[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

TitleStructural and functional evaluation of de novo-designed, two-component nanoparticle carriers for HIV Env trimer immunogens.
Journal, issue, pagesPLoS Pathog, Vol. 16, Issue 8, Page e1008665, Year 2020
Publish dateAug 11, 2020
AuthorsAleksandar Antanasijevic / George Ueda / Philip J M Brouwer / Jeffrey Copps / Deli Huang / Joel D Allen / Christopher A Cottrell / Anila Yasmeen / Leigh M Sewall / Ilja Bontjer / Thomas J Ketas / Hannah L Turner / Zachary T Berndsen / David C Montefiori / Per Johan Klasse / Max Crispin / David Nemazee / John P Moore / Rogier W Sanders / Neil P King / David Baker / Andrew B Ward /
PubMed AbstractTwo-component, self-assembling nanoparticles represent a versatile platform for multivalent presentation of viral antigens. Computational design of protein nanoparticles with differing sizes and ...Two-component, self-assembling nanoparticles represent a versatile platform for multivalent presentation of viral antigens. Computational design of protein nanoparticles with differing sizes and geometries enables combination with antigens of choice to test novel multimerization concepts in immunization strategies where the goal is to improve the induction and maturation of neutralizing antibody lineages. Here, we describe detailed antigenic, structural, and functional characterization of computationally designed tetrahedral, octahedral, and icosahedral nanoparticle immunogens displaying trimeric HIV envelope glycoprotein (Env) ectodomains. Env trimers, based on subtype A (BG505) or consensus group M (ConM) sequences and engineered with SOSIP stabilizing mutations, were fused to an underlying trimeric building block of each nanoparticle. Initial screening yielded one icosahedral and two tetrahedral nanoparticle candidates, capable of presenting twenty or four copies of the Env trimer. A number of analyses, including detailed structural characterization by cryo-EM, demonstrated that the nanoparticle immunogens possessed the intended structural and antigenic properties. When the immunogenicity of ConM-SOSIP trimers presented on a two-component tetrahedral nanoparticle or as soluble proteins were compared in rabbits, the two immunogens elicited similar serum antibody binding titers against the trimer component. Neutralizing antibody titers were slightly elevated in the animals given the nanoparticle immunogen and were initially more focused to the trimer apex. Altogether, our findings indicate that tetrahedral nanoparticles can be successfully applied for presentation of HIV Env trimer immunogens; however, the optimal implementation to different immunization strategies remains to be determined.
External linksPLoS Pathog / PubMed:32780770 / PubMed Central
MethodsEM (single particle)
Resolution4.14 - 19.68 Å
Structure data

EMDB-21175:
EM-Based Polyclonal Epitope Mapping. ConM-SOSIP Complexed with Purified Polyclonal Fab (Grp 1, ID r2381 Wk4)
Method: EM (single particle) / Resolution: 17.24 Å

EMDB-21176:
EM-Based Polyclonal Epitope Mapping. ConM-SOSIP Complexed with Purified Polyclonal Fab (Grp 1, ID r2382, Wk4)
Method: EM (single particle) / Resolution: 16.52 Å

EMDB-21177:
EM-Based Polyclonal Epitope Mapping. ConM-SOSIP Complexed with Purified Polyclonal Fab (Grp 2, ID r2383 Wk4)
Method: EM (single particle) / Resolution: 17.23 Å

EMDB-21178:
EM-Based Polyclonal Epitope Mapping. ConM-SOSIP Complexed with Purified Polyclonal Fab (Grp 2, ID r2385 Wk4)
Method: EM (single particle) / Resolution: 18.02 Å

EMDB-21179:
EM-Based Polyclonal Epitope Mapping. ConM-SOSIP Complexed with Purified Polyclonal Fab (Grp 1, ID r2381 Wk22)
Method: EM (single particle) / Resolution: 17.89 Å

EMDB-21180:
EM-Based Polyclonal Epitope Mapping. ConM-SOSIP Complexed with Purified Polyclonal Fab (Grp 1, ID r2382 Wk22)
Method: EM (single particle) / Resolution: 19.68 Å

EMDB-21181:
EM-Based Polyclonal Epitope Mapping. ConM-SOSIP Complexed with Purified Polyclonal Fab (Grp 2, ID r2383 Wk22)
Method: EM (single particle) / Resolution: 17.11 Å

EMDB-21182:
EM-Based Polyclonal Epitope Mapping. ConM-SOSIP Complexed with Purified Polyclonal Fab (Grp 2, ID r2385 Wk22)
Method: EM (single particle) / Resolution: 17.11 Å

EMDB-21183:
De novo designed icosahedral nanoparticle I53_dn5 presenting BG505-SOSIP, Cryo-EM Map
Method: EM (single particle) / Resolution: 12.46 Å

EMDB-21184:
BG505-SOSIP map reconstructed by subparticle extraction and refinement from an icosahedral nanoparticle (I53_dn5)
Method: EM (single particle) / Resolution: 6.68 Å

EMDB-21185, PDB-6vfk:
De novo designed tetrahedral nanoparticle T33_dn10 displaying 4 copies of BG505-SOSIP trimer on the surface
Method: EM (single particle) / Resolution: 4.25 Å

EMDB-21186, PDB-6vfl:
BG505-SOSIP model reconstructed by subparticle extraction and refinement from a tetrahedral nanoparticle T33_dn10
Method: EM (single particle) / Resolution: 4.14 Å

Chemicals

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

Source
  • synthetic construct (others)
KeywordsDE NOVO PROTEIN / Nanoparticle / Rosetta / De novo protein design / HIV Env

+
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