9XE6 | pdb_00009xe6

Crimean-Congo hemorrhagic fever virus RNA polymerase containing a 10-bp RNA product and incorporated 2FC

• PDB DOI: https://doi.org/10.2210/pdb9XE6/pdb
• EM Map EMD-66783: EMDB EMDataResource
• NAKB: 9XE6

• Classification: VIRAL PROTEIN/RNA
• Organism(s): Crimean-Congo hemorrhagic fever virus strain IbAr10200
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2025-10-27 Released: 2026-05-06 
• Deposition Author(s): Xue, L., Gui, J., Pan, H., Chang, T., Xiong, X.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.09 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

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 

• PubMed: 42486991 
• 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.

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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.
The Guangdong-Hong Kong-Macao Joint Laboratory for Cell Fate Regulation and Diseases, GMU-GIBH Joint School of Life Sciences, Guangdong Provincial Key Laboratory of Protein Modification and Disease, Guangzhou Medical University, Guangzhou, China.
University of Chinese Academy of Sciences, Beijing, China.
State Key Laboratory of Virology and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.
Department of Medicinal Chemistry, State Key Laboratory of Discovery and Utilization of Functional Components in Traditional Chinese Medicine, Shandong Key Laboratory of Druggability Optimization and Evaluation for Lead Compounds, Shandong Basic Science Special Academic Zone (Pharmacy), School of Pharmaceutical Sciences, Shandong University, Jinan, China.
Guangzhou National Laboratory, Guangzhou, China.
Tianjin Cisen Pharmaceutical Research Co. Ltd, Tianjin, China.
Departments of Microbiology and Immunology, College of Medicine, University of Illinois Chicago, Chicago, IL, USA.
State Key Laboratory of Virology and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China. [e-mail].
State Key Laboratory of Virology and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China. [e-mail].
Department of Medicinal Chemistry, State Key Laboratory of Discovery and Utilization of Functional Components in Traditional Chinese Medicine, Shandong Key Laboratory of Druggability Optimization and Evaluation for Lead Compounds, Shandong Basic Science Special Academic Zone (Pharmacy), School of Pharmaceutical Sciences, Shandong University, Jinan, China. [e-mail].
Guangzhou National Laboratory, Guangzhou, China. [e-mail].
State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China. [e-mail].
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. [e-mail].
The Guangdong-Hong Kong-Macao Joint Laboratory for Cell Fate Regulation and Diseases, GMU-GIBH Joint School of Life Sciences, Guangdong Provincial Key Laboratory of Protein Modification and Disease, Guangzhou Medical University, Guangzhou, China. [e-mail].
Guangzhou National Laboratory, Guangzhou, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 471.91 kDa 
• Atom Count: 26,455 
• Modeled Residue Count: 3,226 
• Deposited Residue Count: 4,016 
• Unique protein chains: 1
• Unique nucleic acid chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-directed RNA polymerase L	A	3,945	Crimean-Congo hemorrhagic fever virus strain IbAr10200	Mutation(s): 0  EC: 3.4.19.12 (PDB Primary Data), 3.4.22 (PDB Primary Data), 3.1 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
UniProt
Find proteins for Q6TQR6 (Crimean-Congo hemorrhagic fever virus (strain Nigeria/IbAr10200/1970)) Explore Q6TQR6  Go to UniProtKB:  Q6TQR6

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*UP*UP*CP*CP*AP*AP*AP*AP*AP*AP*AP*UP*CP*GP*UP*UP*CP*CP*C)-3')	B	19	Crimean-Congo hemorrhagic fever virus strain IbAr10200

Entity ID: 3
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*GP*GP*GP*AP*UP*UP*GP*AP*AP*GP*UP*CP*UP*UP*UP*GP*AP*GP*A)-3')	C, E	19	Crimean-Congo hemorrhagic fever virus strain IbAr10200

Entity ID: 4
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*UP*CP*UP*CP*AP*AP*AP*GP*A)-D(P*(CFZ))-3')	D	10	Crimean-Congo hemorrhagic fever virus strain IbAr10200

Entity ID: 5
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*UP*CP*UP*C)-3')	F	4	Crimean-Congo hemorrhagic fever virus strain IbAr10200

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2KH (Subject of Investigation/LOI)	G [auth A]	5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine C9 H16 N3 O14 P3 OZIBFYOFLVBDIY-XVFCMESISA-N
ZN (Subject of Investigation/LOI)	L [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MN (Subject of Investigation/LOI)	H [auth A], I [auth A], J [auth A], K [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.09 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-05-06 
Deposition Author(s): Xue, L., Gui, J., Pan, H., Chang, T., Xiong, X.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32400116 to L.X, 82341085 to X.X

Revision History  

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