[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

TitleN-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2.
Journal, issue, pagesCell, Vol. 184, Issue 9, Page 2332-2347.e16, Year 2021
Publish dateApr 29, 2021
AuthorsMatthew McCallum / Anna De Marco / Florian A Lempp / M Alejandra Tortorici / Dora Pinto / Alexandra C Walls / Martina Beltramello / Alex Chen / Zhuoming Liu / Fabrizia Zatta / Samantha Zepeda / Julia di Iulio / John E Bowen / Martin Montiel-Ruiz / Jiayi Zhou / Laura E Rosen / Siro Bianchi / Barbara Guarino / Chiara Silacci Fregni / Rana Abdelnabi / Shi-Yan Caroline Foo / Paul W Rothlauf / Louis-Marie Bloyet / Fabio Benigni / Elisabetta Cameroni / Johan Neyts / Agostino Riva / Gyorgy Snell / Amalio Telenti / Sean P J Whelan / Herbert W Virgin / Davide Corti / Matteo Samuele Pizzuto / David Veesler /
PubMed AbstractThe SARS-CoV-2 spike (S) glycoprotein contains an immunodominant receptor-binding domain (RBD) targeted by most neutralizing antibodies (Abs) in COVID-19 patient plasma. Little is known about ...The SARS-CoV-2 spike (S) glycoprotein contains an immunodominant receptor-binding domain (RBD) targeted by most neutralizing antibodies (Abs) in COVID-19 patient plasma. Little is known about neutralizing Abs binding to epitopes outside the RBD and their contribution to protection. Here, we describe 41 human monoclonal Abs (mAbs) derived from memory B cells, which recognize the SARS-CoV-2 S N-terminal domain (NTD) and show that a subset of them neutralize SARS-CoV-2 ultrapotently. We define an antigenic map of the SARS-CoV-2 NTD and identify a supersite (designated site i) recognized by all known NTD-specific neutralizing mAbs. These mAbs inhibit cell-to-cell fusion, activate effector functions, and protect Syrian hamsters from SARS-CoV-2 challenge, albeit selecting escape mutants in some animals. Indeed, several SARS-CoV-2 variants, including the B.1.1.7, B.1.351, and P.1 lineages, harbor frequent mutations within the NTD supersite, suggesting ongoing selective pressure and the importance of NTD-specific neutralizing mAbs for protective immunity and vaccine design.
External linksCell / PubMed:33761326 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.2 - 6.5 Å
Structure data

23577

7lxw

EMDB-23577, PDB-7lxw:
SARS-CoV-2 S/S2M11/S2X333 Local Refinement
Method: EM (single particle) / Resolution: 2.8 Å

23578

7lxx

EMDB-23578, PDB-7lxx:
SARS-CoV-2 S/S2M11/S2L28 Local Refinement
Method: EM (single particle) / Resolution: 3.0 Å

23579

7lxy

EMDB-23579, PDB-7lxy:
SARS-CoV-2 S/S2M11/S2X333 Global Refinement
Method: EM (single particle) / Resolution: 2.2 Å

23580

7lxz

EMDB-23580, PDB-7lxz:
SARS-CoV-2 S/S2M11/S2L28 Global Refinement
Method: EM (single particle) / Resolution: 2.6 Å

23581

7ly0

EMDB-23581, PDB-7ly0:
SARS-CoV-2 S/S2M11/S2M28 Local Refinement
Method: EM (single particle) / Resolution: 2.6 Å

23582

7ly2

EMDB-23582, PDB-7ly2:
SARS-CoV-2 S/S2M11/S2M28 Global Refinement
Method: EM (single particle) / Resolution: 2.5 Å

EMDB-23583:
SARS-CoV-2 S/S2M11/S2M24 map
Method: EM (single particle) / Resolution: 6.5 Å

EMDB-23584:
SARS-CoV-2 S/S2X28 map
Method: EM (single particle) / Resolution: 3.5 Å

EMDB-23585:
SARS-CoV-2 S/S2M11/S2X316 map
Method: EM (single particle) / Resolution: 6.0 Å

EMDB-23586:
SARS-CoV-2 S/S2M11/S2L20 map
Method: EM (single particle) / Resolution: 6.3 Å

PDB-7ly3:
Crystal structure of SARS-CoV-2 S NTD bound to S2M28 Fab
Method: X-RAY DIFFRACTION / Resolution: 3 Å

Chemicals

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

ChemComp-HOH:
WATER

ChemComp-UNX:
Unknown entry

ChemComp-XYL:
Xylitol

ChemComp-SO4:
SULFATE ION

Source
  • homo sapiens (human)
  • severe acute respiratory syndrome coronavirus 2
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Antibody / VIRAL PROTEIN / Structural Genomics / Structural Genomics Consortium / SGC / Seattle Structural Genomics Center for Infectious Disease / SSGCID / 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