[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

TitleThe step-by-step assembly mechanism of secreted flavivirus NS1 tetramer and hexamer captured at atomic resolution.
Journal, issue, pagesSci Adv, Vol. 10, Issue 18, Page eadm8275, Year 2024
Publish dateMay 3, 2024
AuthorsQi Pan / Haizhan Jiao / Wanqin Zhang / Qiang Chen / Geshu Zhang / Jianhai Yu / Wei Zhao / Hongli Hu /
PubMed AbstractFlaviviruses encode a conserved, membrane-associated nonstructural protein 1 (NS1) with replication and immune evasion functions. The current knowledge of secreted NS1 (sNS1) oligomers is based on ...Flaviviruses encode a conserved, membrane-associated nonstructural protein 1 (NS1) with replication and immune evasion functions. The current knowledge of secreted NS1 (sNS1) oligomers is based on several low-resolution structures, thus hindering the development of drugs and vaccines against flaviviruses. Here, we revealed that recombinant sNS1 from flaviviruses exists in a dynamic equilibrium of dimer-tetramer-hexamer states. Two DENV4 hexameric NS1 structures and several tetrameric NS1 structures from multiple flaviviruses were solved at atomic resolution by cryo-EM. The stacking of the tetrameric NS1 and hexameric NS1 is facilitated by the hydrophobic β-roll and connector domains. Additionally, a triacylglycerol molecule located within the central cavity may play a role in stabilizing the hexamer. Based on differentiated interactions between the dimeric NS1, two distinct hexamer models (head-to-head and side-to-side hexamer) and the step-by-step assembly mechanisms of NS1 dimer into hexamer were proposed. We believe that our study sheds light on the understanding of the NS1 oligomerization and contributes to NS1-based therapies.
External linksSci Adv / PubMed:38691607 / PubMed Central
MethodsEM (single particle)
Resolution2.9 - 3.2 Å
Structure data

EMDB-37419, PDB-8wbb:
CryoEM structure of non-structural protein 1 dimer from dengue virus type 4
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-37420, PDB-8wbc:
CryoEM structure of non-structural protein 1 tetramer from dengue virus type 4
Method: EM (single particle) / Resolution: 3.03 Å

EMDB-37421, PDB-8wbd:
CryoEM structure of non-structural protein 1 hexamer 1 from dengue virus type 4
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-37422, PDB-8wbe:
CryoEM structure of non-structural protein 1 hexamer 2 from dengue virus type 4
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-37423, PDB-8wbf:
CryoEM structure of non-structural protein 1 tetramer from ZIKA virus
Method: EM (single particle) / Resolution: 2.99 Å

EMDB-37424, PDB-8wbg:
CryoEM structure of non-structural protein 1 tetramer from ZIKA virus
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-37425, PDB-8wbh:
CryoEM structure of non-structural protein 1 tetramer from Japanese encephalitis virus
Method: EM (single particle) / Resolution: 3.2 Å

Chemicals

ChemComp-TGL:
TRISTEAROYLGLYCEROL

Source
  • dengue virus type 4
  • dengue virus 4 philippines/h241/1956
  • japanese encephalitis virus
KeywordsVIRAL PROTEIN / flavivirus / non-structural protein 1 / dimer

+
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