[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

TitleTailored design of protein nanoparticle scaffolds for multivalent presentation of viral glycoprotein antigens.
Journal, issue, pagesElife, Vol. 9, Year 2020
Publish dateAug 4, 2020
AuthorsGeorge Ueda / Aleksandar Antanasijevic / Jorge A Fallas / William Sheffler / Jeffrey Copps / Daniel Ellis / Geoffrey B Hutchinson / Adam Moyer / Anila Yasmeen / Yaroslav Tsybovsky / Young-Jun Park / Matthew J Bick / Banumathi Sankaran / Rebecca A Gillespie / Philip Jm Brouwer / Peter H Zwart / David Veesler / Masaru Kanekiyo / Barney S Graham / Rogier W Sanders / John P Moore / Per Johan Klasse / Andrew B Ward / Neil P King / David Baker /
PubMed AbstractMultivalent presentation of viral glycoproteins can substantially increase the elicitation of antigen-specific antibodies. To enable a new generation of anti-viral vaccines, we designed self- ...Multivalent presentation of viral glycoproteins can substantially increase the elicitation of antigen-specific antibodies. To enable a new generation of anti-viral vaccines, we designed self-assembling protein nanoparticles with geometries tailored to present the ectodomains of influenza, HIV, and RSV viral glycoprotein trimers. We first designed trimers tailored for antigen fusion, featuring N-terminal helices positioned to match the C termini of the viral glycoproteins. Trimers that experimentally adopted their designed configurations were incorporated as components of tetrahedral, octahedral, and icosahedral nanoparticles, which were characterized by cryo-electron microscopy and assessed for their ability to present viral glycoproteins. Electron microscopy and antibody binding experiments demonstrated that the designed nanoparticles presented antigenically intact prefusion HIV-1 Env, influenza hemagglutinin, and RSV F trimers in the predicted geometries. This work demonstrates that antigen-displaying protein nanoparticles can be designed from scratch, and provides a systematic way to investigate the influence of antigen presentation geometry on the immune response to vaccination.
External linksElife / PubMed:32748788 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.303 - 34.17 Å
Structure data

EMDB-21162:
De novo designed tetrahedral nanoparticle T33_dn2
Method: EM (single particle) / Resolution: 17.11 Å

EMDB-21163:
De novo designed tetrahedral nanoparticle T33_dn5
Method: EM (single particle) / Resolution: 19.68 Å

EMDB-21164:
De novo designed tetrahedral nanoparticle T33_dn10
Method: EM (single particle) / Resolution: 19.13 Å

EMDB-21165:
De novo designed octahedral nanoparticle O43_dn18
Method: EM (single particle) / Resolution: 16.4 Å

EMDB-21166:
De novo designed icosahedral nanoparticle I53_dn5
Method: EM (single particle) / Resolution: 18.74 Å

EMDB-21167:
BG505-SOSIP-T33_dn2A nanoparticle fusion component
Method: EM (single particle) / Resolution: 15.62 Å

EMDB-21168:
BG505-SOSIP-T33_dn2A nanoparticle fusion component in complex with VRC01-Fab
Method: EM (single particle) / Resolution: 15.62 Å

EMDB-21169:
De novo designed tetrahedral nanoparticle T33_dn2 presenting BG505-SOSIP
Method: EM (single particle) / Resolution: 34.17 Å

EMDB-21170:
Tetrahedral nanoparticle T33_dn10 presenting BG505-SOSIP
Method: EM (single particle) / Resolution: 25.67 Å

EMDB-21171:
Icosahedral Nanoparticle I53_dn5 presenting BG505-SOSIP
Method: EM (single particle) / Resolution: 23.48 Å

21172

6vfh

EMDB-21172, PDB-6vfh:
De novo designed tetrahedral nanoparticle T33_dn10
Method: EM (single particle) / Resolution: 3.86 Å

21173

6vfi

EMDB-21173, PDB-6vfi:
De novo designed octahedral nanoparticle O43_dn18
Method: EM (single particle) / Resolution: 4.54 Å

21174

6vfj

EMDB-21174, PDB-6vfj:
De novo designed icosahedral nanoparticle I53_dn5
Method: EM (single particle) / Resolution: 5.35 Å

PDB-6v8e:
Computationally designed C3-symmetric homotrimer from TPR repeat protein
Method: X-RAY DIFFRACTION / Resolution: 2.53 Å

PDB-6veh:
Computationally designed C3-symmetric homotrimer from HEAT repeat protein
Method: X-RAY DIFFRACTION / Resolution: 2.303 Å

Chemicals

ChemComp-HOH:
WATER

Source
  • synthetic construct (others)
KeywordsDE NOVO PROTEIN / designed trimers / designed nanoparticles / ribosome-binding site / designed protein / vaccine / De novo / Nanoparticle

+
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