[English] 日本語
EMN Papers
- Database of articles cited by 3DEM data entries -

+
Search query

Keywords
Author
Journal
IF

-
Structure paper

TitleStructural mapping of antibody landscapes to human betacoronavirus spike proteins.
Journal, issue, pagesSci Adv, Vol. 8, Issue 18, Page eabn2911, Year 2022
Publish dateMay 6, 2022
AuthorsSandhya Bangaru / Aleksandar Antanasijevic / Nurgun Kose / Leigh M Sewall / Abigail M Jackson / Naveenchandra Suryadevara / Xiaoyan Zhan / Jonathan L Torres / Jeffrey Copps / Alba Torrents de la Peña / James E Crowe / Andrew B Ward /
PubMed AbstractPreexisting immunity against seasonal coronaviruses (CoVs) represents an important variable in predicting antibody responses and disease severity to severe acute respiratory syndrome CoV-2 (SARS-CoV- ...Preexisting immunity against seasonal coronaviruses (CoVs) represents an important variable in predicting antibody responses and disease severity to severe acute respiratory syndrome CoV-2 (SARS-CoV-2) infections. We used electron microscopy-based polyclonal epitope mapping (EMPEM) to characterize the antibody specificities against β-CoV spike proteins in prepandemic (PP) sera or SARS-CoV-2 convalescent (SC) sera. We observed that most PP sera had antibodies specific to seasonal human CoVs (HCoVs) OC43 and HKU1 spike proteins while the SC sera showed reactivity across all human β-CoVs. Detailed molecular mapping of spike-antibody complexes revealed epitopes that were differentially targeted by preexisting antibodies and SC serum antibodies. Our studies provide an antigenic landscape to β-HCoV spikes in the general population serving as a basis for cross-reactive epitope analyses in SARS-CoV-2-infected individuals.
External linksSci Adv / PubMed:35507649 / PubMed Central
MethodsEM (single particle)
Resolution3.0 - 30.0 Å
Structure data

24968

7sb3

EMDB-24968, PDB-7sb3:
Structure of OC43 spike in complex with polyclonal Fab1 (Donor 269)
Method: EM (single particle) / Resolution: 3.3 Å

24969

7sb4

EMDB-24969, PDB-7sb4:
Structure of OC43 spike in complex with polyclonal Fab2 (Donor 1412)
Method: EM (single particle) / Resolution: 4.7 Å

24970

7sb5

EMDB-24970, PDB-7sb5:
Structure of OC43 spike in complex with polyclonal Fab3 (Donor 1412)
Method: EM (single particle) / Resolution: 4.2 Å

24989

7sbv

EMDB-24989, PDB-7sbv:
Structure of OC43 spike in complex with polyclonal Fab4 (Donor 269)
Method: EM (single particle) / Resolution: 3.1 Å

24990

7sbw

EMDB-24990, PDB-7sbw:
Structure of OC43 spike in complex with polyclonal Fab5 (Donor 1051)
Method: EM (single particle) / Resolution: 3.2 Å

24991

7sbx

EMDB-24991, PDB-7sbx:
Structure of OC43 spike in complex with polyclonal Fab6 (Donor 1051)
Method: EM (single particle) / Resolution: 3.0 Å

24992

7sby

EMDB-24992, PDB-7sby:
Structure of OC43 spike in complex with polyclonal Fab7 (Donor 269)
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-24993: Structure of OC43 spike in complex with polyclonal Fab8 (Donor 1412)
Method: EM (single particle) / Resolution: 8.0 Å

EMDB-24994: Structure of OC43 spike in complex with polyclonal Fab9 (Donor 1412)
Method: EM (single particle) / Resolution: 7.1 Å

EMDB-24995: Structure of OC43 spike in complex with polyclonal Fab10 (Donor 1412)
Method: EM (single particle) / Resolution: 5.0 Å

EMDB-24996: Structure of SARS-CoV-2 spike in complex with polyclonal Fab11
Method: EM (single particle) / Resolution: 3.9 Å

EMDB-24997: Structure of SARS-CoV-2 spike in complex with polyclonal Fab12
Method: EM (single particle) / Resolution: 4.2 Å

EMDB-24998: Structure of SARS-CoV-2 spike in complex with polyclonal Fab13
Method: EM (single particle) / Resolution: 4.3 Å

EMDB-24999: Structure of SARS-CoV-2 spike in complex with polyclonal Fab14
Method: EM (single particle) / Resolution: 4.4 Å

EMDB-25000: Structure of SARS-CoV-2 spike in complex with polyclonal Fab15
Method: EM (single particle) / Resolution: 4.1 Å

EMDB-25001: Spike proteins from OC43, HKU1, MERS, and SARS CoVs complexed with polyclonal Fab from donor 1051
Method: EM (single particle) / Resolution: 20.0 Å

EMDB-25002: Spike proteins from OC43, HKU1, MERS, and SARS CoVs complexed with polyclonal Fab from donor 1056
Method: EM (single particle) / Resolution: 20.0 Å

