2020-12-30 REL PDBe PDBe PDBe 2020-07-28 2020-08-05 2020-08-05 2020-12-30 European Research Council (ERC) ERC-CoG-648432 European Union Medical Research Council (MRC, United Kingdom) MC_UP_A025_1013 United Kingdom Medical Research Council (MRC, United Kingdom) MC_UP_1201/16 United Kingdom Japan Society for the Promotion of Science (JSPS) Japan German Research Foundation (DFG) 240245660-SFB 1129 Germany Subtomogram averaging of SARS-CoV-2 spike protein from unconcentrated virions: Prefusion Class (2 open RBDs) Ke Z Oton J Zivanov J Lu JM Peukes J Cortese M Zila V Scheres SHW Briggs JAG Ke Z Oton J Qu K Cortese M Zila V McKeane L Nakane T Zivanov J Neufeldt CJ Cerikan B Lu JM Peukes J Xiong X Krausslich HG Scheres SHW Bartenschlager R Briggs JAG Structures and distributions of SARS-CoV-2 spike proteins on intact virions. Nature UK 588 498 502 2020 32805734 doi:10.1038/s41586-020-2665-2 1476-4687 0006 NATUAS EMD-11496 associated EM volume EMD-11493 other EM volume EMD-11494 other EM volume EMD-11495 other EM volume EMD-11497 other EM volume EMD-11498 other EM volume Severe acute respiratory syndrome coronavirus 2 Severe acute respiratory syndrome coronavirus 2 0 1
Unconcentrated supernatant of SARS-CoV-2 virions produced from infected VeroE6 cells.
Severe acute respiratory syndrome coronavirus 2 VIRION STRAIN true false SARS-CoV-2 Spike proteins on virions Severe acute respiratory syndrome coronavirus 2 Germany/BavPat1/2020 LEVO MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEE(NAG)(NAG)(NAG)(NAG)(NAG)(NAG)(NAG)(NAG)(NAG)(NAG)(NAG)(NAG)(NAG)(NAG)(NAG)(NAG)(NAG)(NAG)(NAG)(NAG)(NAG)LDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT subtomogramAveraging particle 7.4 C-flat-2/2 CARBON HOLEY ARRAY GLOW DISCHARGE ETHANE LEICA EM GP FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 2.0 6.0 81000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 20 GATAN K2 SUMMIT (4k x 4k) COUNTING 3710 3838 5.0 1-10 1.25 3.0 1 C1 FOURIER SPACE 9.9 FSC 0.143 CUT-OFF RELION 3.1.0 subtomogram averaging
Modified version of RELION for subtomogram averaging
525 156 4104 MATLAB 2016b RELION 3.1.0
Matlab Relion dedicated python scripts
 NOVACTF 1.0.0 IMOD 4.10.30 RELION 3.1.0
novaCTF Relion dedicated python script
 RELION 3.1.0 subtomogram averaging
Focused classification without alignment and with partial signal subtraction of the RBD region. Selection of 2 open RBDs spikes.
 MAXIMUM LIKELIHOOD RELION 3.1.0 subtomogram averaging
Modified version of RELION for subtomogram averaging
 emd_11496.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 128 128 128 0 0 0 128 128 128 392.192 392.192 392.192 90.0 90.0 90.0 X Y Z -3.9059904 15.108139 -0.025958644 0.8509294 3.064 3.064 3.064 3.4 AUTHOR prefusion 2 open RBDs emd_11496_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 128 128 128 0 0 0 128 128 128 392.192 392.192 392.192 90.0 90.0 90.0 X Y Z -29.651192 35.12002 -0.012720135 4.919918 3.064 3.064 3.064 AUTHOR prefusion 2 open RBDs, half2 emd_11496_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 128 128 128 0 0 0 128 128 128 392.192 392.192 392.192 90.0 90.0 90.0 X Y Z -39.294407 35.817093 -0.004524154 5.246794 3.064 3.064 3.064 AUTHOR prefusion 2 open RBDs, half1