[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

TitleEvolution of the SARS-CoV-2 spike protein in the human host.
Journal, issue, pagesNat Commun, Vol. 13, Issue 1, Page 1178, Year 2022
Publish dateMar 4, 2022
AuthorsAntoni G Wrobel / Donald J Benton / Chloë Roustan / Annabel Borg / Saira Hussain / Stephen R Martin / Peter B Rosenthal / John J Skehel / Steven J Gamblin /
PubMed AbstractRecently emerged variants of SARS-CoV-2 contain in their surface spike glycoproteins multiple substitutions associated with increased transmission and resistance to neutralising antibodies. We have ...Recently emerged variants of SARS-CoV-2 contain in their surface spike glycoproteins multiple substitutions associated with increased transmission and resistance to neutralising antibodies. We have examined the structure and receptor binding properties of spike proteins from the B.1.1.7 (Alpha) and B.1.351 (Beta) variants to better understand the evolution of the virus in humans. Spikes of both variants have the same mutation, N501Y, in the receptor-binding domains. This substitution confers tighter ACE2 binding, dependent on the common earlier substitution, D614G. Each variant spike has acquired other key changes in structure that likely impact virus pathogenesis. The spike from the Alpha variant is more stable against disruption upon binding ACE2 receptor than all other spikes studied. This feature is linked to the acquisition of a more basic substitution at the S1-S2 furin site (also observed for the variants of concern Delta, Kappa, and Omicron) which allows for near-complete cleavage. In the Beta variant spike, the presence of a new substitution, K417N (also observed in the Omicron variant), in combination with the D614G, stabilises a more open spike trimer, a conformation required for receptor binding. Our observations suggest ways these viruses have evolved to achieve greater transmissibility in humans.
External linksNat Commun / PubMed:35246509 / PubMed Central
MethodsEM (single particle)
Resolution2.8 - 4.1 Å
Structure data

14225

7r0z

EMDB-14225, PDB-7r0z:
Dissociated S1 domain of Alpha Variant SARS-CoV-2 Spike bound to ACE2 (Non-Uniform Refinement)
Method: EM (single particle) / Resolution: 3.5 Å

14226

7r10

EMDB-14226, PDB-7r10:
Dissociated S1 domain of Alpha Variant SARS-CoV-2 Spike bound to ACE2
Method: EM (single particle) / Resolution: 4.0 Å

14227

7r11

EMDB-14227, PDB-7r11:
Dissociated S1 domain of Beta Variant SARS-CoV-2 Spike bound to ACE2 (Non-Uniform Refinement)
Method: EM (single particle) / Resolution: 3.5 Å

14228

7r12

EMDB-14228, PDB-7r12:
Dissociated S1 domain of Mink Variant SARS-CoV-2 Spike bound to ACE2 (Non-Uniform Refinement)
Method: EM (single particle) / Resolution: 3.3 Å

14229

7r13

EMDB-14229, PDB-7r13:
Alpha Variant SARS-CoV-2 Spike in Closed conformation
Method: EM (single particle) / Resolution: 3.6 Å

14230

7r14

EMDB-14230, PDB-7r14:
Alpha Variant SARS-CoV-2 Spike with 1 Erect RBD
Method: EM (single particle) / Resolution: 3.4 Å

14231

7r15

EMDB-14231, PDB-7r15:
Alpha Variant SARS-CoV-2 Spike with 2 Erect RBDs
Method: EM (single particle) / Resolution: 4.1 Å

14232

7r16

EMDB-14232, PDB-7r16:
Beta Variant SARS-CoV-2 Spike with 1 Erect RBD
Method: EM (single particle) / Resolution: 3.5 Å

14233

7r17

EMDB-14233, PDB-7r17:
Beta Variant SARS-CoV-2 Spike with 2 Erect RBDs
Method: EM (single particle) / Resolution: 3.7 Å

14234

7r18

EMDB-14234, PDB-7r18:
Mink Variant SARS-CoV-2 Spike in Closed conformation
Method: EM (single particle) / Resolution: 3.0 Å

14235

7r19

EMDB-14235, PDB-7r19:
Mink Variant SARS-CoV-2 Spike with 2 Erect RBDs
Method: EM (single particle) / Resolution: 3.3 Å

14236

7r1a

EMDB-14236, PDB-7r1a:
Furin Cleaved Alpha Variant SARS-CoV-2 Spike in complex with 3 ACE2
Method: EM (single particle) / Resolution: 3.9 Å

14237

7r1b

EMDB-14237, PDB-7r1b:
Mink Variant SARS-CoV-2 Spike with 1 Erect RBD
Method: EM (single particle) / Resolution: 2.8 Å

Chemicals

ChemComp-ZN:
Unknown entry

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

ChemComp-HOH:
WATER / Water

Source
  • homo sapiens (human)
  • severe acute respiratory syndrome coronavirus 2
KeywordsVIRAL PROTEIN / Spike / SARS-CoV-2

+
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