[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

TitleThe buried S2 apex of SARS-CoV-2 spike elicits an immunodominant germline-restricted public antibody response.
Journal, issue, pagesbioRxiv, Year 2026
Publish dateFeb 19, 2026
AuthorsSuncheol Park / Jacob Mischka / Nisreen Okba / Anass Abbad / Meng Yuan / Komal Srivastava / Charles Gleason / Lubbertus C F Mulder / Jeffrey Copps / Katrina Saam / Sandhya Bangaru / Florian Krammer / Ian A Wilson / Viviana Simon / Andrew B Ward
PubMed AbstractThe continued mutational pressure on the SARS-CoV-2 S1 subunit underscores the need to target the conserved S2 region for pan-coronavirus vaccine development. A detailed molecular understanding of S2- ...The continued mutational pressure on the SARS-CoV-2 S1 subunit underscores the need to target the conserved S2 region for pan-coronavirus vaccine development. A detailed molecular understanding of S2-directed immune responses is therefore essential. In this study, we identified the S2 apex as the most immunodominant epitope within the S2 subunit, eliciting robust antibody responses despite occlusion by S1, using electron-microscopy-based polyclonal epitope mapping (EMPEM) of plasma from infected and vaccinated individuals. Structure-guided sequence analysis with antibody databases revealed that antibodies targeting a poorly characterized S2 Apex-B site form a convergent public clonotype, which is predominantly derived from the IGHV3-30 germline with a 14-residue CDRH3 containing a G/S-G-S/N-Y motif. This clonotype is extensively expanded, accounting for up to 40% of total spike-reactive antibody sequence counts in individual vaccinated donors. This study elucidates the molecular basis the high-frequency elicitation of this non-neutralizing clonotype emphasizing that its immunodominance acts as a primary hurdle for universal coronavirus vaccines and underscore the need for precision antigen design to redirect immunity toward more potent neutralizing targets.
External linksbioRxiv / PubMed:41756886 / PubMed Central
MethodsEM (single particle)
Resolution2.75 - 24.0 Å
Structure data

73884

9z80

EMDB-73884, PDB-9z80:
SARS-CoV-2 S2 in complex with polyclonal Fab_Donor1
Method: EM (single particle) / Resolution: 3.17 Å

74737

9zt5

EMDB-74737, PDB-9zt5:
SARS-CoV-2 S2 in complex with polyclonal Fab-B_Donor3
Method: EM (single particle) / Resolution: 3.21 Å

74738

9zt6

EMDB-74738, PDB-9zt6:
SARS-CoV-2 S2 in complex with polyclonal Fab-B_Donor8
Method: EM (single particle) / Resolution: 2.83 Å

74739

9zt7

EMDB-74739, PDB-9zt7:
SARS-CoV-2 S2 in complex with COV2-2509
Method: EM (single particle) / Resolution: 3.11 Å

74740

9zt8

EMDB-74740, PDB-9zt8:
Stabilized SARS-CoV-2 S2 apo
Method: EM (single particle) / Resolution: 2.75 Å

EMDB-75193: SARS-CoV-2 spike S2 subunit in complex with polyclonal Fabs (Apex-A epitope)
Method: EM (single particle) / Resolution: 22.0 Å

EMDB-75194: SARS-CoV-2 spike S2 subunit in complex with polyclonal Fabs (Apex-B epitope)
Method: EM (single particle) / Resolution: 24.0 Å

75295

10mu

EMDB-75295, PDB-10mu:
SARS-CoV-2 S2 in complex with polyclonal Fab_Donor2
Method: EM (single particle) / Resolution: 3.16 Å

Chemicals

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

Source
  • homo sapiens (human)
  • severe acute respiratory syndrome coronavirus 2
KeywordsVIRAL PROTEIN/Immune System / SARS-CoV-2 / Coronavirus / Immune system / antibody / VIRAL PROTEIN / VIRAL PROTEIN-Immune System complex / VIRUS

+
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