2023-08-30 REL RCSB RCSB RCSB 2022-05-20 2022-08-10 2022-08-10 2023-08-30 Bill & Melinda Gates Foundation INV-021989 United States National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) UM1-AI144371 United States National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) AI158571 United States Edwards RJ Mansouri K SARS-CoV2 spike, antibody Fab, VIRAL PROTEIN Luo S Zhang J Kreutzberger AJB Eaton A Edwards RJ Jing C Dai HQ Sempowski GD Cronin K Parks R Ye AY Mansouri K Barr M Pishesha N Williams AC Vieira Francisco L Saminathan A Peng H Batra H Bellusci L Khurana S Alam SM Montefiori DC Saunders KO Tian M Ploegh H Kirchhausen T Chen B Haynes BF Alt FW Sci Immunol US 7 eadd5446 eadd5446 2022 35951767 doi:10.1126/sciimmunol.add5446 2470-9468 EMD-27043 other EM volume Complex of SARS-CoV2 2P spike with VHH7-7-53 antibody Fab Complex of SARS-CoV2 2P spike with VHH7-7-53 antibody Fab 0 1 2 3 0.048 SARS-CoV2 2P spike 1 1 Severe acute respiratory syndrome coronavirus VHH7-7-53 Antibody Fab Light Chain, VHH7-7-53 Antibody Fab Heavy Chain 1 2 3 Mus musculus SARS-CoV2 2P spike Severe acute respiratory syndrome coronavirus Homo sapiens LEVO MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHV SGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPF LGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPI NLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYN ENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASV YAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIAD YNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYF PLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFL PFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLT PTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPGSASSVASQSIIAYTMSLG AENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGI AVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDC LGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIG VTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDI LSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLM SFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNT FVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVA KNLNESLIDLQELGKYEQGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGRSLEVLFQGPGHHHHHHHHSAW SHPQFEKGGGSGGGGSGGSAWSHPQFEK VHH7-7-53 Antibody Heavy Chain Mus musculus Homo sapiens LEVO QVQLVQSGAEVKKPGASVRVSCKASGFTFTGYQIHWVRQAPGQGLEWMGWINPKSGGTNYAQKFQGRVTMTRDTSISTAYMELSRLRSDDTAVYYCARRNCDYWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT VHH7-7-53 antibody light chain Mus musculus Homo sapiens LEVO DIQMTQSPSSLSASVGDRVTITCQASQDISTYLNWYQQKPGKAPKLLIYDASNLETGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCQQYDNLPYTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC singleParticle particle 7.4 150.0 NaCl Sodium Chloride 20.0 HEPES HEPES buffer 5.0 glycerol glycerol NEGATIVE Uranyl formate

For negative staining, 5 microliter of the diluted and quenched sample was applied to a freshly glow-discharged, 300 mesh, carbon-coated EM grid and incubated 10-12 s, then rinsed with 70 microliter of 2% uranyl formate delivered in one smooth ejection from a pipet. The drop of uranyl formate remaining on the grid was allowed to incubate for 60 s, then the grid was blotted with filter paper and allowed to air dry.

Homemade COPPER 300 CARBON CONTINUOUS 5.0 GLOW DISCHARGE 30

To form the Fab-spike complex, spike was mixed with Fab at a 9:1 molar ratio of fab to spike and incubated at 37 degrees C for 1 h. Then complex was cross-linked by diluting to 200 micrograms/ml spike with 5 g/dl Glycerol in HEPES buffered saline (HBS), containing 20 mM HEPES pH 7.4 and 150 mM NaCl, augmented with 8 mM glutaraldehyde, then incubated 5 min and quenched by addition of sufficient 1 M Tris stock to give 75 mM final Tris concentration and incubated for an additional 5 min.

FEI/PHILIPS EM420 FLOOD BEAM BRIGHT FIELD LAB6 120 50.0 2.0 0.2 1.5 49000.0 SIDE ENTRY, EUCENTRIC NITROGEN OTHER 8736 8740 1 101 0.25 32.0

Images were collected with a minimal dose approach with the beam blanked except during initial grid orientation and image collection. To create an initial atlas, the entire grid was imaged once at 49x magnification at very low beam intensity by decreasing the emission current, strongly focusing C1 (Spot Size 6) and defocusing C2 (Intensity knob fully clockwise). The stage was then quickly translated to center the desired gridsquare, with an estimated exposure of < 2 s at this very low illumination level, at which point the beam was blanked. A 3,300x magnification was then selected so that a single gridsquare approximately fills the scintillator screen. The beam was then unblanked and the stage manually tilted and the eucentric height quickly adjusted by noting the movement of the gridbars, and then the stage was translated to center on the lower-left corner of the gridsquare, with an estimated exposure of < 2 s at this very low illumination level, at which point the beam was blanked. A magnfication of 49,000x was then selected and C2 focused by a known number of clicks of the Intensity knob so that the beam would approximately fill the scintillator screen. The beam was then unblanked, the objective lens focused by eye and then adjusted to approximately 0.5 micron underfocused, and C2 adjusted so the beam just filled the scintillator screen. Because this focusing step involved a long exposure to the focused beam, no data was collected in this area. For data collection, the stage was translated blindly, with the beam blanked, by noting the micrometer markings on the left-hand stage control, to move to an un-irradiated area that was approximately two screen-widths vertically away from the initial position. The beam was then unblanked, an image captured with 0.25 s exposure to the focused beam without any adjustment of the objective lens focus, and the beam then re-blanked. The FFT of the collected image was examined and the position of the first Thon ring noted and the objective lens focus adjusted if needed for subsequent images. The stage was then moved blindly in the same direction to an un-irradiated area and a new image collected. In this way images were collected until the gridbar was encountered, at which point the beam was unblanked and the stage moved so that the gridbar occluded all of the beam except a small sliver of the gridsquare at the bottom or top of the screen, and the right hand stage control was used to translate the specimen to a new location at least two screen widths away horizontally. In this way the entire gridsquare could be imaged in a rastered fashion with each area only irradiated with the full strength beam during the 0.25 s image capture.

1 565030 An unliganded (no Fab) Env trimer homology model was built with SwissModel using the CH505 sequence and PDB 5UM8 as template, then converted to a map using UCSF Chimera's molmap function with 15 angstrom resolution and 2.4 angstrom gridspacing

The starting model was further low-pass filtered to 60 angstroms for use in 3D classification. Resulting 3D classification map was used for as starting model for final 3d refinements.

1 C1 BACK PROJECTION 14.2 FSC 0.143 CUT-OFF RELION 3.0 11357 MAXIMUM LIKELIHOOD RELION 3.0 MAXIMUM LIKELIHOOD RELION 3.0 12 15605.0 RELION 3.0 emd_27044_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 160 160 160 0 0 0 160 160 160 384.0 384.0 384.0 90.0 90.0 90.0 X Y Z -0.049755182 0.08825818 0.00026208747 0.0076500806 2.4 2.4 2.4 AUTHOR ::::EMDATABANK.org::::EMD-27044:::: Half-map 2 of negative stain electron microscopy single particle reconstruction of monoclonal antibody VHH7-7-53 Fab in complex with SARS-CoV2 2P spike emd_27044_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 160 160 160 0 0 0 160 160 160 384.0 384.0 384.0 90.0 90.0 90.0 X Y Z -0.053502493 0.08722641 0.00026542068 0.007651302 2.4 2.4 2.4 AUTHOR ::::EMDATABANK.org::::EMD-27044:::: Half-map 1 of negative stain electron microscopy single particle reconstruction of monoclonal antibody VHH7-7-53 Fab in complex with SARS-CoV2 2P spike