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TitleConformational dynamics of the Beta and Kappa SARS-CoV-2 spike proteins and their complexes with ACE2 receptor revealed by cryo-EM.
Journal, issue, pagesNat Commun, Vol. 12, Issue 1, Page 7345, Year 2021
Publish dateDec 20, 2021
AuthorsYifan Wang / Cong Xu / Yanxing Wang / Qin Hong / Chao Zhang / Zuyang Li / Shiqi Xu / Qinyu Zuo / Caixuan Liu / Zhong Huang / Yao Cong /
PubMed AbstractThe emergence of SARS-CoV-2 Kappa and Beta variants with enhanced transmissibility and resistance to neutralizing antibodies has created new challenges for the control of the ongoing COVID-19 ...The emergence of SARS-CoV-2 Kappa and Beta variants with enhanced transmissibility and resistance to neutralizing antibodies has created new challenges for the control of the ongoing COVID-19 pandemic. Understanding the structural nature of Kappa and Beta spike (S) proteins and their association with ACE2 is of significant importance. Here we present two cryo-EM structures for each of the Kappa and Beta spikes in the open and open-prone transition states. Compared with wild-type (WT) or G614 spikes, the two variant spikes appear more untwisted/open especially for Beta, and display a considerable population shift towards the open state as well as more pronounced conformational dynamics. Moreover, we capture four conformational states of the S-trimer/ACE2 complex for each of the two variants, revealing an enlarged conformational landscape for the Kappa and Beta S-ACE2 complexes and pronounced population shift towards the three RBDs up conformation. These results implicate that the mutations in Kappa and Beta may modify the kinetics of receptor binding and viral fusion to improve virus fitness. Combined with biochemical analysis, our structural study shows that the two variants are enabled to efficiently interact with ACE2 receptor despite their sensitive ACE2 binding surface is modified to escape recognition by some potent neutralizing MAbs. Our findings shed new light on the pathogenicity and immune evasion mechanism of the Beta and Kappa variants.
External linksNat Commun / PubMed:34930910 / PubMed Central
MethodsEM (single particle)
Resolution3.2 - 4 Å
Structure data

EMDB-32167, PDB-7vx1:
SARS-CoV-2 Beta variant spike protein in open state
Method: EM (single particle) / Resolution: 3.5 Å

EMDB-32168, PDB-7vx4:
ACE2-RBD in SARS-CoV-2 Beta variant S-ACE2 complex
Method: EM (single particle) / Resolution: 3.9 Å

EMDB-32169, PDB-7vx5:
ACE2-RBD in SARS-CoV-2 Kappa variant S-ACE2 complex
Method: EM (single particle) / Resolution: 3.8 Å

EMDB-32170: SARS-CoV-2 Beta variant spike protein in transition state
PDB-7wev: SARS-COV-2 BETA VARIANT SPIKE PROTEIN IN TRANSITION STATE
Method: EM (single particle) / Resolution: 3.6 Å

EMDB-32172, PDB-7vx9:
SARS-CoV-2 Kappa variant spike protein in complex wth ACE2, state C1
Method: EM (single particle) / Resolution: 4 Å

EMDB-32173, PDB-7vxa:
SARS-CoV-2 Kappa variant spike protein in complex with ACE2, state C2a
Method: EM (single particle) / Resolution: 3.9 Å

EMDB-32174, PDB-7vxb:
SARS-CoV-2 Kappa variant spike protein in C2b state
Method: EM (single particle) / Resolution: 3.9 Å

EMDB-32175, PDB-7vxc:
SARS-CoV-2 Kappa variant spike protein in C3 state
Method: EM (single particle) / Resolution: 3.9 Å

EMDB-32176, PDB-7vxd:
SARS-CoV-2 spike protein in complex with ACE2, Beta variant, C1 state
Method: EM (single particle) / Resolution: 4 Å

EMDB-32177, PDB-7vxe:
SARS-CoV-2 Kappa variant spike protein in open state
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-32178, PDB-7vxf:
SARS-CoV-2 spike protein in complex with ACE2, Beta variant, C2B state
Method: EM (single particle) / Resolution: 3.6 Å

EMDB-32180, PDB-7vxi:
SARS-CoV-2 Kappa variant spike protein in transition state
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-32182, PDB-7vxk:
SARS-CoV-2 spike protein in complex with ACE2, Beta variant, C2A state
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-32184, PDB-7vxm:
SARS-CoV-2 spike protein in complex with ACE2, Beta variant, C3 state
Method: EM (single particle) / Resolution: 3.6 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

Source
  • severe acute respiratory syndrome coronavirus 2
  • homo sapiens (human)
  • omo sapiens (human)
KeywordsVIRAL PROTEIN / SARS-CoV-2 / coronavirus / Beta variant / B.1.351 lineage / spike protein / Angiotensin-converting enzyme 2 / Kappa variant / B.1.617.1 lineage / VIRAL PROTEIN/HYDROLASE / VIRAL PROTEIN-HYDROLASE complex / SPIK PROTEIN

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