9XF9 | pdb_00009xf9

Crystal structure of Kasokero virus cap- snatching endonuclease in complex with WXS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.214 (Depositor), 0.214 (DCC) 
  • R-Value Work: 
    0.179 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 
    0.180 (Depositor) 

Starting Model: in silico
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Structures and inhibition of the Crimean-Congo haemorrhagic fever virus polymerase.

Xue, L.Gui, J.Pan, H.Wu, F.Gao, S.Kuang, W.Chang, T.Li, Z.Zou, B.Zhao, H.Li, M.Zhou, M.Yuan, H.Rong, L.Gong, P.He, J.Deng, Z.Wang, M.Zhan, P.Chen, X.Xiong, X.

(2026) Nature 

  • DOI: https://doi.org/10.1038/s41586-026-10701-6
  • Primary Citation Related Structures: 
    9XD4, 9XD5, 9XD6, 9XE6, 9XE7, 9XE9, 9XEC, 9XF9

  • PubMed Abstract: 

    Crimean-Congo haemorrhagic fever virus (CCHFV) is a tick-borne virus and causes severe, often fatal, human infections. Lacking licensed vaccines or drugs, CCHFV is a World Health Organization priority pathogen requiring urgent development of medical countermeasures 1,2 . The CCHFV Large (L) protein functions as the viral RNA-dependent RNA polymerase CCHFV-L, representing a promising antiviral target, and is among the largest viral polymerases in the order Bunyavirales. Here we define the cofactors required for CCHFV-L RNA synthesis in vitro, enabling capture and determination of elongating CCHFV-L-RNA complex structures. The structures show a markedly enlarged polymerase architecture, revealing that CCHFV-L RNA synthesis is accompanied by ordering of the polymerase peripheral domains. We also define how the baloxavir-derived experimental drug WXSH0208 (ref. 3 ) and the nucleoside analogue 2'-deoxy-2'-fluorocytidine 4,5 , which has nanomolar cellular potency, inhibit this polymerase through endonuclease inhibition and post-translocation chain termination, respectively. Together, these results should structurally guide rational optimization of inhibitors directed against CCHFV-L.


  • Organizational Affiliation
    • State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.

Macromolecule Content 

  • Total Structure Weight: 83.6 kDa 
  • Atom Count: 5,892 
  • Modeled Residue Count: 677 
  • Deposited Residue Count: 749 
  • Unique protein chains: 3

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA-directed RNA polymerase L300Kasokero virusMutation(s): 0 
EC: 2.7.7.48
UniProt
Find proteins for A0A0M5KLS1 (Kasokero virus)
Explore A0A0M5KLS1 
Go to UniProtKB:  A0A0M5KLS1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0M5KLS1
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
mAb 2E9 Fab heavy chainB [auth H]230Mus musculusMutation(s): 0 
Gene Names: Fab heavy chain
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
mAb 2E9 Fab light chainC [auth L]219Mus musculusMutation(s): 0 
Gene Names: Fab light chain
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.214 (Depositor), 0.214 (DCC) 
  • R-Value Work:  0.179 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 0.180 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.32α = 90
b = 80.6β = 93.19
c = 116.14γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2026-05-06
    Type: Initial release
  • Version 1.1: 2026-07-29
    Changes: Database references
  • Version 1.2: 2026-08-05
    Changes: Database references