Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Structural conservation among variants of the SARS-CoV-2 spike postfusion bundle.
Journal, issue, pages	Proc Natl Acad Sci U S A, Vol. 119, Issue 16, Page e2119467119, Year 2022
Publish date	Apr 19, 2022
Authors	Kailu Yang / Chuchu Wang / K Ian White / Richard A Pfuetzner / Luis Esquivies / Axel T Brunger /
PubMed Abstract	Variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) challenge currently available COVID-19 vaccines and monoclonal antibody therapies due to structural and dynamic changes of the ...Variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) challenge currently available COVID-19 vaccines and monoclonal antibody therapies due to structural and dynamic changes of the viral spike glycoprotein (S). The heptad repeat 1 (HR1) and heptad repeat 2 (HR2) domains of S drive virus–host membrane fusion by assembly into a six-helix bundle, resulting in delivery of viral RNA into the host cell. We surveyed mutations of currently reported SARS-CoV-2 variants and selected eight mutations, including Q954H, N969K, and L981F from the Omicron variant, in the postfusion HR1HR2 bundle for functional and structural studies. We designed a molecular scaffold to determine cryogenic electron microscopy (cryo-EM) structures of HR1HR2 at 2.2–3.8 Å resolution by linking the trimeric N termini of four HR1 fragments to four trimeric C termini of the Dps4 dodecamer from Nostoc punctiforme. This molecular scaffold enables efficient sample preparation and structure determination of the HR1HR2 bundle and its mutants by single-particle cryo-EM. Our structure of the wild-type HR1HR2 bundle resolves uncertainties in previously determined structures. The mutant structures reveal side-chain positions of the mutations and their primarily local effects on the interactions between HR1 and HR2. These mutations do not alter the global architecture of the postfusion HR1HR2 bundle, suggesting that the interfaces between HR1 and HR2 are good targets for developing antiviral inhibitors that should be efficacious against all known variants of SARS-CoV-2 to date. We also note that this work paves the way for similar studies in more distantly related viruses.
External links	Proc Natl Acad Sci U S A / PubMed:35363556 / PubMed Central
Methods	EM (single particle)
Resolution	2.09 - 2.52 Å
Structure data	24774 7rzq EMDB-24774, PDB-7rzq: Cryo-EM structure of the SARS-CoV-2 HR1HR2 fusion core complex Method: EM (single particle) / Resolution: 2.09 Å 24775 7rzr EMDB-24775, PDB-7rzr: Cryo-EM structure of the SARS-CoV-2 HR1HR2 fusion core complex with D936Y mutation Method: EM (single particle) / Resolution: 2.27 Å 24776 7rzs EMDB-24776, PDB-7rzs: Cryo-EM structure of the SARS-CoV-2 HR1HR2 fusion core complex with L938F mutation Method: EM (single particle) / Resolution: 2.52 Å 24777 7rzt EMDB-24777, PDB-7rzt: Cryo-EM structure of the SARS-CoV-2 HR1HR2 fusion core complex with S940F mutation Method: EM (single particle) / Resolution: 2.35 Å 24778 7rzu EMDB-24778, PDB-7rzu: Cryo-EM structure of the SARS-CoV-2 HR1HR2 fusion core complex with A942S mutation Method: EM (single particle) / Resolution: 2.3 Å 24779 7rzv EMDB-24779, PDB-7rzv: Cryo-EM structure of the SARS-CoV-2 HR1HR2 fusion core complex with V1176F mutation Method: EM (single particle) / Resolution: 2.11 Å
Source	severe acute respiratory syndrome coronavirus 2 nostoc punctiforme (strain atcc 29133 / pcc 73102) (bacteria)
Keywords	VIRAL PROTEIN / spike / HR1HR2 / fusion / scaffold / D936Y / L938F / S940F / A942S / V1176F