[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

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 - 4.0 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: 4.0 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: 4.0 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

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

+
About Yorodumi Papers

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more