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| Title | Detergent modulates the conformational equilibrium of SARS-CoV-2 Spike during cryo-EM structural determination. |
|---|---|
| Journal, issue, pages | Nat Commun, Vol. 14, Issue 1, Page 2527, Year 2023 |
| Publish date | May 3, 2023 |
 Authors | Shawn B Egri / Xue Wang / Marco A Díaz-Salinas / Jeremy Luban / Natalya V Dudkina / James B Munro / Kuang Shen /   |
| PubMed Abstract | The Spike glycoprotein of SARS-CoV-2 mediates viral entry into the host cell via the interaction between its receptor binding domain (RBD) and human angiotensin-converting enzyme 2 (ACE2). Spike RBD ...The Spike glycoprotein of SARS-CoV-2 mediates viral entry into the host cell via the interaction between its receptor binding domain (RBD) and human angiotensin-converting enzyme 2 (ACE2). Spike RBD has been reported to adopt two primary conformations, a closed conformation in which the binding site is shielded and unable to interact with ACE2, and an open conformation that is capable of binding ACE2. Many structural studies have probed the conformational space of the homotrimeric Spike from SARS-CoV-2. However, how sample buffer conditions used during structural determination influence the Spike conformation is currently unclear. Here, we systematically explored the impact of commonly used detergents on the conformational space of Spike. We show that in the presence of detergent, the Spike glycoprotein predominantly occupies a closed conformational state during cryo-EM structural determination. However, in the absence of detergent, such conformational compaction was neither observed by cryo-EM, nor by single-molecule FRET designed to visualize the movement of RBD in solution in real-time. Our results highlight the highly sensitive nature of the Spike conformational space to buffer composition during cryo-EM structural determination, and emphasize the importance of orthogonal biophysical approaches to validate the structural models obtained. |
 External links | Nat Commun / PubMed:37137903 / PubMed Central |
| Methods | EM (single particle) |
| Resolution | 2.7 - 7.0 Å |
| Structure data |  EMDB-29428: SARS-CoV-2 Spike D614G variant, pH 7.4, 0.01% CHAPS, Fully Closed  EMDB-29430: SARS-CoV-2 Spike D614G variant, pH 7.4, 0.01% CHAPS, One RBD Open  EMDB-29431: SARS-CoV-2 Spike D614G variant, pH 7.4, 0.01% CHAPS, Two RBD Open  EMDB-29432: SARS-CoV-2 Spike D614G variant, pH 7.4, 0.01% CHAPS, Three RBD Open  EMDB-29434: SARS-CoV-2 Spike D614G variant, pH 7.4, 0.5% CHAPS, Fully Closed  EMDB-29435: SARS-CoV-2 Spike D614G variant, pH 7.4, 0.5% CHAPS, One RBD Open  EMDB-29436: SARS-CoV-2 Spike D614G variant, pH 7.4, 0.5% CHAPS, Two RBD Open  EMDB-29438: SARS-CoV-2 Spike D614G variant, pH 7.4, 0.5% CHAPS, Three RBD Open  EMDB-29444: SARS-CoV-2 Spike D614G variant, pH 7.4, 0.01% DDM, Fully Closed  EMDB-29445: SARS-CoV-2 Spike D614G variant, pH 7.4, 0.01% DDM, One RBD Open  EMDB-29446: SARS-CoV-2 Spike D614G variant, pH 7.4, 0.01% DDM, Two RBD Open  EMDB-29460: SARS-CoV-2 Spike D614G variant, pH 7.4, 0.5% DDM, Fully Closed  EMDB-29461: SARS-CoV-2 Spike D614G variant, pH 7.4, 0.5% DDM, One RBD Open  EMDB-29462: SARS-CoV-2 Spike D614G variant, pH 7.4, 0.5% DDM, Two RBD Open  EMDB-29463: SARS-CoV-2 Spike D614G variant, pH 7.4, 0.5% DDM, Three RBD Open  EMDB-29464: SARS-CoV-2 Spike D614G variant, pH 5.0, Fully Closed  EMDB-29465: SARS-CoV-2 Spike D614G variant, pH 5.0, One RBD Open (RBD observed)  EMDB-29466: SARS-CoV-2 Spike D614G variant, pH 5.0, One RBD Open (RBD scattered)  EMDB-29467: SARS-CoV-2 Spike D614G variant, pH 5.0, Two RBD Open (two RBD observed)  EMDB-29468: SARS-CoV-2 Spike D614G variant, pH 5.0, Two RBD Open (one RBD observed, one RBD scattered)  EMDB-29469: SARS-CoV-2 Spike D614G variant, pH 5.0, Two RBD Open (two RBD scattered)  EMDB-29470: SARS-CoV-2 Spike D614G variant, pH 5.0, Three RBD Open (three RBD observed)  EMDB-29471: SARS-CoV-2 Spike D614G variant, pH 5.0, Three RBD Open (two RBD observed, one RBD scattered)  EMDB-29472: SARS-CoV-2 Spike D614G variant, pH 5.0, Three RBD Open (one RBD observed, two RBD scattered)  EMDB-29473: SARS-CoV-2 Spike D614G variant, pH 5.0, Three RBD Open (three RBD scattered)  EMDB-29474: SARS-CoV-2 Spike D614 variant, pH 5.0, Fully Closed  EMDB-29475: SARS-CoV-2 Spike D614 variant, pH 5.0, One RBD Open  EMDB-29476: SARS-CoV-2 Spike D614 variant, pH 5.0, Two RBD Open  EMDB-29477: SARS-CoV-2 Spike D614 variant, pH 5.0, Three RBD Open  EMDB-29478: SARS-CoV-2 Spike D614G variant, pH 5.0, 0.5% CHAPS, Fully Closed  EMDB-29479: SARS-CoV-2 Spike D614 variant, pH 5.0, 0.5% CHAPS, Fully Closed  EMDB-29525: SARS-CoV-2 Spike D614G variant, pH 7.4, Fully Closed  EMDB-29527: SARS-CoV-2 Spike D614G variant, pH 7.4, One RBD Open  EMDB-29528: SARS-CoV-2 Spike D614G variant, pH 7.4, Two RBD Open  EMDB-29529: SARS-CoV-2 Spike D614G variant, pH 7.4, Three RBD Open |
| Source |
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Homo sapiens (human)
Severe acute respiratory syndrome coronavirus 2