[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

TitleCryo-EM structures reveal two distinct conformational states in a picornavirus cell entry intermediate.
Journal, issue, pagesPLoS Pathog, Vol. 16, Issue 9, Page e1008920, Year 2020
Publish dateSep 30, 2020
AuthorsPranav N M Shah / David J Filman / Krishanthi S Karunatilaka / Emma L Hesketh / Elisabetta Groppelli / Mike Strauss / James M Hogle /
PubMed AbstractThe virions of enteroviruses such as poliovirus undergo a global conformational change after binding to the cellular receptor, characterized by a 4% expansion, and by the opening of holes at the two ...The virions of enteroviruses such as poliovirus undergo a global conformational change after binding to the cellular receptor, characterized by a 4% expansion, and by the opening of holes at the two and quasi-three-fold symmetry axes of the capsid. The resultant particle is called a 135S particle or A-particle and is thought to be on the pathway to a productive infection. Previously published studies have concluded that the membrane-interactive peptides, namely VP4 and the N-terminus of VP1, are irreversibly externalized in the 135S particle. However, using established protocols to produce the 135S particle, and single particle cryo-electron microscopy methods, we have identified at least two unique states that we call the early and late 135S particle. Surprisingly, only in the "late" 135S particles have detectable levels of the VP1 N-terminus been trapped outside the capsid. Moreover, we observe a distinct density inside the capsid that can be accounted for by VP4 that remains associated with the genome. Taken together our results conclusively demonstrate that the 135S particle is not a unique conformation, but rather a family of conformations that could exist simultaneously.
External linksPLoS Pathog / PubMed:32997730 / PubMed Central
MethodsEM (single particle)
Resolution2.9 - 3.6 Å
Structure data

20275

6p9o

EMDB-20275, PDB-6p9o:
Poliovirus 135S-like expanded particle in complex with a monoclonal antibody directed against the N-terminal extension of capsid protein VP1
Method: EM (single particle) / Resolution: 2.9 Å

20276

6p9w

EMDB-20276, PDB-6p9w:
Poliovirus (Type 1 Mahoney), receptor catalysed 135S particle map
Method: EM (single particle) / Resolution: 3.2 Å

20469

6psz

EMDB-20469, PDB-6psz:
Poliovirus (Type 1 Mahoney), heat-catalysed 135S particle
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-20474:
Poliovirus Type-1 Mahoney receptor catalysed 135S particle incubated with anti-VP1 mAb for 1 hour at 37 degrees C
Method: EM (single particle) / Resolution: 3.6 Å

20546

6q0b

EMDB-20546, PDB-6q0b:
Poliovirus (Type 1 Mahoney), receptor-catalysed 135S particle incubated with anti-VP1 mAb at RT for 1 hr
Method: EM (single particle) / Resolution: 3.4 Å

Source
  • poliovirus type 1 (strain mahoney)
  • mouse (mice)
  • mus musculus (house mouse)
KeywordsVIRUS / Virus-antibody complex / poliovirus / cell-entry intermediate / expanded virus / a-particle / VIRUS/IMMUNE SYSTEM / VIRUS-IMMUNE SYSTEM complex

+
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