[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

TitleStructure of the Nipah virus polymerase complex.
Journal, issue, pagesEMBO J, Year 2024
Publish dateDec 30, 2024
AuthorsEsra Balıkçı / Franziska Günl / Loïc Carrique / Jeremy R Keown / Ervin Fodor / Jonathan M Grimes /
PubMed AbstractNipah virus is a highly virulent zoonotic paramyxovirus causing severe respiratory and neurological disease. Despite its lethality, there is no approved treatment for Nipah virus infection. The viral ...Nipah virus is a highly virulent zoonotic paramyxovirus causing severe respiratory and neurological disease. Despite its lethality, there is no approved treatment for Nipah virus infection. The viral polymerase complex, composed of the polymerase (L) and phosphoprotein (P), replicates and transcribes the viral RNA genome. Here, we describe structures of the Nipah virus L-P polymerase complex and the L-protein's Connecting Domain (CD). The cryo-electron microscopy L-P complex structure reveals the organization of the RNA-dependent RNA polymerase (RdRp) and polyribonucleotidyl transferase (PRNTase) domains of the L-protein, and shows how the P-protein, which forms a tetramer, interacts with the RdRp-domain of the L-protein. The crystal structure of the CD-domain alone reveals binding of three Mg ions. Modelling of this domain onto an AlphaFold 3 model of an RNA-L-P complex suggests a catalytic role for one Mg ion in mRNA capping. These findings offer insights into the structural details of the L-P polymerase complex and the molecular interactions between L-protein and P-protein, shedding light on the mechanisms of the replication machinery. This work will underpin efforts to develop antiviral drugs that target the polymerase complex of Nipah virus.
External linksEMBO J / PubMed:39739115
MethodsEM (single particle) / X-ray diffraction
Resolution1.85 - 2.75 Å
Structure data

50781

9fux

EMDB-50781, PDB-9fux:
Cryo-EM structure of the Nipah virus polymerase (L) bound to the tetrameric phosphoprotein (P)
Method: EM (single particle) / Resolution: 2.49 Å

EMDB-50805: Cryo-EM structure of the Nipah virus polymerase (L) bound to the tetrameric phosphoprotein (P)- Local map for L
Method: EM (single particle) / Resolution: 2.52 Å

EMDB-50807: Cryo-EM structure of the Nipah virus polymerase (L) bound to the tetrameric phosphoprotein (P)- Local map for P
Method: EM (single particle) / Resolution: 2.75 Å

EMDB-50808: Cryo-EM structure of the Nipah virus polymerase (L) bound to the tetrameric phosphoprotein (P) - Consensus Map
Method: EM (single particle) / Resolution: 2.49 Å

PDB-9ftf:
Crystal structure of the Connecting Domain of the Nipah virus Large protein
Method: X-RAY DIFFRACTION / Resolution: 1.85 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-HOH:
WATER

ChemComp-ZN:
Unknown entry

Source
  • henipavirus nipahense
KeywordsVIRAL PROTEIN / Nipah virus L / Connecting Domain / Polymerase / Replicase / Transcriptase

+
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