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- PDB-25xo: Cryo-EM structure of the Crimean-Congo hemorrhagic fever virus fu... -

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Basic information

Entry
Database: PDB / ID: 25xo
TitleCryo-EM structure of the Crimean-Congo hemorrhagic fever virus full-length L protein RdRP elongation complex (EC14b form)
Components
  • RNA (38-MER)
  • RNA (5'-R(*GP*GP*AP*UP*AP*UP*AP*AP*UP*CP*AP*AP*AP*A)-3')
  • RNA (5'-R(*GP*GP*GP*A)-3')
  • RNA (5'-R(*UP*CP*UP*CP*AP*AP*AP*GP*AP*UP*AP*UP*CP*AP*AP*UP*CP*C)-3')
  • RNA-directed RNA polymerase L
KeywordsVIRAL PROTEIN/RNA / negative-strand RNA virus / Crimean-Congo hemorrhagic fever virus / RNA-dependent RNA polymerase / elongation complex / VIRAL PROTEIN-RNA complex
Function / homology
Function and homology information


protein deubiquitination / endoplasmic reticulum unfolded protein response / ERAD pathway / symbiont-mediated suppression of host ISG15-protein conjugation / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / nucleotide binding / RNA-directed RNA polymerase ...protein deubiquitination / endoplasmic reticulum unfolded protein response / ERAD pathway / symbiont-mediated suppression of host ISG15-protein conjugation / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / nucleotide binding / RNA-directed RNA polymerase / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / metal ion binding
Similarity search - Function
RNA-directed RNA polymerase, nairovirus / : / OTU-like cysteine protease / RNA-directed RNA polymerase L, N-terminal / L protein N-terminus / OTU domain / OTU domain profile. / RNA-dependent RNA polymerase, bunyaviral / Bunyavirus RNA dependent RNA polymerase / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile.
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesOrthonairovirus haemorrhagiae
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsJia, H. / Tang, B. / Gong, P.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFC2303300 China
National Natural Science Foundation of China (NSFC)32300139 China
CitationJournal: Nature / Year: 2026
Title: RNA synthesis and substrate analogue inhibition in the CCHFV polymerase.
Authors: Hengxia Jia / Bo Tang / Shunli Liu / Xin Wen / Fan Wu / Xiao Hu / Hu Zhou / Tingting Chong / Lincan Lv / Qiaojie Liu / Guibo Rao / Mingyu Wei / Xuping Jing / Sheng Cao / Fei Deng / Zhihong ...Authors: Hengxia Jia / Bo Tang / Shunli Liu / Xin Wen / Fan Wu / Xiao Hu / Hu Zhou / Tingting Chong / Lincan Lv / Qiaojie Liu / Guibo Rao / Mingyu Wei / Xuping Jing / Sheng Cao / Fei Deng / Zhihong Hu / Bo Shu / Rui Gong / Jiqin Wu / Manli Wang / Peng Gong /
Abstract: The about 4,000-residue L proteins from the Nairoviridae are the largest known viral polymerases, lacking global structural information and promising nucleotide analogue inhibitors. Here we report ...The about 4,000-residue L proteins from the Nairoviridae are the largest known viral polymerases, lacking global structural information and promising nucleotide analogue inhibitors. Here we report structures of full-length Nairoviridae Crimean-Congo haemorrhagic fever virus (CCHFV) L, including a 3.0 Å resolution polymerase elongation complex that elucidates mechanisms of both early and late elongation stages. Large additions and insertions are found in all three major functional regions that contain the endonuclease RNA-dependent RNA polymerase (RdRP) and cap-binding domain of CCHFV L, extending RNA-binding paths on both sides of the RdRP active site and creating interaction networks critical for viral replication, as suggested by CCHFV minigenome assay data. Nucleotide analogues with ribose-2' modifications identical to the hepatitis C drug sofosbuvir are found to specifically and efficiently inhibit CCHFV RdRP through an immediate chain termination mechanism. Using a sofosbuvir-hepatitis C virus RdRP system as the reference, the potency of these nucleotide analogues is further demonstrated in competition assays in the presence of corresponding nucleoside triphosphates.
History
DepositionApr 22, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 5, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2026Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update
Revision 1.1Sep 9, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: citation / em_admin / Data content type: EM metadata / EM metadata / EM metadata
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA-directed RNA polymerase L
B: RNA (38-MER)
C: RNA (5'-R(*GP*GP*AP*UP*AP*UP*AP*AP*UP*CP*AP*AP*AP*A)-3')
D: RNA (5'-R(*UP*CP*UP*CP*AP*AP*AP*GP*AP*UP*AP*UP*CP*AP*AP*UP*CP*C)-3')
E: RNA (5'-R(*GP*GP*GP*A)-3')
F: RNA (38-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)489,28212
Polymers488,9216
Non-polymers3616
Water543
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 1 types, 1 molecules A

#1: Protein RNA-directed RNA polymerase L / Large structural protein / Replicase / Transcriptase


Mass: 453202.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orthonairovirus haemorrhagiae / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: A0A068JD44, RNA-directed RNA polymerase, ubiquitinyl hydrolase 1

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RNA chain , 4 types, 5 molecules BFCDE

#2: RNA chain RNA (38-MER)


Mass: 12117.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain RNA (5'-R(*GP*GP*AP*UP*AP*UP*AP*AP*UP*CP*AP*AP*AP*A)-3')


Mass: 4502.780 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: RNA chain RNA (5'-R(*UP*CP*UP*CP*AP*AP*AP*GP*AP*UP*AP*UP*CP*AP*AP*UP*CP*C)-3')


Mass: 5661.427 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: RNA chain RNA (5'-R(*GP*GP*GP*A)-3')


Mass: 1319.866 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 9 molecules

#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Crimean-Congo hemorrhagic fever virus RNA-dependent RNA polymerase elongation complex
Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Source (natural)Organism: Orthonairovirus haemorrhagiae
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv4.6.2particle selection
9PHENIX1.20.1_4487model refinement
13cryoSPARCv4.6.23D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 84438 / Symmetry type: POINT
RefinementHighest resolution: 3.18 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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