[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 the molecular basis of receptor-initiated coxsackievirus uncoating.
Journal, issue, pagesCell Host Microbe, Vol. 29, Issue 3, Page 448-462.e5, Year 2021
Publish dateMar 10, 2021
AuthorsLongfa Xu / Qingbing Zheng / Rui Zhu / Zhichao Yin / Hai Yu / Yu Lin / Yuanyuan Wu / Maozhou He / Yang Huang / Yichao Jiang / Hui Sun / Zhenghui Zha / Hongwei Yang / Qiongzi Huang / Dongqing Zhang / Zhenqin Chen / Xiangzhong Ye / Jinle Han / Lisheng Yang / Che Liu / Yuqiong Que / Mujin Fang / Ying Gu / Jun Zhang / Wenxin Luo / Z Hong Zhou / Shaowei Li / Tong Cheng / Ningshao Xia /
PubMed AbstractEnterovirus uncoating receptors bind at the surface depression ("canyon") that encircles each capsid vertex causing the release of a host-derived lipid called "pocket factor" that is buried in a ...Enterovirus uncoating receptors bind at the surface depression ("canyon") that encircles each capsid vertex causing the release of a host-derived lipid called "pocket factor" that is buried in a hydrophobic pocket formed by the major viral capsid protein, VP1. Coxsackievirus and adenovirus receptor (CAR) is a universal uncoating receptor of group B coxsackieviruses (CVB). Here, we present five high-resolution cryoEM structures of CVB representing different stages of virus infection. Structural comparisons show that the CAR penetrates deeper into the canyon than other uncoating receptors, leading to a cascade of events: collapse of the VP1 hydrophobic pocket, high-efficiency release of the pocket factor and viral uncoating and genome release under neutral pH, as compared with low pH. Furthermore, we identified a potent therapeutic antibody that can neutralize viral infection by interfering with virion-CAR interactions, destabilizing the capsid and inducing virion disruption. Together, these results define the structural basis of CVB cell entry and antibody neutralization.
External linksCell Host Microbe / PubMed:33539764 / PubMed Central
MethodsEM (single particle)
Resolution3.2 - 3.8 Å
Structure data

30805

7dpf

EMDB-30805, PDB-7dpf:
Cryo-EM structure of Coxsackievirus B1 mature virion
Method: EM (single particle) / Resolution: 3.2 Å

30806

7dpg

EMDB-30806, PDB-7dpg:
Cryo-EM structure of Coxsackievirus B1 empty particle
Method: EM (single particle) / Resolution: 3.4 Å

30812

7dpz

EMDB-30812, PDB-7dpz:
Cryo-EM structure of Coxsackievirus B1 virion in complex with CAR
Method: EM (single particle) / Resolution: 3.8 Å

30813

7dq1

EMDB-30813, PDB-7dq1:
Cryo-EM structure of Coxsackievirus B1 virion in complex with CAR at physiological temperature
Method: EM (single particle) / Resolution: 3.6 Å

30814

7dq4

EMDB-30814, PDB-7dq4:
Cryo-EM structure of CAR triggered Coxsackievirus B1 A-particle
Method: EM (single particle) / Resolution: 3.8 Å

30815

7dq7

EMDB-30815, PDB-7dq7:
Cryo-EM structure of Coxsackievirus B1 mature virion in complex with nAb 5F5
Method: EM (single particle) / Resolution: 3.2 Å

Chemicals

ChemComp-PLM:
PALMITIC ACID / Palmitic acid

Source
  • coxsackievirus b1
  • Human (human)
  • mus musculus (house mouse)
  • homo sapiens (human)
KeywordsVIRUS / Coxsackievirus B1 / mature virion / Cryo-EM / empty particle / CAR / A-particle / VIRUS/IMMUNE SYSTEM / neutralizing antibody / 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