25XM | pdb_000025xm

Cryo-EM structure of the Crimean-Congo hemorrhagic fever virus L protein (5'-cRNA-bound form)

PDB DOI: https://doi.org/10.2210/pdb25XM/pdb
EM Map EMD-80448: EMDB EMDataResource

Classification: VIRAL PROTEIN/RNA
Organism(s): Orthonairovirus haemorrhagiae, synthetic construct
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2026-04-22 Released: 2026-08-05
Deposition Author(s): Jia, H., Liu, S., Gong, P.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.67 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 25XM

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

Literature

RNA synthesis and substrate analog 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

Macromolecule Content

Total Structure Weight: 457.75 kDa
Atom Count: 11,860
Modeled Residue Count: 1,560
Deposited Residue Count: 4,003
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	3,989	Orthonairovirus haemorrhagiae	Mutation(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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A068JD44
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism	Image
Entity ID: 2
RNA (5'-R(UPCPUPCPAPAPAPGPAPUPAPUPCPA)-3')	B	14	synthetic construct
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] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.67 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487
RECONSTRUCTION	cryoSPARC

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-08-05

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	(2022YFC2303300)
National Natural Science Foundation of China (NSFC)	China	32300139

Revision History (Full details and data files)

Version 1.0: 2026-08-05
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.