[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

TitleHierarchical design of pseudosymmetric protein nanocages.
Journal, issue, pagesNature, Year 2024
Publish dateDec 18, 2024
AuthorsQuinton M Dowling / Young-Jun Park / Chelsea N Fries / Neil C Gerstenmaier / Sebastian Ols / Erin C Yang / Adam J Wargacki / Annie Dosey / Yang Hsia / Rashmi Ravichandran / Carl D Walkey / Anika L Burrell / David Veesler / David Baker / Neil P King /
PubMed AbstractDiscrete protein assemblies ranging from hundreds of kilodaltons to hundreds of megadaltons in size are a ubiquitous feature of biological systems and perform highly specialized functions. Despite ...Discrete protein assemblies ranging from hundreds of kilodaltons to hundreds of megadaltons in size are a ubiquitous feature of biological systems and perform highly specialized functions. Despite remarkable recent progress in accurately designing new self-assembling proteins, the size and complexity of these assemblies has been limited by a reliance on strict symmetry. Here, inspired by the pseudosymmetry observed in bacterial microcompartments and viral capsids, we developed a hierarchical computational method for designing large pseudosymmetric self-assembling protein nanomaterials. We computationally designed pseudosymmetric heterooligomeric components and used them to create discrete, cage-like protein assemblies with icosahedral symmetry containing 240, 540 and 960 subunits. At 49, 71 and 96 nm diameter, these nanocages are the largest bounded computationally designed protein assemblies generated to date. More broadly, by moving beyond strict symmetry, our work substantially broadens the variety of self-assembling protein architectures that are accessible through design.
External linksNature / PubMed:39695230
MethodsEM (single particle)
Resolution3.1 - 14.9 Å
Structure data

EMDB-47034: Pseudosymmetric protein nanocages: GI4-F7 nanocage
Method: EM (single particle) / Resolution: 4.4 Å

47036

9dnd

EMDB-47036, PDB-9dnd:
Pseudosymmetric protein nanocage GI4 -F7 (local refinement)
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-47037: Pseudosymmetric protein nanocage GI9-F7
Method: EM (single particle) / Resolution: 6.7 Å

47038

9dne

EMDB-47038, PDB-9dne:
Pseudosymmetric protein nanocage GI9-F7 (local refinement)
Method: EM (single particle) / Resolution: 4.0 Å

EMDB-47039: Pseudosymmetric protein nanocage GI16-F7
Method: EM (single particle) / Resolution: 14.9 Å

Source
  • synthetic construct (others)
KeywordsVIRAL PROTEIN / Fusion protein / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / pseudosymmetric protein nanocages

+
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