2024-11-13 REL RCSB RCSB RCSB 2023-05-18 2024-05-22 2024-05-22 2024-11-13 Bill & Melinda Gates Foundation OPP1170236 United States National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) P01 AI144462 United States Local refinement of SARS-CoV-2 (HP-GSAS-Mut7) spike NTD in complex with TXG-0078 Fab Bangaru B Ward A SARS-CoV-2, spike, COVID, monoclonal antibody, complex, NTD, VIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex Hurtado J Rogers TF Jaffe DB Adams BA Bangaru S Garcia E Capozzola T Messmer T Sharma P Song G Beutler N He W Dueker K Musharrafieh R Burbach S Truong A Stubbington MJT Burton DR Andrabi R Ward AB McDonnell WJ Briney B Deep repertoire mining uncovers ultra-broad coronavirus neutralizing antibodies targeting multiple spike epitopes. Cell Rep US 43 114307 114307 2024 38848216 doi:10.1016/j.celrep.2024.114307 2211-1247 8swh FULLOVERLAP Structure of SARS-CoV-2(HP-GSAS-Mut7) spike in complex with TXG-0078 Fab- Local refinement Structure of SARS-CoV-2(HP-GSAS-Mut7) spike in complex with TXG-0078 Fab- Local refinement 0 1 2 3 Severe acute respiratory syndrome coronavirus 2 Spike glycoprotein Severe acute respiratory syndrome coronavirus 2 0.141328359 1 Homo sapiens LEVO MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFD NPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVY SSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQT LLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRV QPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSF VIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPC NGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFL PFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGS NVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPGSASSVASQSIIAYTMSLGAENSCAYSNNSIAIPTNFTI SVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGF NFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAG TICSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAQALN TLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRV DFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNT FVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDL QELGKYEQGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGRSLEVLFQGPGSAWSHPQFEKGGGSGGGGSGGSAWSHPQFEK P0DTC2 TXG-0078 Fab Heavy chain Homo sapiens 0.016115957 1 Homo sapiens LEVO MDCTWRILFLVAAATGTHAQVQVIQSGAEVKKPGASVKVSCKVSGYTLTELSIHWVRQAPGKGLEWMGGFDPEDAETIYA QQFQGRVSMTEDTSTDTAYMELSSLRSEDTAVYYCATAFAITTVGTNYYYYYGMDVWGQGTTVTVSS TXG-0078 Fab Light chain Homo sapiens 0.014484453999999999 1 Homo sapiens LEVO MRLLAQLLGLLMLWVPESSGDIVLTQTPLSSPVTLGQPASISCRSSQSLVHSDGNTYLSWLQQRPGQPPRLLIYKISNRF SGVPDRFSGSGAGTDFTLKISRVEAEDVGLYYCTQATQFPHTFGQGTRLDIK 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 2 NAG singleParticle particle 1 7.4 50.0 Tris-Cl Tris Chloride 150.0 NaCl Sodium Chloride
1X TBS
 Quantifoil R1.2/1.3 COPPER 300 CARBON PLASMA CLEANING ETHANE 100 283 FEI VITROBOT MARK IV
The spike protein was incubated with a 3-fold molar excess of TXG-0078 Fab for 30 minutes and mixed with 0.04 mM Lauryl maltose neopentyl glycol solution immediately prior to sample deposition.
 TFS GLACIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 2.7 0.5 1.5 190000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN FEI FALCON IV (4k x 4k) COUNTING 1 4257 50.0 1 C1 3.88 FSC 0.143 CUT-OFF cryoSPARC 188799 PROJECTION MATCHING cryoSPARC ANGULAR RECONSTITUTION cryoSPARC cryoSPARC emd_40814.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 520 520 520 0 0 0 520 520 520 377.0 377.0 377.0 90.0 90.0 90.0 X Y Z -0.44826058 0.83388567 -0.00027640047 0.007445381 0.725 0.725 0.725 0.1 AUTHOR EM map 7c2l PDB experimental model
Initial fitting in chimera followed by relaxing in Coot
REAL emd_40814_msk_1.map emd_40814_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 520 520 520 0 0 0 520 520 520 377.0 377.0 377.0 90.0 90.0 90.0 X Y Z -0.2613139 0.5562058 0.00016613127 0.021151867 0.725 0.725 0.725 AUTHOR Half map 2 emd_40814_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 520 520 520 0 0 0 520 520 520 377.0 377.0 377.0 90.0 90.0 90.0 X Y Z -0.2139879 0.46249136 0.0001662826 0.021345025 0.725 0.725 0.725 AUTHOR half map 1