[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

TitleStructural basis for broad coronavirus neutralization.
Journal, issue, pagesNat Struct Mol Biol, Vol. 28, Issue 6, Page 478-486, Year 2021
Publish dateMay 12, 2021
AuthorsMaximilian M Sauer / M Alejandra Tortorici / Young-Jun Park / Alexandra C Walls / Leah Homad / Oliver J Acton / John E Bowen / Chunyan Wang / Xiaoli Xiong / Willem de van der Schueren / Joel Quispe / Benjamin G Hoffstrom / Berend-Jan Bosch / Andrew T McGuire / David Veesler /
PubMed AbstractThree highly pathogenic β-coronaviruses have crossed the animal-to-human species barrier in the past two decades: SARS-CoV, MERS-CoV and SARS-CoV-2. To evaluate the possibility of identifying ...Three highly pathogenic β-coronaviruses have crossed the animal-to-human species barrier in the past two decades: SARS-CoV, MERS-CoV and SARS-CoV-2. To evaluate the possibility of identifying antibodies with broad neutralizing activity, we isolated a monoclonal antibody, termed B6, that cross-reacts with eight β-coronavirus spike glycoproteins, including all five human-infecting β-coronaviruses. B6 broadly neutralizes entry of pseudotyped viruses from lineages A and C, but not from lineage B, and the latter includes SARS-CoV and SARS-CoV-2. Cryo-EM, X-ray crystallography and membrane fusion assays reveal that B6 binds to a conserved cryptic epitope located in the fusion machinery. The data indicate that antibody binding sterically interferes with the spike conformational changes leading to membrane fusion. Our data provide a structural framework explaining B6 cross-reactivity with β-coronaviruses from three lineages, along with a proof of concept for antibody-mediated broad coronavirus neutralization elicited through vaccination. This study unveils an unexpected target for next-generation structure-guided design of a pan-β-coronavirus vaccine.
External linksNat Struct Mol Biol / PubMed:33981021
MethodsEM (single particle) / X-ray diffraction
Resolution1.4 - 4.7 Å
Structure data

EMDB-23672:
Structural basis for broad coronavirus neutralization
Method: EM (single particle) / Resolution: 4.7 Å

23674

7m5e

EMDB-23674, PDB-7m5e:
MERS-CoV S bound to the broadly neutralizing B6 Fab fragment (C3 refinement)
Method: EM (single particle) / Resolution: 2.5 Å

PDB-7m51:
B6 Fab fragment bound to the OC43 spike stem helix peptide
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-7m52:
B6 Fab fragment bound to the HKU4 spike stem helix peptide
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-7m53:
B6 Fab fragment bound to the SARS-CoV/SARS-CoV-2 spike stem helix peptide
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-7m55:
B6 Fab fragment bound to the MERS-CoV spike stem helix peptide
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

Chemicals

ChemComp-GOL:
GLYCEROL / Glycerol

ChemComp-HOH:
WATER / Water

ChemComp-FOL:
FOLIC ACID / Folate

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

ChemComp-SIA:
N-acetyl-alpha-neuraminic acid / Sialic acid

Source
  • middle east respiratory syndrome-related coronavirus
  • mus musculus (house mouse)
  • human coronavirus oc43
  • bat coronavirus hku4
  • severe acute respiratory syndrome coronavirus 2
KeywordsANTIVIRAL PROTEIN / IMMUNE SYSTEM / Broadly neutralizing antibody / Structural genomics / SSGCID / Seattle Structural Genomics Center for Infectious Disease / Center for Structural Genomics of Infectious Diseases / CSGID / VIRAL PROTEIN / MERS-CoV / coronaviruses / antibody

+
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