SARS-CoV-2 Spike protein Beta Variant at 37C structural flexibility / heterogeneity analyses

2025-05-07 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY citation citation_author em_admin _em_admin.last_update EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update DATA_COLLECTION em_admin _em_admin.last_update PDBe PDBe 2024-08-06 2024-10-30 2024-10-30 2025-05-07 Ministerio de Ciencia e Innovacion (MCIN) rant PID2022-136594NB-I00 funded by MICIU /AEI/ 10.13039/501100011033/ Spain European Research Council (ERC) HighResCells (ERC-2018-SyG, Proposal: 810057 European Union iNEXT-Discovery iNEXT-Discovery (Proposal: 871037) European Union Academia Sinica (Taiwan) (AS-KPQ-109-TPP2) Taiwan Academia Sinica (Taiwan) NSTC 113-2740-B-006-004 Taiwan Academia Sinica (Taiwan) AS-CFII-108-110 Taiwan SARS-CoV-2 Spike protein Beta Variant at 37C structural flexibility / heterogeneity analyses Herreros D Mata CP Noddings C Irene D Agard DA Tsai M-D Sorzano COS Carazo JM SARS-CoV-2, Spike Protein, temperature dependence, VIRAL PROTEIN Herreros D Mata CP Noddings C Irene D Krieger J Agard DA Tsai MD Sorzano COS Carazo JM Real-space heterogeneous reconstruction, refinement, and disentanglement of CryoEM conformational states with HetSIREN. Nat Commun UK 16 3751 3751 2025 40263313 doi:10.1038/s41467-025-59135-0 2041-1723 Herreros D Mata CP Noddings C Irene D Krieger J Agard DA Tsai MD Sorzano COS Carazo JM Real-space heterogeneous reconstruction, refinement, and disentanglement of CryoEM conformational states with HetSIREN. Biorxiv US 2024 39345408 doi:10.1101/2024.09.16.613176 2692-8205 9gdy FULLOVERLAP SARS-CoV-2 Spike protein Beta Variant at 37C SARS-CoV-2 Spike protein Beta Variant at 37C 0 1 Severe acute respiratory syndrome coronavirus 2 0.54 Spike glycoprotein,Fibritin Enterobacteria phage T4 0.136142703 3 Cricetulus griseus LEVO QCVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFA STEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQ PFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHISYLTPGDSSS GWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLC PFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTG NIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVKGFNCYFPLQSYG FQPTYGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAV RDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHV NNSYECDIPIGAGICASYQTQTNSPGSASSVASQSIIAYTMSLGVENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSV DCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRS FIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQI PFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSV LNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSA PHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNT VYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQGSGYIPEA PRDGQAYVRKDGEWVLLSTFLGRSLEVLFQ P0DTC2 P10104 singleParticle particle 0.25 5.5 100.0 C6H9Na3O9 Trisodium Citrate Dihydrate ETHANE 100 37 FEI VITROBOT MARK IV TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.5 2.2 81000.0 FEI TITAN KRIOS AUTOGRID HOLDER GATAN K3 BIOQUANTUM (6k x 4k) 7064 50.0 1 CTFFIND Gctf NONE C1 2.8 FSC 0.143 CUT-OFF 309062 MAXIMUM LIKELIHOOD cryoSPARC OTHER

