[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

TitlePotent Omicron-neutralizing antibodies isolated from a patient vaccinated 6 months before Omicron emergence.
Journal, issue, pagesCell Rep, Vol. 42, Issue 5, Page 112421, Year 2023
Publish dateApr 10, 2023
AuthorsKathryn M Hastie / Xiaoying Yu / Fernanda Ana-Sosa-Batiz / Dawid S Zyla / Stephanie S Harkins / Chitra Hariharan / Hal Wasserman / Michelle A Zandonatti / Robyn Miller / Erin Maule / Kenneth Kim / Kristen M Valentine / Sujan Shresta / Erica Ollmann Saphire /
PubMed AbstractTherapeutic antibodies are an important tool in the arsenal against coronavirus infection. However, most antibodies developed early in the pandemic have lost most or all efficacy against newly ...Therapeutic antibodies are an important tool in the arsenal against coronavirus infection. However, most antibodies developed early in the pandemic have lost most or all efficacy against newly emergent strains of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), particularly those of the Omicron lineage. Here, we report the identification of a panel of vaccinee-derived antibodies that have broad-spectrum neutralization activity. Structural and biochemical characterization of the three broadest-spectrum antibodies reveal complementary footprints and differing requirements for avidity to overcome variant-associated mutations in their binding footprints. In the K18 mouse model of infection, these three antibodies exhibit protective efficacy against BA.1 and BA.2 infection. This study highlights the resilience and vulnerabilities of SARS-CoV-2 antibodies and provides road maps for further development of broad-spectrum therapeutics.
External linksCell Rep / PubMed:37083327 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.57 - 25.0 Å
Structure data

28756

8f0g

EMDB-28756, PDB-8f0g:
Structure of SARS-CoV-2 Omicron BA.1 spike in complex with antibody Fab 1C3
Method: EM (single particle) / Resolution: 3.35 Å

28757

8f0h

EMDB-28757, PDB-8f0h:
Structure of SARS-CoV-2 spike with antibody Fabs 2A10 and 1H2 (Local refinement of the RBD and Fabs 1H2 and 2A10)
Method: EM (single particle) / Resolution: 3.18 Å

EMDB-28763: Negative stain EM map of SARS-CoV-2 D614G Spike in complex with 2A10 IgG
Method: EM (single particle) / Resolution: 17.0 Å

EMDB-28764: Negative stain EM map of SARS-CoV-2 D614G Spike in complex with 4H4 IgG
Method: EM (single particle) / Resolution: 18.0 Å

EMDB-28765: Negative stain EM map of SARS-CoV-2 D614G Spike in complex with 1C3 IgG
Method: EM (single particle) / Resolution: 20.0 Å

EMDB-28769: Negative stain EM map of SARS-CoV-2 Omicron BA.1 Spike in complex with 1C3 IgG
Method: EM (single particle) / Resolution: 25.0 Å

EMDB-28770: Negative stain EM map of SARS-CoV-2 D614G Spike in complex with 2G3 IgG
Method: EM (single particle) / Resolution: 25.0 Å

EMDB-28771: Negative stain EM map of SARS-CoV-2 D614G Spike in complex with 2E6 IgG
Method: EM (single particle) / Resolution: 25.0 Å

EMDB-28772: Negative stain EM map of SARS-CoV-2 D614G Spike in complex with 1H2 Fab
Method: EM (single particle) / Resolution: 20.0 Å

EMDB-28773: Negative stain EM map of SARS-CoV-2 D614G Spike in complex with 1G8 IgG
Method: EM (single particle) / Resolution: 25.0 Å

PDB-8e1g:
SARS-CoV-2 RBD in complex with Omicron-neutralizing antibody 2A10
Method: X-RAY DIFFRACTION / Resolution: 2.57 Å

Chemicals

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

Source
  • homo sapiens (human)
  • severe acute respiratory syndrome coronavirus 2
KeywordsVIRAL PROTEIN / SARS-CoV-2 / Omicron / antibody / neutralizing / VIRAL PROTEIN/IMMUNE SYSTEM / glycoprotein / immune system / COVID / VIRAL PROTEIN-Immune System complex / coronavirus

+
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