[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

TitleBroadly neutralizing antibodies to SARS-related viruses can be readily induced in rhesus macaques.
Journal, issue, pagesSci Transl Med, Vol. 14, Issue 657, Page eabl9605, Year 2022
Publish dateAug 10, 2022
AuthorsWan-Ting He / Meng Yuan / Sean Callaghan / Rami Musharrafieh / Ge Song / Murillo Silva / Nathan Beutler / Wen-Hsin Lee / Peter Yong / Jonathan L Torres / Mariane Melo / Panpan Zhou / Fangzhu Zhao / Xueyong Zhu / Linghang Peng / Deli Huang / Fabio Anzanello / James Ricketts / Mara Parren / Elijah Garcia / Melissa Ferguson / William Rinaldi / Stephen A Rawlings / David Nemazee / Davey M Smith / Bryan Briney / Yana Safonova / Thomas F Rogers / Jennifer M Dan / Zeli Zhang / Daniela Weiskopf / Alessandro Sette / Shane Crotty / Darrell J Irvine / Andrew B Ward / Ian A Wilson / Dennis R Burton / Raiees Andrabi /
PubMed AbstractTo prepare for future coronavirus (CoV) pandemics, it is desirable to generate vaccines capable of eliciting broadly neutralizing antibody responses to CoVs. Here, we show that immunization of ...To prepare for future coronavirus (CoV) pandemics, it is desirable to generate vaccines capable of eliciting broadly neutralizing antibody responses to CoVs. Here, we show that immunization of macaques with SARS-CoV-2 spike (S) protein with a two-shot protocol generated potent serum receptor binding domain cross-neutralizing antibody responses to both SARS-CoV-2 and SARS-CoV-1. Furthermore, responses were equally effective against most SARS-CoV-2 variants of concern (VOCs) and some were highly effective against Omicron. This result contrasts with human infection or many two-shot vaccination protocols where responses were typically more SARS-CoV-2 specific and where VOCs were less well neutralized. Structural studies showed that cloned macaque neutralizing antibodies, particularly using a given heavy chain germline gene, recognized a relatively conserved region proximal to the angiotensin converting enzyme 2 receptor binding site (RBS), whereas many frequently elicited human neutralizing antibodies targeted more variable epitopes overlapping the RBS. B cell repertoire differences between humans and macaques appeared to influence the vaccine response. The macaque neutralizing antibodies identified a pan-SARS-related virus epitope region less well targeted by human antibodies that could be exploited in rational vaccine design.
External linksSci Transl Med / PubMed:35947674 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution1.95 - 25.0 Å
Structure data

EMDB-26522: SARS-CoV-2 6P Mut7 in complex with K398.25 Fab
Method: EM (single particle) / Resolution: 25.0 Å

EMDB-26523: SARS-CoV-1 in complex with K398.25 Fab
Method: EM (single particle) / Resolution: 25.0 Å

EMDB-26524: SARS-CoV-2 6P Mut7 in complex with K398.16 Fab
Method: EM (single particle) / Resolution: 25.0 Å

EMDB-26525: SARS-CoV-2 6P Mut7 in complex with K398.16 Fab (3 bound)
Method: EM (single particle) / Resolution: 25.0 Å

EMDB-26526: SARS-CoV-1 in complex with K398.16 Fab
Method: EM (single particle) / Resolution: 25.0 Å

EMDB-26527: SARS-CoV-2 6P Mut7 in complex with K288.2 Fab
Method: EM (single particle) / Resolution: 25.0 Å

EMDB-26528: SARS-CoV-2 6P Mut7 in complex with K398.8 Fab
Method: EM (single particle) / Resolution: 25.0 Å

EMDB-26529: SARS-CoV-2 6P Mut7 in complex with K398.8 Fab (2 bound)
Method: EM (single particle) / Resolution: 25.0 Å

EMDB-26530: SARS-CoV-2 6P Mut7 in complex with K398.18 Fab
Method: EM (single particle) / Resolution: 25.0 Å

EMDB-26531: SARS-CoV-2 6P Mut7 in complex with K398.18 Fabs (2 bound)
Method: EM (single particle) / Resolution: 25.0 Å

EMDB-26532: SARS-CoV-2 6P Mut7 in complex with K398.22 Fab
Method: EM (single particle) / Resolution: 25.0 Å

EMDB-26533: SARS-CoV-2 6P Mut7 in complex with K398.22 Fab (2 bound)
Method: EM (single particle) / Resolution: 25.0 Å

EMDB-26534: SARS-CoV-1 in complex with K398.8 Fab
Method: EM (single particle) / Resolution: 25.0 Å

EMDB-26535: SARS-CoV-1 in complex with K398.8 Fab (2 bound)
Method: EM (single particle) / Resolution: 25.0 Å

EMDB-26536: SARS-CoV-1 in complex with K398.18 Fab (2 bound)
Method: EM (single particle) / Resolution: 25.0 Å

EMDB-26537: SARS-CoV-1 in complex with K398.18 Fab (3 bound)
Method: EM (single particle) / Resolution: 25.0 Å

EMDB-26538: SARS-CoV-1 in complex with K288.2 Fab
Method: EM (single particle) / Resolution: 25.0 Å

EMDB-26539: SARS-CoV-1 in complex with K398.22 Fab
Method: EM (single particle) / Resolution: 25.0 Å

PDB-7tp3:
Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody K288.2
Method: X-RAY DIFFRACTION / Resolution: 2.33 Å

PDB-7tp4:
Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody K398.22
Method: X-RAY DIFFRACTION / Resolution: 1.95 Å

Chemicals

ChemComp-CAC:
CACODYLATE ION

ChemComp-HOH:
WATER

ChemComp-EDO:
1,2-ETHANEDIOL

Source
  • severe acute respiratory syndrome coronavirus 2
  • macaca mulatta (Rhesus monkey)
  • Severe acute respiratory syndrome coronavirus
KeywordsIMMUNE SYSTEM / SARS-CoV-2 / antibody / neutralizing antibody / Fab / COVID-19 / coronavirus / receptor-binding domain / RBD / VIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex

+
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