HetSIREN

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7VX1

7WEV PDB experimental model

7WEV

FLEXIBLE FIT REAL emd_51280_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 224 224 224 -112 -112 -112 224 224 224 313.6 313.6 313.6 90.0 90.0 90.0 X Y Z -0.12975974 1.1363759 0.0014827535 0.022425361 1.4 1.4 1.4 AUTHOR ::::EMDATABANK.org::::EMD-51280:::: SARS-CoV-2 Spike protein Beta Variant at 37C flexibility map 18 3down emd_51280_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 224 224 224 -112 -112 -112 224 224 224 313.6 313.6 313.6 90.0 90.0 90.0 X Y Z -0.13122118 1.1103172 0.0012019724 0.02149251 1.4 1.4 1.4 AUTHOR ::::EMDATABANK.org::::EMD-51280:::: SARS-CoV-2 Spike protein Beta Variant at 37C flexibility map 15 3down emd_51280_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 224 224 224 -112 -112 -112 224 224 224 313.6 313.6 313.6 90.0 90.0 90.0 X Y Z -0.13484575 0.9397567 0.0006896478 0.016632633 1.4 1.4 1.4 AUTHOR ::::EMDATABANK.org::::EMD-51280:::: SARS-CoV-2 Spike protein Beta Variant at 37C flexibility map 16 3down emd_51280_additional_4.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 224 224 224 -112 -112 -112 224 224 224 313.6 313.6 313.6 90.0 90.0 90.0 X Y Z -0.13879094 1.1314034 0.0012247926 0.022022875 1.4 1.4 1.4 AUTHOR ::::EMDATABANK.org::::EMD-51280:::: SARS-CoV-2 Spike protein Beta Variant at 37C flexibility map 19 3down emd_51280_additional_5.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 224 224 224 -112 -112 -112 224 224 224 313.6 313.6 313.6 90.0 90.0 90.0 X Y Z -0.12854582 1.0639322 0.0012127075 0.020850182 1.4 1.4 1.4 AUTHOR ::::EMDATABANK.org::::EMD-51280:::: SARS-CoV-2 Spike protein Beta Variant at 37C flexibility map 20 3down emd_51280_additional_6.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 224 224 224 -112 -112 -112 224 224 224 313.6 313.6 313.6 90.0 90.0 90.0 X Y Z -0.16019145 1.0267507 -0.0040550516 0.021724794 1.4 1.4 1.4 AUTHOR ::::EMDATABANK.org::::EMD-51280:::: SARS-CoV-2 Spike protein Beta Variant at 37C flexibility map 17 3down emd_51280_additional_7.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 224 224 224 -112 -112 -112 224 224 224 313.6 313.6 313.6 90.0 90.0 90.0 X Y Z -0.13284582 1.0632994 0.0009902474 0.018569054 1.4 1.4 1.4 AUTHOR ::::EMDATABANK.org::::EMD-51280:::: SARS-CoV-2 Spike protein Beta Variant at 37C flexibility map 02 1UP emd_51280_additional_8.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 224 224 224 -112 -112 -112 224 224 224 313.6 313.6 313.6 90.0 90.0 90.0 X Y Z -0.120761804 1.0145955 0.001332883 0.019733466 1.4 1.4 1.4 AUTHOR ::::EMDATABANK.org::::EMD-51280:::: SARS-CoV-2 Spike protein Beta Variant at 37C flexibility map 03 3down emd_51280_additional_9.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 224 224 224 -112 -112 -112 224 224 224 313.6 313.6 313.6 90.0 90.0 90.0 X Y Z -0.14767373 1.1618825 0.0013840805 0.023077458 1.4 1.4 1.4 AUTHOR ::::EMDATABANK.org::::EMD-51280:::: SARS-CoV-2 Spike protein Beta Variant at 37C flexibility map 04 3down emd_51280_additional_10.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 224 224 224 -112 -112 -112 224 224 224 313.6 313.6 313.6 90.0 90.0 90.0 X Y Z -0.15304601 0.94937307 -0.0034890447 0.018178781 1.4 1.4 1.4 AUTHOR ::::EMDATABANK.org::::EMD-51280:::: SARS-CoV-2 Spike protein Beta Variant at 37C flexibility map 05 3down emd_51280_additional_11.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 224 224 224 -112 -112 -112 224 224 224 313.6 313.6 313.6 90.0 90.0 90.0 X Y Z -0.13652743 1.0718696 0.0012504049 0.020396171 1.4 1.4 1.4 AUTHOR ::::EMDATABANK.org::::EMD-51280:::: SARS-CoV-2 Spike protein Beta Variant at 37C flexibility map 08 3down emd_51280_additional_12.