[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

TitleBypassing pan-enterovirus host factor PLA2G16.
Journal, issue, pagesNat Commun, Vol. 10, Issue 1, Page 3171, Year 2019
Publish dateJul 18, 2019
AuthorsJim Baggen / Yue Liu / Heyrhyoung Lyoo / Arno L W van Vliet / Maryam Wahedi / Jost W de Bruin / Richard W Roberts / Pieter Overduin / Adam Meijer / Michael G Rossmann / Hendrik Jan Thibaut / Frank J M van Kuppeveld /
PubMed AbstractEnteroviruses are a major cause of human disease. Adipose-specific phospholipase A2 (PLA2G16) was recently identified as a pan-enterovirus host factor and potential drug target. In this study, we ...Enteroviruses are a major cause of human disease. Adipose-specific phospholipase A2 (PLA2G16) was recently identified as a pan-enterovirus host factor and potential drug target. In this study, we identify a possible mechanism of PLA2G16 evasion by employing a dual glycan receptor-binding enterovirus D68 (EV-D68) strain. We previously showed that this strain does not strictly require the canonical EV-D68 receptor sialic acid. Here, we employ a haploid screen to identify sulfated glycosaminoglycans (sGAGs) as its second glycan receptor. Remarkably, engagement of sGAGs enables this virus to bypass PLA2G16. Using cryo-EM analysis, we reveal that, in contrast to sialic acid, sGAGs stimulate genome release from virions via structural changes that enlarge the putative openings for genome egress. Together, we describe an enterovirus that can bypass PLA2G16 and identify additional virion destabilization as a potential mechanism to circumvent PLA2G16.
External linksNat Commun / PubMed:31320648 / PubMed Central
MethodsEM (single particle)
Resolution2.43 - 3.56 Å
Structure data

7632

6cv1

EMDB-7632, PDB-6cv1:
CryoEM structure of human enterovirus D68 full particle (after incubation with heparin-derived hexasaccharide)
Method: EM (single particle) / Resolution: 2.76 Å

7633

6cv2

EMDB-7633, PDB-6cv2:
CryoEM structure of human enterovirus D68 full virion
Method: EM (single particle) / Resolution: 2.86 Å

7634

6cv3

EMDB-7634, PDB-6cv3:
CryoEM structure of human enterovirus D68 emptied particle
Method: EM (single particle) / Resolution: 3.56 Å

7635

6cv4

EMDB-7635, PDB-6cv4:
CryoEM structure of human enterovirus D68 emptied particle (after incubation with low molecular weight heparin)
Method: EM (single particle) / Resolution: 3.03 Å

7636

6cv5

EMDB-7636, PDB-6cv5:
CryoEM structure of human enterovirus D68 full particle (after incubation with low molecular weight heparin)
Method: EM (single particle) / Resolution: 2.79 Å

7638

6cvb

EMDB-7638, PDB-6cvb:
CryoEM structure of human enterovirus D68 in complex with 6'-sialyl-N-acetyllactosamine
Method: EM (single particle) / Resolution: 2.43 Å

Chemicals

ChemComp-HOH:
WATER

Source
  • enterovirus d68
KeywordsVIRUS / genome release / receptor

+
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