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 basis for SARS-CoV-2 Delta variant recognition of ACE2 receptor and broadly neutralizing antibodies.
Journal, issue, pages	Nat Commun, Vol. 13, Issue 1, Page 871, Year 2022
Publish date	Feb 15, 2022
Authors	Yifan Wang / Caixuan Liu / Chao Zhang / Yanxing Wang / Qin Hong / Shiqi Xu / Zuyang Li / Yong Yang / Zhong Huang / Yao Cong /
PubMed Abstract	The SARS-CoV-2 Delta variant is currently the dominant circulating strain in the world. Uncovering the structural basis of the enhanced transmission and altered immune sensitivity of Delta is ...The SARS-CoV-2 Delta variant is currently the dominant circulating strain in the world. Uncovering the structural basis of the enhanced transmission and altered immune sensitivity of Delta is particularly important. Here we present cryo-EM structures revealing two conformational states of Delta spike and S/ACE2 complex in four states. Our cryo-EM analysis suggests that RBD destabilizations lead to population shift towards the more RBD-up and S1 destabilized fusion-prone state, beneficial for engagement with ACE2 and shedding of S1. Noteworthy, we find the Delta T478K substitution plays a vital role in stabilizing and reshaping the RBM loop, enhancing interaction with ACE2. Collectively, increased propensity for more RBD-up states and the affinity-enhancing T478K substitution together contribute to increased ACE2 binding, providing structural basis of rapid spread of Delta. Moreover, we identify a previously generated MAb 8D3 as a cross-variant broadly neutralizing antibody and reveal that 8D3 binding induces a large K478 side-chain orientation change, suggesting 8D3 may use an "induced-fit" mechanism to tolerate Delta T478K mutation. We also find that all five RBD-targeting MAbs tested remain effective on Delta, suggesting that Delta well preserves the neutralizing antigenic landscape in RBD. Our findings shed new lights on the pathogenicity and antibody neutralization of Delta.
External links	Nat Commun / PubMed:35169135 / PubMed Central
Methods	EM (single particle)
Resolution	3.1 - 3.6 Å
Structure data	32359 7w92 EMDB-32359, PDB-7w92: Open state of SARS-CoV-2 Delta variant spike protein Method: EM (single particle) / Resolution: 3.1 Å 32360 7w94 EMDB-32360, PDB-7w94: Transition state of SARS-CoV-2 Delta variant spike protein Method: EM (single particle) / Resolution: 3.4 Å 32361 7w98 EMDB-32361, PDB-7w98: SARS-CoV-2 Delta S-ACE2-C1 Method: EM (single particle) / Resolution: 3.6 Å 32362 7w99 EMDB-32362, PDB-7w99: SARS-CoV-2 Delta S-ACE2-C2a Method: EM (single particle) / Resolution: 3.4 Å 32363 7w9b EMDB-32363, PDB-7w9b: SARS-CoV-2 Delta S-ACE2-C2b Method: EM (single particle) / Resolution: 3.4 Å 32364 7w9c EMDB-32364, PDB-7w9c: SARS-CoV-2 Delta S-ACE2-C3 Method: EM (single particle) / Resolution: 3.2 Å 32365 7w9e EMDB-32365, PDB-7w9e: SARS-CoV-2 Delta S-8D3 Method: EM (single particle) / Resolution: 3.1 Å 32366 7w9f EMDB-32366, PDB-7w9f: SARS-CoV-2 Delta S-RBD-8D3 Method: EM (single particle) / Resolution: 3.6 Å 32367 7w9i EMDB-32367, PDB-7w9i: SARS-CoV-2 Delta S-RBD-ACE2 Method: EM (single particle) / Resolution: 3.4 Å
Source	severe acute respiratory syndrome coronavirus 2 homo sapiens (human) severe acute respiratory syndrome-related coronavirus mus musculus (house mouse)
Keywords	VIRAL PROTEIN / SARS-CoV-2 Delta variant spike protein / ACE2