[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 epitope arrangement on flavivirus particles contributes to Mab C10's extraordinary neutralization breadth across Zika and dengue viruses.
Journal, issue, pagesCell, Vol. 184, Issue 25, Page 6052-6066.e18, Year 2021
Publish dateDec 9, 2021
AuthorsArvind Sharma / Xiaokang Zhang / Wanwisa Dejnirattisai / Xinghong Dai / Danyang Gong / Wiyada Wongwiwat / Stéphane Duquerroy / Alexander Rouvinski / Marie-Christine Vaney / Pablo Guardado-Calvo / Ahmed Haouz / Patrick England / Ren Sun / Z Hong Zhou / Juthathip Mongkolsapaya / Gavin R Screaton / Felix A Rey /
PubMed AbstractThe human monoclonal antibody C10 exhibits extraordinary cross-reactivity, potently neutralizing Zika virus (ZIKV) and the four serotypes of dengue virus (DENV1-DENV4). Here we describe a comparative ...The human monoclonal antibody C10 exhibits extraordinary cross-reactivity, potently neutralizing Zika virus (ZIKV) and the four serotypes of dengue virus (DENV1-DENV4). Here we describe a comparative structure-function analysis of C10 bound to the envelope (E) protein dimers of the five viruses it neutralizes. We demonstrate that the C10 Fab has high affinity for ZIKV and DENV1 but not for DENV2, DENV3, and DENV4. We further show that the C10 interaction with the latter viruses requires an E protein conformational landscape that limits binding to only one of the three independent epitopes per virion. This limited affinity is nevertheless counterbalanced by the particle's icosahedral organization, which allows two different dimers to be reached by both Fab arms of a C10 immunoglobulin. The epitopes' geometric distribution thus confers C10 its exceptional neutralization breadth. Our results highlight the importance not only of paratope/epitope complementarity but also the topological distribution for epitope-focused vaccine design.
External linksCell / PubMed:34852239 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.1 - 3.6 Å
Structure data

30465

7cth

EMDB-30465, PDB-7cth:
Cryo-EM structure of dengue virus serotype 2 in complex with the scFv fragment of the broadly neutralizing antibody EDE1 C10
Method: EM (single particle) / Resolution: 3.5 Å

PDB-7a3n:
Crystal structure of Zika virus envelope glycoprotein in complex with the Fab fragment of the broadly neutralizing human antibody EDE1 C10
Method: X-RAY DIFFRACTION / Resolution: 2.1 Å

PDB-7a3o:
Crystal structure of dengue 1 virus envelope glycoprotein in complex with the scFv fragment of the broadly neutralizing human antibody EDE1 C10
Method: X-RAY DIFFRACTION / Resolution: 2.8 Å

PDB-7a3p:
Crystal structure of dengue 3 virus envelope glycoprotein in complex with the scFv fragment of the broadly neutralizing human antibody EDE1 C10
Method: X-RAY DIFFRACTION / Resolution: 3.19 Å

PDB-7a3q:
Crystal structure of dengue 4 virus envelope glycoprotein in complex with the scFv fragment of the broadly neutralizing human antibody EDE1 C10
Method: X-RAY DIFFRACTION / Resolution: 2.7 Å

PDB-7a3r:
Crystal structure of dengue 1 virus envelope glycoprotein
Method: X-RAY DIFFRACTION / Resolution: 3.6 Å

PDB-7a3s:
Crystal structure of dengue 3 virus envelope glycoprotein
Method: X-RAY DIFFRACTION / Resolution: 2.8 Å

PDB-7a3t:
Crystal structure of dengue 3 virus envelope glycoprotein in complex with the Fab fragment of the broadly neutralizing human antibody EDE1 C8
Method: X-RAY DIFFRACTION / Resolution: 2.65 Å

PDB-7a3u:
Crystal structure of Zika virus envelope glycoprotein in complex with the divalent F(ab')2 fragment of the broadly neutralizing human antibody EDE1 C10
Method: X-RAY DIFFRACTION / Resolution: 3 Å

Chemicals

ChemComp-CA:
Unknown entry

ChemComp-HOH:
WATER

ChemComp-GOL:
GLYCEROL

ChemComp-SO4:
SULFATE ION

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

ChemComp-3CX:
(2S)-3-(cyclohexylamino)-2-hydroxypropane-1-sulfonic acid

Source
  • dengue virus 2
  • homo sapiens (human)
  • zika virus
  • dengue virus 1
  • dengue virus 3
  • dengue virus 4
  • dengue virus 3 philippines/h87/1956
KeywordsVIRAL PROTEIN / FLAVIVIRUS / CLASS 2 FUSION PROTEIN / ANTIBODY / Fab / IMMUNOCOMPLEX / ZIKA / broadly neutralising antibody / DENGUE / F(ab')2 / VIRUS / Dengue virus / broadly neutralizing

+
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