimeric spike revealed features attributable to a bound Fab molecule. Next, 3,772,722 particles were picked using 2D class averages of the dissociated spikes. Following two rounds of 2D classification in cryoSPARC-2, 753,837 particles, re-extracted with pixel size of 2.2 A, were subjected to 3D classification in Relion-3.1 into 9 classes using an initial model obtained by Ab-initio reconstruction in cryoSPARC-2. The procedure revealed a single well-defined 3D class containing 208,343 particles (27.4%) of S1 protein with a bound Fab molecule. The particles, re-extracted without binning (with a pixel size 1.1 A), were subjected to two rounds of 3D classification using Ab-initio reconstruction in cryoSPARC-2 with 2 classes and class similarity set to 0. At the end of each round, the most populated class was selected, resulting in the final set of 166,619 particles.
Starting model was generating using ab-initio procedure in cryoSPARC
 1 C1 FOURIER SPACE 4.31 FSC 0.143 CUT-OFF cryoSPARC 2
Non Uniform refinement in cryoSPARC
166619 PROJECTION MATCHING PROJECTION MATCHING 2 RELION 3.1
Particles were subjected to two rounds of 3D classification using ab-initio reconstruction in cryoSPARC-2 with 2 classes and class similarity set to 0. At the end of each round, the most populated class was selected, resulting in the final set of 166,619 particles.
 emd_14591.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 340 340 340 0 0 0 340 340 340 374.0 374.0 374.0 90.0 90.0 90.0 X Y Z -0.0017089208 1.8422732 0.0004936652 0.015751675 1.1 1.1 1.1 0.03 AUTHOR DeepEMenhancer map 7A92 A PDB experimental model 5WI9 E PDB experimental model 5WI9 F PDB experimental model OTHER
The atomistic models of monomeric SARS-CoV-2 S1 protein and a Fab molecule, extracted from PDB entries 7A92 and 5WI9, were docked in the cryo-EM map using Chimera. The NTD and the RBD of the spike subunit were replaced with the crystal structures from PDB entries 7B62 and 7OAO, respectively. Guided by the cryo-EM map, the model was adjusted and extended interactively in Coot and refined using phenix.real_space_refine.
Correlation coefficient REAL 81.0 emd_14591_msk_1.map emd_14591_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 340 340 340 0 0 0 340 340 340 374.0 374.0 374.0 90.0 90.0 90.0 X Y Z -0.18044688 0.98389864 -0.000042736796 0.027029967 1.1 1.1 1.1 AUTHOR original map, no modifications emd_14591_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 340 340 340 0 0 0 340 340 340 374.0 374.0 374.0 90.0 90.0 90.0 X Y Z -0.32068327 1.1211324 0.00073349656 0.039653238 1.1 1.1 1.1 AUTHOR half map B emd_14591_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 340 340 340 0 0 0 340 340 340 374.0 374.0 374.0 90.0 90.0 90.0 X Y Z -0.32376912 1.0819782 0.000734251 0.039826963 1.1 1.1 1.1 AUTHOR half map A