9IP4 | pdb_00009ip4

Cryo-EM structure of the RNA-dependent RNA polymerase complex from Marburg virus


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.84 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Structural insights into the RNA-dependent RNA polymerase complexes from highly pathogenic Marburg and Ebola viruses.

Li, G.Du, T.Wang, J.Jie, K.Ren, Z.Zhang, X.Zhang, L.Wu, S.Ru, H.

(2025) Nat Commun 16: 3080-3080

  • DOI: https://doi.org/10.1038/s41467-025-58308-1
  • Primary Citation Related Structures: 
    9IP2, 9IP3, 9IP4

  • PubMed Abstract: 

    The Ebola and the Marburg viruses belong to the Filoviridae family, a group of filamentous, single-stranded, negative-sensed RNA viruses. Upon infection, uncontrolled propagation of the Ebola and the Marburg viruses causes severe hemorrhagic fevers with high mortality rates. The replication and transcription of viral genomes are mediated by a polymerase complex consisting of two proteins: L and its cofactor VP35. However, the molecular mechanism of filovirus RNA synthesis remains understudied due to the lack of high-resolution structures of L and VP35 complexes from these viruses. Here, we present the cryo-EM structures of the polymerase complexes for the Marburg virus and the Ebola virus at 2.7 Å and 3.1 Å resolutions respectively. Despite the similar assembly and overall structures between these two viruses, we identify virus-specific L-VP35 interactions. Our data show that intergeneric exchange of VP35 would diminish these interactions and prevent the formation of a functional chimeric polymerase complex between L protein and heterologous VP35. Additionally, we identify a contracted conformation of the Ebola virus polymerase structure, revealing the structural dynamics of the polymerase during RNA synthesis. These insights enhance our understanding of filovirus RNA synthesis mechanisms and may facilitate the development of antiviral drugs targeting filovirus polymerase.


  • Organizational Affiliation
    • Life Sciences Institute, Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang Key Laboratory of Molecular Cancer Biology, Zhejiang University, Hangzhou, China.

Macromolecule Content 

  • Total Structure Weight: 504.84 kDa 
  • Atom Count: 13,615 
  • Modeled Residue Count: 1,702 
  • Deposited Residue Count: 4,535 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA-directed RNA polymerase L,Maltose/maltodextrin-binding periplasmic protein1,851Marburg virus - Musoke, Kenya, 1980Escherichia coli K-12
This entity is chimeric
Mutation(s): 0 
EC: 2.7.7.48 (PDB Primary Data), 3.6.1 (PDB Primary Data), 2.7.7.88 (PDB Primary Data), 2.1.1.375 (PDB Primary Data)
UniProt
Find proteins for P31352 (Lake Victoria marburgvirus (strain Musoke-80))
Explore P31352 
Go to UniProtKB:  P31352
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31352
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Maltose/maltodextrin-binding periplasmic protein,Polymerase cofactor VP35
B, C, D, E
671Escherichia coli K-12Marburg virus - Musoke, Kenya, 1980
This entity is chimeric
Mutation(s): 0 
Gene Names: malEb4034JW3994VP35
UniProt
Find proteins for P35259 (Lake Victoria marburgvirus (strain Musoke-80))
Explore P35259 
Go to UniProtKB:  P35259
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35259
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.84 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32371344

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-09
    Type: Initial release
  • Version 1.1: 2025-04-16
    Changes: Data collection, Database references