2024-11-20 REL RCSB RCSB RCSB 2021-05-20 2021-06-16 2021-06-16 2024-11-20 National Institutes of Health/National Cancer Institute (NIH/NCI) HSSN261200800001E United States Xu K Kwong PD SARS-CoV2, nanobody, neutralizing, spike, IMMUNE SYSTEM-VIRAL PROTEIN complex Xu J Xu K Jung S Conte A Lieberman J Muecksch F Lorenzi JCC Park S Schmidt F Wang Z Huang Y Luo Y Nair MS Wang P Schulz JE Tessarollo L Bylund T Chuang GY Olia AS Stephens T Teng IT Tsybovsky Y Zhou T Munster V Ho DD Hatziioannou T Bieniasz PD Nussenzweig MC Kwong PD Casellas R Nature UK 595 278 282 2021 34098567 doi:10.1038/s41586-021-03676-z 1476-4687 0006 NATUAS 7my2 FULLOVERLAP SARS-CoV2 spike in complex with nanobody Nb30 SARS-CoV2 spike in complex with nanobody Nb30 0 1 2 Severe acute respiratory syndrome coronavirus 2 SARS-CoV2 spike 1 1

HexaPro construct

Nanobody Nb30 1 2 Mus musculus Spike glycoprotein Severe acute respiratory syndrome coronavirus 2 0.142427438 3 Homo sapiens LEVO MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFD NPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVY SSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQT LLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRV QPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSF VIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPC NGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFL PFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGS NVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPGSASSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTI SVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGF NFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAG TITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAQALN TLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRV DFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNT FVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDL QELGKYEQGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGRSLEVLFQGPGHHHHHHHHSAWSHPQFEKGGGSGGGGSGGSA WSHPQFEK P0DTC2 Nanobody Nb30 Mus musculus 0.014210730999999999 3 Escherichia coli LEVO QVQLVESGGGLVQAGGSLRLSCAASGLTFSKYAMGWFRQAPGKERKFVATISWSGDSAFYADSVKGRFTISRDNARNTVY LQMNSLKPEDTAVYYCAADRGMGYGDFMDYWGQGTSVTASSASGAHHHHHH 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 29 NAG singleParticle particle 0.5 7.4 HBS

5mM Hepes pH7.4, 150mM NaCl

Quantifoil R2/2 GOLD 400 CARBON HOLEY GLOW DISCHARGE 30 AIR ETHANE 95 293 FEI VITROBOT MARK IV FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K3 (6k x 4k) 1 6796 2.0 40.3 1 1666677 6XKL 48 C1 2.65 FSC 0.143 CUT-OFF cryoSPARC 2.15 333232 NOT APPLICABLE MAXIMUM LIKELIHOOD cryoSPARC 2.15 cryoSPARC 2.15 6XKL A PDB experimental model FLEXIBLE FIT REAL emd_24077_msk_1.map emd_24077_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 105 89 114 192 218 259 114 89 105 97.47 76.095 89.775 90.0 90.0 90.0 Z Y X -8.258018 33.330629999999999 0.000000000022178 1.0 0.855 0.855 0.855 AUTHOR ::::EMDATABANK.org::::EMD-24077:::: Local refined map focused on one RBD and nanobody complex region emd_24077_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 0 0 0 600 600 600 513.0 513.0 513.0 90.0 90.0 90.0 X Y Z -1.7379049 2.5532224 0.00025355926 0.19216621 0.855 0.855 0.855 AUTHOR ::::EMDATABANK.org::::EMD-24077:::: emd_24077_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 0 0 0 600 600 600 513.0 513.0 513.0 90.0 90.0 90.0 X Y Z -1.7154207 2.430921 0.00025125002 0.19176456 0.855 0.855 0.855 AUTHOR ::::EMDATABANK.org::::EMD-24077::::