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Yorodumi- EMDB-11222: Structure of SARS-CoV-2 spike glycoprotein (S) trimer determined ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11222 | |||||||||
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Title | Structure of SARS-CoV-2 spike glycoprotein (S) trimer determined by sub-tomogram averaging | |||||||||
Map data | Structure of the SARS-CoV-2 S glycoprotein trimer | |||||||||
Sample |
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Function / homology | Function and homology information Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / symbiont-mediated suppression of host innate immune response / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 7.9 Å | |||||||||
Authors | Turonova B / Sikora M / Schurmann C / Hagen W / Welsch S / Blanc FEC / von Bulow S / Gecht M / Bagola K / Horner C ...Turonova B / Sikora M / Schurmann C / Hagen W / Welsch S / Blanc FEC / von Bulow S / Gecht M / Bagola K / Horner C / van Zandbergen G / Landry J / de Azevedo NTD / Mosalaganti S / Schwarz A / Covino R / Muhlebach M / Hummer G / Locker JK / Beck M | |||||||||
Citation | Journal: Science / Year: 2020 Title: In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges. Authors: Beata Turoňová / Mateusz Sikora / Christoph Schürmann / Wim J H Hagen / Sonja Welsch / Florian E C Blanc / Sören von Bülow / Michael Gecht / Katrin Bagola / Cindy Hörner / Ger van ...Authors: Beata Turoňová / Mateusz Sikora / Christoph Schürmann / Wim J H Hagen / Sonja Welsch / Florian E C Blanc / Sören von Bülow / Michael Gecht / Katrin Bagola / Cindy Hörner / Ger van Zandbergen / Jonathan Landry / Nayara Trevisan Doimo de Azevedo / Shyamal Mosalaganti / Andre Schwarz / Roberto Covino / Michael D Mühlebach / Gerhard Hummer / Jacomine Krijnse Locker / Martin Beck / Abstract: The spike protein (S) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is required for cell entry and is the primary focus for vaccine development. In this study, we combined cryo- ...The spike protein (S) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is required for cell entry and is the primary focus for vaccine development. In this study, we combined cryo-electron tomography, subtomogram averaging, and molecular dynamics simulations to structurally analyze S in situ. Compared with the recombinant S, the viral S was more heavily glycosylated and occurred mostly in the closed prefusion conformation. We show that the stalk domain of S contains three hinges, giving the head unexpected orientational freedom. We propose that the hinges allow S to scan the host cell surface, shielded from antibodies by an extensive glycan coat. The structure of native S contributes to our understanding of SARS-CoV-2 infection and potentially to the development of safe vaccines. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11222.map.gz | 726.6 KB | EMDB map data format | |
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Header (meta data) | emd-11222-v30.xml emd-11222.xml | 17.6 KB 17.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11222_fsc.xml | 4.7 KB | Display | FSC data file |
Images | emd_11222.png | 71.3 KB | ||
Others | emd_11222_additional_1.map.gz emd_11222_half_map_1.map.gz emd_11222_half_map_2.map.gz | 7.4 MB 7.4 MB 7.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11222 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11222 | HTTPS FTP |
-Validation report
Summary document | emd_11222_validation.pdf.gz | 720.9 KB | Display | EMDB validaton report |
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Full document | emd_11222_full_validation.pdf.gz | 720.5 KB | Display | |
Data in XML | emd_11222_validation.xml.gz | 10.3 KB | Display | |
Data in CIF | emd_11222_validation.cif.gz | 13.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11222 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11222 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10453 (Title: Cryo electron tomography - tilt-series of Sars-Cov-2 / Data size: 469.8 / Data #1: Unaligned tilt-series of Sars-Cov-2 [tilt series]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_11222.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Structure of the SARS-CoV-2 S glycoprotein trimer | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.658 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Structure of the SARS-CoV-2 S glycoprotein trimer (unmasked...
File | emd_11222_additional_1.map | ||||||||||||
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Annotation | Structure of the SARS-CoV-2 S glycoprotein trimer (unmasked and unsharpened map) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Structure of the SARS-CoV-2 S glycoprotein trimer (Half...
File | emd_11222_half_map_1.map | ||||||||||||
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Annotation | Structure of the SARS-CoV-2 S glycoprotein trimer (Half map 1, unmasked and unfiltered) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Structure of the SARS-CoV-2 S glycoprotein trimer (Half...
File | emd_11222_half_map_2.map | ||||||||||||
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Annotation | Structure of the SARS-CoV-2 S glycoprotein trimer (Half map 2, unmasked and unfiltered) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Severe acute respiratory syndrome coronavirus 2
Entire | Name: Severe acute respiratory syndrome coronavirus 2 |
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Components |
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-Supramolecule #1: Severe acute respiratory syndrome coronavirus 2
Supramolecule | Name: Severe acute respiratory syndrome coronavirus 2 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 2697049 Sci species name: Severe acute respiratory syndrome coronavirus 2 Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No |
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-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 / Component - Formula: PBS / Component - Name: Phosphate buffered Saline |
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 3.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |