+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27779 | |||||||||
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Title | Structure of the SARS-CoV-2 spike glycoprotein S2 subunit | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information endocytosis involved in viral entry into host cell / membrane => GO:0016020 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane Similarity search - Function | |||||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.67 Å | |||||||||
Authors | Park YJ / Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Veesler D | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Sci Immunol / Year: 2022 Title: SARS-CoV-2 spike conformation determines plasma neutralizing activity elicited by a wide panel of human vaccines. Authors: John E Bowen / Young-Jun Park / Cameron Stewart / Jack T Brown / William K Sharkey / Alexandra C Walls / Anshu Joshi / Kaitlin R Sprouse / Matthew McCallum / M Alejandra Tortorici / Nicholas ...Authors: John E Bowen / Young-Jun Park / Cameron Stewart / Jack T Brown / William K Sharkey / Alexandra C Walls / Anshu Joshi / Kaitlin R Sprouse / Matthew McCallum / M Alejandra Tortorici / Nicholas M Franko / Jennifer K Logue / Ignacio G Mazzitelli / Annalee W Nguyen / Rui P Silva / Yimin Huang / Jun Siong Low / Josipa Jerak / Sasha W Tiles / Kumail Ahmed / Asefa Shariq / Jennifer M Dan / Zeli Zhang / Daniela Weiskopf / Alessandro Sette / Gyorgy Snell / Christine M Posavad / Najeeha Talat Iqbal / Jorge Geffner / Alessandra Bandera / Andrea Gori / Federica Sallusto / Jennifer A Maynard / Shane Crotty / Wesley C Van Voorhis / Carlos Simmerling / Renata Grifantini / Helen Y Chu / Davide Corti / David Veesler / Abstract: Numerous safe and effective coronavirus disease 2019 vaccines have been developed worldwide that use various delivery technologies and engineering strategies. We show here that vaccines containing ...Numerous safe and effective coronavirus disease 2019 vaccines have been developed worldwide that use various delivery technologies and engineering strategies. We show here that vaccines containing prefusion-stabilizing S mutations elicit antibody responses in humans with enhanced recognition of S and the S subunit relative to postfusion S as compared with vaccines lacking these mutations or natural infection. Prefusion S and S antibody binding titers positively and equivalently correlated with neutralizing activity, and depletion of S-directed antibodies completely abrogated plasma neutralizing activity. We show that neutralizing activity is almost entirely directed to the S subunit and that variant cross-neutralization is mediated solely by receptor binding domain-specific antibodies. Our data provide a quantitative framework for guiding future S engineering efforts to develop vaccines with higher resilience to the emergence of variants than current technologies. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27779.map.gz | 101.2 MB | EMDB map data format | |
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Header (meta data) | emd-27779-v30.xml emd-27779.xml | 19.9 KB 19.9 KB | Display Display | EMDB header |
Images | emd_27779.png | 186.9 KB | ||
Others | emd_27779_additional_1.map.gz emd_27779_half_map_1.map.gz emd_27779_half_map_2.map.gz | 53.2 MB 99.6 MB 99.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27779 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27779 | HTTPS FTP |
-Validation report
Summary document | emd_27779_validation.pdf.gz | 632.1 KB | Display | EMDB validaton report |
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Full document | emd_27779_full_validation.pdf.gz | 631.7 KB | Display | |
Data in XML | emd_27779_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | emd_27779_validation.cif.gz | 15.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27779 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27779 | HTTPS FTP |
-Related structure data
Related structure data | 8dyaMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_27779.map.gz / Format: CCP4 / Size: 107.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_27779_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_27779_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_27779_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SARS-CoV-2 spike glycoprotein S2 subunit
Entire | Name: SARS-CoV-2 spike glycoprotein S2 subunit |
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Components |
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-Supramolecule #1: SARS-CoV-2 spike glycoprotein S2 subunit
Supramolecule | Name: SARS-CoV-2 spike glycoprotein S2 subunit / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1 Details: ...Details: MGILPSPGMPALLSLVSLLSVLLMGCVAETGTSVASQSIIAYTMSLGAENSVACSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTICSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAQALNTLVKQLSSNCGAISSVLNDILSRLDKPEAEVQIDRLITCRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGRSLEVLFQGPGSGGLNDIFEAQKIEWHEGSGHHHHHHHH |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-Supramolecule #2: SARS-CoV-2 spike S2 subunit
Supramolecule | Name: SARS-CoV-2 spike S2 subunit / type: complex / ID: 2 / Chimera: Yes / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-Macromolecule #1: Spike glycoprotein
Macromolecule | Name: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 68.178117 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MGILPSPGMP ALLSLVSLLS VLLMGCVAET GTSVASQSII AYTMSLGAEN SVACSNNSIA IPTNFTISVT TEILPVSMTK TSVDCTMYI CGDSTECSNL LLQYGSFCTQ LNRALTGIAV EQDKNTQEVF AQVKQIYKTP PIKDFGGFNF SQILPDPSKP S KRSFIEDL ...String: MGILPSPGMP ALLSLVSLLS VLLMGCVAET GTSVASQSII AYTMSLGAEN SVACSNNSIA IPTNFTISVT TEILPVSMTK TSVDCTMYI CGDSTECSNL LLQYGSFCTQ LNRALTGIAV EQDKNTQEVF AQVKQIYKTP PIKDFGGFNF SQILPDPSKP S KRSFIEDL LFNKVTLADA GFIKQYGDCL GDIAARDLIC AQKFNGLTVL PPLLTDEMIA QYTSALLAGT ICSGWTFGAG PA LQIPFPM QMAYRFNGIG VTQNVLYENQ KLIANQFNSA IGKIQDSLSS TPSALGKLQD VVNQNAQALN TLVKQLSSNC GAI SSVLND ILSRLDKPEA EVQIDRLITC RLQSLQTYVT QQLIRAAEIR ASANLAATKM SECVLGQSKR VDFCGKGYHL MSFP QSAPH GVVFLHVTYV PAQEKNFTTA PAICHDGKAH FPREGVFVSN GTHWFVTQRN FYEPQIITTD NTFVSGNCDV VIGIV NNTV YDPLQPELDS FKEELDKYFK NHTSPDVDLG DISGINASVV NIQKEIDRLN EVAKNLNESL IDLQELGKYE QGSGYI PEA PRDGQAYVRK DGEWVLLSTF LGRSLEVLFQ GPGSGGLNDI FEAQKIEWHE GSGHHHHHHH H |
-Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 18 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.67 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 137737 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |