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 9XEC | pdb_00009xec

Crimean-Congo hemorrhagic fever virus RNA polymerase containing a 9-bp RNA product


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.98 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9XEC

This is version 1.3 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 657: 1073-1083

  • 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: 471.22 kDa 
  • Atom Count: 26,146 
  • Modeled Residue Count: 3,192 
  • Deposited Residue Count: 4,014 
  • 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 L3,945Crimean-Congo hemorrhagic fever virus strain IbAr10200Mutation(s): 0 
Gene Names: L
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 Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6TQR6
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (5'-R(*UP*UP*CP*CP*AP*AP*AP*AP*AP*AP*AP*UP*CP*GP*UP*UP*CP*CP*C)-3')19Crimean-Congo hemorrhagic fever virus strain IbAr10200
Sequence Annotations
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Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
RNA (5'-R(*GP*GP*GP*AP*UP*UP*GP*AP*UP*AP*UP*CP*UP*UP*UP*GP*AP*GP*A)-3')
C, E
19Crimean-Congo hemorrhagic fever virus strain IbAr10200
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 4
MoleculeChains LengthOrganismImage
RNA (5'-R(P*UP*CP*UP*CP*AP*AP*AP*GP*A)-3')9Crimean-Congo hemorrhagic fever virus strain IbAr10200
Sequence Annotations
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Reference Sequence
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Entity ID: 5
MoleculeChains LengthOrganismImage
RNA (5'-R(P*UP*CP*U)-3')3Crimean-Congo hemorrhagic fever virus strain IbAr10200
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2KH
(Subject of Investigation/LOI)

Query on 2KH



Download:Ideal Coordinates CCD File
K [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)

Query on ZN



Download:Ideal Coordinates CCD File
L [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MN
(Subject of Investigation/LOI)

Query on MN



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A],
I [auth A],
J [auth A]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.98 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32400116 to L.X, 82341085 to X.X

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2026-10-07
    Changes: Data collection, Database references