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	Cryo-EM Structures of SARS-CoV-2 Spike without and with ACE2 Reveal a pH-Dependent Switch to Mediate Endosomal Positioning of Receptor-Binding Domains.
Journal, issue, pages	Cell Host Microbe, Vol. 28, Issue 6, Page 867-879.e5, Year 2020
Publish date	Dec 9, 2020
Authors	Tongqing Zhou / Yaroslav Tsybovsky / Jason Gorman / Micah Rapp / Gabriele Cerutti / Gwo-Yu Chuang / Phinikoula S Katsamba / Jared M Sampson / Arne Schön / Jude Bimela / Jeffrey C Boyington / Alexandra Nazzari / Adam S Olia / Wei Shi / Mallika Sastry / Tyler Stephens / Jonathan Stuckey / I-Ting Teng / Pengfei Wang / Shuishu Wang / Baoshan Zhang / Richard A Friesner / David D Ho / John R Mascola / Lawrence Shapiro / Peter D Kwong /
PubMed Abstract	The SARS-CoV-2 spike employs mobile receptor-binding domains (RBDs) to engage the human ACE2 receptor and to facilitate virus entry, which can occur through low-pH-endosomal pathways. To understand ...The SARS-CoV-2 spike employs mobile receptor-binding domains (RBDs) to engage the human ACE2 receptor and to facilitate virus entry, which can occur through low-pH-endosomal pathways. To understand how ACE2 binding and low pH affect spike conformation, we determined cryo-electron microscopy structures-at serological and endosomal pH-delineating spike recognition of up to three ACE2 molecules. RBDs freely adopted "up" conformations required for ACE2 interaction, primarily through RBD movement combined with smaller alterations in neighboring domains. In the absence of ACE2, single-RBD-up conformations dominated at pH 5.5, resolving into a solitary all-down conformation at lower pH. Notably, a pH-dependent refolding region (residues 824-858) at the spike-interdomain interface displayed dramatic structural rearrangements and mediated RBD positioning through coordinated movements of the entire trimer apex. These structures provide a foundation for understanding prefusion-spike mechanics governing endosomal entry; we suggest that the low pH all-down conformation potentially facilitates immune evasion from RBD-up binding antibody.
External links	Cell Host Microbe / PubMed:33271067 / PubMed Central
Methods	EM (single particle)
Resolution	2.4 - 3.93 Å
Structure data	22251 6xlu EMDB-22251, PDB-6xlu: Structure of SARS-CoV-2 spike at pH 4.0 Method: EM (single particle) / Resolution: 2.4 Å 22253 6xm0 EMDB-22253, PDB-6xm0: Consensus structure of SARS-CoV-2 spike at pH 5.5 Method: EM (single particle) / Resolution: 2.7 Å 22254 6xm3 EMDB-22254, PDB-6xm3: Structure of SARS-CoV-2 spike at pH 5.5, single RBD up, conformation 1 Method: EM (single particle) / Resolution: 2.9 Å 22255 6xm4 EMDB-22255, PDB-6xm4: Structure of SARS-CoV-2 spike at pH 5.5, single RBD up, conformation 2 Method: EM (single particle) / Resolution: 2.9 Å 22256 6xm5 EMDB-22256, PDB-6xm5: Structure of SARS-CoV-2 spike at pH 5.5, all RBDs down Method: EM (single particle) / Resolution: 3.1 Å 22515 7jwy EMDB-22515, PDB-7jwy: Structure of SARS-CoV-2 spike at pH 4.5 Method: EM (single particle) / Resolution: 2.5 Å 22922 7kmb EMDB-22922, PDB-7kmb: ACE2-RBD Focused Refinement Using Symmetry Expansion of Applied C3 for Triple ACE2-bound SARS-CoV-2 Trimer Spike at pH 7.4 Method: EM (single particle) / Resolution: 3.39 Å 22927 7kms EMDB-22927, PDB-7kms: Cryo-EM structure of triple ACE2-bound SARS-CoV-2 trimer spike at pH 7.4 Method: EM (single particle) / Resolution: 3.64 Å 22932 7kmz EMDB-22932, PDB-7kmz: Cryo-EM structure of double ACE2-bound SARS-CoV-2 trimer Spike at pH 7.4 Method: EM (single particle) / Resolution: 3.62 Å 22941 7knb EMDB-22941, PDB-7knb: Cryo-EM structure of single ACE2-bound SARS-CoV-2 trimer spike at pH 7.4 Method: EM (single particle) / Resolution: 3.93 Å 22943 7kne EMDB-22943, PDB-7kne: Cryo-EM structure of single ACE2-bound SARS-CoV-2 trimer spike at pH 5.5 Method: EM (single particle) / Resolution: 3.85 Å 22949 7knh EMDB-22949, PDB-7knh: Cryo-EM Structure of Double ACE2-Bound SARS-CoV-2 Trimer Spike at pH 5.5 Method: EM (single particle) / Resolution: 3.74 Å 22950 7kni EMDB-22950, PDB-7kni: Cryo-EM structure of Triple ACE2-bound SARS-CoV-2 Trimer Spike at pH 5.5 Method: EM (single particle) / Resolution: 3.91 Å
Chemicals	ChemComp-NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine ChemComp-HOH: WATER / Water
Source	severe acute respiratory syndrome coronavirus 2 homo sapiens (human)
Keywords	VIRAL PROTEIN / SARS-CoV-2 spike COVID19 / SARS-CoV-2 spike / COVID19 / SARS-CoV-2 COVID19 / Hydrolase/Viral Protein / COVID / SARS-CoV2 / ACE2 / prefusion / Hydrolase-Viral Protein complex / VIRAL PROTEIN/Hydrolase / VIRAL PROTEIN-Hydrolase complex