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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 / RNA-directed RNA polymerase / viral RNA genome replication ...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 / RNA-directed RNA polymerase / viral RNA genome replication / nucleotide binding / 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 analog inhibition in the CCHFV polymerase
Authors: 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.
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

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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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