2025-06-18 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY PDBe PDBe 2024-06-07 2025-06-18 2025-06-18 2025-06-18 Novo Nordisk Foundation Denmark Omicron BA.1 Spike protein with neutralizing NTD specific mAb K501SP6 Bjoernsson KH Walker MR Raghavan SSR Ward AB Barfod LK Neutralizing Antibody, Conserved Epitope, Covid-19, Spike, VIRAL PROTEIN Bjoernsson KH Walker MR Raghavan SSR Ward AB Barfod LK Omicron BA.1 Spike protein with neutralizing NTD specific mAb K501SP6 To Be Published 0353 EMD-50503 consensus EM volume EMD-50721 focused EM volume
Fab of neutralizing mAb K501SP6 binding to the N-terminal domain of Covid-19 BA.1 Spike protein
 9fmw FULLOVERLAP Alphacoronavirus Alphacoronavirus 0 1 2 3
Omicron BA.1 spike trimer with Fab fragment of human monoclonal antibody K501SP6 produced with hybridoma technology
 Antibody 1 2 3
Human monoclonal antibody
Homo sapiens Spike glycoprotein with fibritin 1 1
Omicron BA.1 spike trimer
Severe acute respiratory syndrome coronavirus 2 Omicron BA.1 Spike glycoprotein,Fibritin Enterobacteria phage T4 0.14148103099999998 3 Homo sapiens LEVO MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNP VLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANN CTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPILVREPEDLPQGFSALEPLVDLPIGINITRFQTLLA LHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPT ESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIR GDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGV AGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLKGTGVLTESNKKFLPFQ QFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVF QTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHGSASSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVT TEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFS QILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFKGLTVLPPLLTDEMIAQYTSALLAGTIT SGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNHNAQALNTLV KQLSSKFGAISSVLNDIFSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFC GKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVS GNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQEL GKYEQGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGRSLEVLFQGPGSAWSHPQFEKGGGSGGGGSGGSAWSHPQFEK P0DTC2 P10104 Fab of neutralizing mAb K501SP6 heavy chain Homo sapiens 0.014387906 1 Homo sapiens LEVO QVQLQESGPGLVKPSETLSLTCTVSGGSISSRSYYWGWIRQPPGKGLEWIGSIYYSGSTYYNPSLKSRVTISVDTSKNQF SLKMNSMTAADTAVYYCARLRGDEIYYESSGYYSYFDYWGQGTLVTVSS Fab of neutralizing mAb K501SP6 light chain Homo sapiens 0.014002314 1 Homo sapiens LEVO WAQSALTQPPSVSGAPGQRVAISCTGSSANIGTADDVHWYQQLPRTAPKLLIYGNNNRPSGVPDRFSGSQSGTSASLVIT GLQPEDEADYFCQSYDSSLSGYVFGTGTKVTVLGQPKAAPSVTLFPPSSEELQA singleParticle particle 1.2 7.5
TBS, pH 7.5
 ETHANE 100 277 FEI VITROBOT MARK IV TFS GLACIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 0.8 2.0 195000.0 NITROGEN FEI FALCON IV (4k x 4k) 60.0 1 591736 cryoSPARC 4.3.1 PHASE FLIPPING AND AMPLITUDE CORRECTION 7WP9
Homotimer (spike protein) with Fab region of neutralizing mAb K501SP6
 FOURIER SPACE 3.6 FSC 0.5 CUT-OFF cryoSPARC 4.4.1 87875 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_50574.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 367.616 367.616 367.616 90.0 90.0 90.0 X Y Z -0.38070533 1.0170816 0.0038135212 0.015208475 0.718 0.718 0.718 0.2 AUTHOR Fab of neutralizing mAb K501SP6 in complex with BA.1 spike trimer