25XO | pdb_000025xo

Cryo-EM structure of the Crimean-Congo hemorrhagic fever virus full-length L protein RdRP elongation complex (EC14b form)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.18 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

RNA synthesis and substrate analogue inhibition in the CCHFV polymerase.

Jia, H.Tang, B.Liu, S.Wen, X.Wu, F.Hu, X.Zhou, H.Chong, T.Lv, L.Liu, Q.Rao, G.Wei, M.Jing, X.Cao, S.Deng, F.Hu, Z.Shu, B.Gong, R.Wu, J.Wang, M.Gong, P.

(2026) Nature 

  • DOI: https://doi.org/10.1038/s41586-026-10913-w
  • Primary Citation Related Structures: 
    25XL, 25XM, 25XN, 25XO

  • PubMed Abstract: 

    The about 4,000-residue L proteins from the Nairoviridae are the largest known viral polymerases, lacking global structural information and promising nucleotide analogue inhibitors. Here we report structures of full-length Nairoviridae Crimean-Congo haemorrhagic fever virus (CCHFV) L, including a 3.0 Å resolution polymerase elongation complex that elucidates mechanisms of both early and late elongation stages. Large additions and insertions are found in all three major functional regions that contain the endonuclease RNA-dependent RNA polymerase (RdRP) and cap-binding domain of CCHFV L, extending RNA-binding paths on both sides of the RdRP active site and creating interaction networks critical for viral replication, as suggested by CCHFV minigenome assay data. Nucleotide analogues with ribose-2' modifications identical to the hepatitis C drug sofosbuvir are found to specifically and efficiently inhibit CCHFV RdRP through an immediate chain termination mechanism. Using a sofosbuvir-hepatitis C virus RdRP system as the reference, the potency of these nucleotide analogues is further demonstrated in competition assays in the presence of corresponding nucleoside triphosphates.


  • Organizational Affiliation
    • State Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.

Macromolecule Content 

  • Total Structure Weight: 489.28 kDa 
  • Atom Count: 24,541 
  • Modeled Residue Count: 3,328 
  • Deposited Residue Count: 4,101 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 4

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA-directed RNA polymerase L3,989Orthonairovirus haemorrhagiaeMutation(s): 0 
EC: 2.7.7.48 (PDB Primary Data), 3.4.19.12 (PDB Primary Data)
UniProt
Find proteins for A0A068JD44 (Orthonairovirus haemorrhagiae)
Explore A0A068JD44 
Go to UniProtKB:  A0A068JD44
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A068JD44
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (38-MER)
B, F
38synthetic construct
Sequence Annotations
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Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
RNA (5'-R(*GP*GP*AP*UP*AP*UP*AP*AP*UP*CP*AP*AP*AP*A)-3')14synthetic construct
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Reference Sequence
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Entity ID: 4
MoleculeChains LengthOrganismImage
RNA (5'-R(*UP*CP*UP*CP*AP*AP*AP*GP*AP*UP*AP*UP*CP*AP*AP*UP*CP*C)-3')18synthetic construct
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Reference Sequence
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Entity ID: 5
MoleculeChains LengthOrganismImage
RNA (5'-R(*GP*GP*GP*A)-3')4synthetic construct
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.18 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487
RECONSTRUCTIONcryoSPARCv4.6.2

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2022YFC2303300
National Natural Science Foundation of China (NSFC)China32300139

Revision History  (Full details and data files)

  • Version 1.0: 2026-08-05
    Type: Initial release
  • Version 1.1: 2026-09-09
    Changes: Data collection, Database references