9XD5 | pdb_00009xd5

Crimean-Congo hemorrhagic fever virus RNA polymerase in complex with the 5' vRNA

PDB DOI: https://doi.org/10.2210/pdb9XD5/pdb
NAKB: 9XD5
EM Map EMD-66755: EMDB EMDataResource

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)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.72 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9XD5

This is version 1.0 of the entry. See complete history.

Literature

Structural basis of RNA Synthesis and Inhibition by Small-Molecules in the Crimean-Congo Hemorrhagic Fever Virus Polymerase

Xue, L., Gui, J., Pan, H., Chang, T., Xiong, X.

To be published.

Macromolecule Content

Total Structure Weight: 454.58 kDa
Atom Count: 12,810
Modeled Residue Count: 1,582
Deposited Residue Count: 3,964
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

Find similar proteins by:

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6TQR6
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism	Image
Entity ID: 2
RNA (5'-R(UPCPUPCPAPAPAPGPAPAPAPUPCPGPUPUPCPCP*C)-3')	B [auth C]	19	Crimean-Congo hemorrhagic fever virus strain IbAr10200
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.72 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

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-05-06

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2026-05-06
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.