[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

TitleNeutralizing monoclonal antibodies elicited by mosaic RBD nanoparticles bind conserved sarbecovirus epitopes.
Journal, issue, pagesImmunity, Vol. 55, Issue 12, Page 2419-2435.e10, Year 2022
Publish dateDec 13, 2022
AuthorsChengcheng Fan / Alexander A Cohen / Miso Park / Alfur Fu-Hsin Hung / Jennifer R Keeffe / Priyanthi N P Gnanapragasam / Yu E Lee / Han Gao / Leesa M Kakutani / Ziyan Wu / Harry Kleanthous / Kathryn E Malecek / John C Williams / Pamela J Bjorkman /
PubMed AbstractIncreased immune evasion by SARS-CoV-2 variants of concern highlights the need for new therapeutic neutralizing antibodies. Immunization with nanoparticles co-displaying spike receptor-binding ...Increased immune evasion by SARS-CoV-2 variants of concern highlights the need for new therapeutic neutralizing antibodies. Immunization with nanoparticles co-displaying spike receptor-binding domains (RBDs) from eight sarbecoviruses (mosaic-8 RBD-nanoparticles) efficiently elicits cross-reactive polyclonal antibodies against conserved sarbecovirus RBD epitopes. Here, we identified monoclonal antibodies (mAbs) capable of cross-reactive binding and neutralization of animal sarbecoviruses and SARS-CoV-2 variants by screening single mouse B cells secreting IgGs that bind two or more sarbecovirus RBDs. Single-particle cryo-EM structures of antibody-spike complexes, including a Fab-Omicron complex, mapped neutralizing mAbs to conserved class 1/4 RBD epitopes. Structural analyses revealed neutralization mechanisms, potentials for intra-spike trimer cross-linking by IgGs, and induced changes in trimer upon Fab binding. In addition, we identified a mAb-resembling Bebtelovimab, an EUA-approved human class 3 anti-RBD mAb. These results support using mosaic RBD-nanoparticle vaccination to generate and identify therapeutic pan-sarbecovirus and pan-variant mAbs.
External linksImmunity / PubMed:36370711 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.2 - 4.1 Å
Structure data

26878

7uz4

EMDB-26878, PDB-7uz4:
Structure of the SARS-CoV-2 S 6P trimer in complex with the mouse antibody Fab fragment, M8a-3
Method: EM (single particle) / Resolution: 3.1 Å

26879

7uz5

EMDB-26879, PDB-7uz5:
Structure of the SARS-CoV-2 S 6P trimer in complex with the mouse antibody Fab fragment, M8a-6
Method: EM (single particle) / Resolution: 3.2 Å

26880

7uz6

EMDB-26880, PDB-7uz6:
Structure of the SARS-CoV-2 S 6P trimer in complex with the mouse antibody Fab fragment, M8a-28
Method: EM (single particle) / Resolution: 2.8 Å

26881

7uz7

EMDB-26881, PDB-7uz7:
Structure of the SARS-CoV-2 S 6P trimer in complex with the mouse antibody Fab fragment, M8a-31
Method: EM (single particle) / Resolution: 2.9 Å

26882

7uz8

EMDB-26882, PDB-7uz8:
Structure of the SARS-CoV-2 Omicron BA.1 S 6P trimer in complex with the mouse antibody Fab fragment, M8a-31
Method: EM (single particle) / Resolution: 3.1 Å

26883

7uz9

EMDB-26883, PDB-7uz9:
Structure of the SARS-CoV-2 S 6P trimer in complex with the mouse antibody Fab fragment, M8a-34
Method: EM (single particle) / Resolution: 3.5 Å

26884

7uza

EMDB-26884, PDB-7uza:
Structure of the SARS-CoV-2 S 6P trimer in complex with the mouse antibody Fab fragment, HSW-1
Method: EM (single particle) / Resolution: 3.1 Å

26885

7uzb

EMDB-26885, PDB-7uzb:
Structure of the SARS-CoV-2 S S1 doamin in complex with the mouse antibody Fab fragment, HSW-2
Method: EM (single particle) / Resolution: 4.1 Å

PDB-7uzc:
Structure of the SARS-CoV-2 RBD in complex with the mouse antibody Fab fragment, M8a-34
Method: X-RAY DIFFRACTION / Resolution: 2.2 Å

PDB-7uzd:
Structure of the SARS-CoV-2 RBD in complex with the mouse antibody Fab fragment, HSW-2
Method: X-RAY DIFFRACTION / Resolution: 3.0 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

ChemComp-HOH:
WATER

Source
  • severe acute respiratory syndrome coronavirus 2
  • mus musculus (house mouse)
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / immune system / neutralizing antibody / IMMUNE SYSTEM-VIRAL PROTEIN 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://pdbjlvh1.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