EMDB-25003: Spike proteins from OC43, HKU1, MERS, and SARS CoVs complexed with polyclonal Fab from donor 1057
Method: EM (single particle) / Resolution: 20.0 Å

EMDB-25004: Spike proteins from OC43, HKU1, MERS, and SARS CoVs complexed with polyclonal Fab from donor 1124
Method: EM (single particle) / Resolution: 20.0 Å

EMDB-25005: Spike proteins from OC43, HKU1, MERS, and SARS CoVs complexed with polyclonal Fab from donor 1383
Method: EM (single particle) / Resolution: 20.0 Å

EMDB-25006: Spike proteins from OC43, HKU1, MERS, and SARS CoVs complexed with polyclonal Fab from donor 1386
Method: EM (single particle) / Resolution: 20.0 Å

EMDB-25009: Spike proteins from OC43, HKU1, MERS, and SARS CoVs complexed with polyclonal Fab from donor 1412
Method: EM (single particle) / Resolution: 20.0 Å

EMDB-25010: Spike proteins from OC43, HKU1, MERS, and SARS CoVs complexed with polyclonal Fab from donor 269
Method: EM (single particle) / Resolution: 20.0 Å

EMDB-25011: Spike proteins from OC43, HKU1, MERS, SARS, and SARS-2 CoVs complexed with polyclonal Fab from donor 1988
Method: EM (single particle) / Resolution: 20.0 Å

EMDB-25012: Spike proteins from OC43, HKU1, MERS, SARS, and SARS-2 CoVs complexed with polyclonal Fab from donor 1989
Method: EM (single particle) / Resolution: 20.0 Å

EMDB-25013: Spike proteins from OC43, HKU1, MERS, SARS, and SARS-2 CoVs complexed with polyclonal Fab from donor 1992
Method: EM (single particle) / Resolution: 20.0 Å

EMDB-25014: HKU1 spike protein with foldon domain
Method: EM (single particle) / Resolution: 25.9 Å

EMDB-25015: OC43 spike protein with foldon domain
Method: EM (single particle) / Resolution: 28.9 Å

EMDB-25016: MERS spike protein with foldon domain
Method: EM (single particle) / Resolution: 24.6 Å

EMDB-25017: SARS spike protein with foldon domain
Method: EM (single particle) / Resolution: 30.0 Å

EMDB-25018: SARS-2 Hexapro stabilized spike with foldon domain (furin cleavage resistant)
Method: EM (single particle) / Resolution: 26.0 Å

EMDB-25019: SARS-2 Hexapro mut2 (S383C and D985C) stabilized spike with foldon domain (furin cleavage resistant)
Method: EM (single particle) / Resolution: 25.0 Å

EMDB-25020: SARS-2 Hexapro mut4 (A570C and L966C) stabilized spike with foldon domain (furin cleavage resistant)
Method: EM (single particle) / Resolution: 26.0 Å

EMDB-25021: SARS-2 Hexapro mut7 (V705C and T883C) stabilized spike with foldon domain (furin cleavage resistant)
Method: EM (single particle) / Resolution: 25.0 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

ChemComp-8Z9:
Sapienic acid / Sapienic acid

ChemComp-PLM:
PALMITIC ACID / Palmitic acid

Source
  • human coronavirus oc43
  • homo sapiens (human)
  • Severe acute respiratory syndrome coronavirus 2
  • Human coronavirus HKU1
  • Middle East respiratory syndrome-related coronavirus
  • Severe acute respiratory syndrome-related coronavirus
KeywordsVIRAL PROTEIN/Immune System / HCoV / spike / OC43 / polyclonal antibody / EMPEM / VIRAL PROTEIN / VIRAL PROTEIN-Immune System complex

+
About EMN 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

-
Oct 5, 2021. Nobel Prize for mechanically activated and temperature-gated ion channels

Nobel Prize for mechanically activated and temperature-gated ion channels

  • The Nobel Prize in Physiology or Medicine 2021 was awarded jointly to David Julius and Ardem Patapoutian "for their discoveries of receptors for temperature and touch."
  • EM Navigator can help to find cryo-EM structure data by both pioneers.

External links:The Nobel Prize in Physiology or Medicine 2021 - NobelPrize.org / Structure data by Ardem Patapoutian / Structure data by David Julius

+
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

+
Jul 5, 2019. Downlodablable text data

Downlodablable text data

Some data of EM Navigator services can be downloaded as text file. Software such as Excel can load the data files.

PageDataFormat
EMN Searchsearch resultCSV, TSV, or JSON
EMN statisticsdata tableCSV or TSV

Related info.:EMN Search / EMN Statistics

-
EMN Papers

Database of articles cited by 3DEM data entries

  • Database of articles cited by 3DEM data entries in EMDB and PDB
  • Using PubMed data

Related info.:EMDB / PDB / Q: What are the data sources of EM Navigator? / EM Navigator / Yorodumi Papers / Changes in new EM Navigator and Yorodumi

Read more