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 224 224 224 -112 -112 -112 224 224 224 313.6 313.6 313.6 90.0 90.0 90.0 X Y Z -0.1347018 1.108607 0.0010478282 0.020385152 1.4 1.4 1.4 AUTHOR ::::EMDATABANK.org::::EMD-51280:::: SARS-CoV-2 Spike protein Beta Variant at 37C flexibility map 07 3down emd_51280_additional_13.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 224 224 224 -112 -112 -112 224 224 224 313.6 313.6 313.6 90.0 90.0 90.0 X Y Z -0.12632139 1.0224282 0.0009419402 0.018936737 1.4 1.4 1.4 AUTHOR ::::EMDATABANK.org::::EMD-51280:::: SARS-CoV-2 Spike protein Beta Variant at 37C flexibility map 10 3down emd_51280_additional_14.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 224 224 224 -112 -112 -112 224 224 224 313.6 313.6 313.6 90.0 90.0 90.0 X Y Z -0.11112977 1.0229207 0.0012251459 0.018780151 1.4 1.4 1.4 AUTHOR ::::EMDATABANK.org::::EMD-51280:::: SARS-CoV-2 Spike protein Beta Variant at 37C flexibility map 11 1UP emd_51280_additional_15.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 224 224 224 -112 -112 -112 224 224 224 313.6 313.6 313.6 90.0 90.0 90.0 X Y Z -0.12264101 1.0643376 0.001545296 0.020252926 1.4 1.4 1.4 AUTHOR ::::EMDATABANK.org::::EMD-51280:::: SARS-CoV-2 Spike protein Beta Variant at 37C flexibility map 12 3down emd_51280_additional_16.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 224 224 224 -112 -112 -112 224 224 224 313.6 313.6 313.6 90.0 90.0 90.0 X Y Z -0.12361333 1.0352796 0.000823649 0.018743416 1.4 1.4 1.4 AUTHOR ::::EMDATABANK.org::::EMD-51280:::: SARS-CoV-2 Spike protein Beta Variant at 37C flexibility map 13 3down emd_51280_additional_17.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 224 224 224 -112 -112 -112 224 224 224 313.6 313.6 313.6 90.0 90.0 90.0 X Y Z -0.12741461 1.1252469 0.001320079 0.022305472 1.4 1.4 1.4 AUTHOR ::::EMDATABANK.org::::EMD-51280:::: SARS-CoV-2 Spike protein Beta Variant at 37C flexibility map 14 3down emd_51280_additional_18.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 224 224 224 -112 -112 -112 224 224 224 313.6 313.6 313.6 90.0 90.0 90.0 X Y Z -0.0016718688 1.3166025 0.0016890379 0.024304723 1.4 1.4 1.4 AUTHOR ::::EMDATABANK.org::::EMD-51280:::: SARS-CoV-2 Spike protein Beta Variant at 37C sharpened map emd_51280_additional_19.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 224 224 224 -112 -112 -112 224 224 224 313.6 313.6 313.6 90.0 90.0 90.0 X Y Z -0.12837753 1.0211706 0.0011961863 0.019334255 1.4 1.4 1.4 AUTHOR ::::EMDATABANK.org::::EMD-51280:::: SARS-CoV-2 Spike protein Beta Variant at 37C flexibility map 06 3down emd_51280_additional_20.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 224 224 224 -112 -112 -112 224 224 224 313.6 313.6 313.6 90.0 90.0 90.0 X Y Z -0.14444144 1.0960642 0.0011041245 0.02065572 1.4 1.4 1.4 AUTHOR ::::EMDATABANK.org::::EMD-51280:::: SARS-CoV-2 Spike protein Beta Variant at 37C flexibility map 01 1UP emd_51280_additional_21.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 224 224 224 -112 -112 -112 224 224 224 313.6 313.6 313.6 90.0 90.0 90.0 X Y Z -0.12790641 1.0068804 0.00073314446 0.018255139 1.4 1.4 1.4 AUTHOR ::::EMDATABANK.org::::EMD-51280:::: SARS-CoV-2 Spike protein Beta Variant at 37C flexibility map 09 1UP emd_51280_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 224 224 224 -112 -112 -112 224 224 224 313.6 313.6 313.6 90.0 90.0 90.0 X Y Z -0.36579973 1.4614176 0.0030306194 0.059556536 1.4 1.4 1.4 AUTHOR ::::EMDATABANK.org::::EMD-51280:::: SARS-CoV-2 Spike protein Beta Variant at 37C half map 02 emd_51280_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 224 224 224 -112 -112 -112 224 224 224 313.6 313.6 313.6 90.0 90.0 90.0 X Y Z -0.34697312 1.3991494 0.002998724 0.059581395 1.4 1.4 1.4 AUTHOR ::::EMDATABANK.org::::EMD-51280:::: SARS-CoV-2 Spike protein Beta Variant at 37C half map 01