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- PDB-9t0e: Structure of Crimean Congo hemorrhagic fever virus (CCHFV) L prot... -

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Basic information

Entry
Database: PDB / ID: 9t0e
TitleStructure of Crimean Congo hemorrhagic fever virus (CCHFV) L protein bound to 5' vRNA and nanobody 20096.
Components
  • Nanobody 20096
  • RNA (5'-R(P*UP*CP*UP*CP*AP*AP*AP*GP*AP*UP*AP*UP*A)-3')
  • RNA-directed RNA polymerase L
KeywordsVIRAL PROTEIN / RNA-dependent RNA polymerase / CCHF / CCHFV / CCHFV-L / Crimean Congo hemorrhagic fever virus / Bunyavirales
Function / homology
Function and homology information


RNA-templated viral transcription / negative stranded viral RNA replication / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / protein deubiquitination / endoplasmic reticulum unfolded protein response / ERAD pathway / symbiont-mediated suppression of host ISG15-protein conjugation / Hydrolases; Acting on ester bonds / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 ...RNA-templated viral transcription / negative stranded viral RNA replication / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / protein deubiquitination / endoplasmic reticulum unfolded protein response / ERAD pathway / symbiont-mediated suppression of host ISG15-protein conjugation / Hydrolases; Acting on ester bonds / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA-directed RNA polymerase / 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 ...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. / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesLama glama (llama)
Crimean-Congo hemorrhagic fever virus strain IbAr10200
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsKeown, J.R. / Carrique, L. / Grimes, J.M.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome Trust200835/Z/16/Z United Kingdom
University of Oxford, Medical Sciences Internal Fund (MSIF)BDR00281 United Kingdom
Royal Society242315 United Kingdom
CitationJournal: To Be Published
Title: Structure of Crimean Congo hemorrhagic fever virus (CCHFV) L protein bound to 5' vRNA and nanobody 20096.
Authors: Keown, J.R. / Carrique, L. / Grimes, J.M.
History
DepositionOct 17, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 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

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Assembly

Deposited unit
C: Nanobody 20096
R: RNA (5'-R(P*UP*CP*UP*CP*AP*AP*AP*GP*AP*UP*AP*UP*A)-3')
A: RNA-directed RNA polymerase L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)472,9377
Polymers472,7583
Non-polymers1794
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Antibody / RNA chain / Protein , 3 types, 3 molecules CRA

#1: Antibody Nanobody 20096


Mass: 14180.771 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#2: RNA chain RNA (5'-R(P*UP*CP*UP*CP*AP*AP*AP*GP*AP*UP*AP*UP*A)-3')


Mass: 5090.103 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Crimean-Congo hemorrhagic fever virus strain IbAr10200
#3: Protein RNA-directed RNA polymerase L / Protein L / Large structural protein / Replicase / Transcriptase


Mass: 453487.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Crimean-Congo hemorrhagic fever virus strain IbAr10200
Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q6TQR6, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, Hydrolases; Acting on ester bonds, RNA-directed RNA polymerase

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Non-polymers , 3 types, 297 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / 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: CCHFV-L protein bound to 5' vRNA and nanobody 20096. / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 0.466 MDa / Experimental value: YES
Source (natural)Organism: Crimean-Congo hemorrhagic fever virus strain IbAr10200
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mM2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acidHEPES1
2500 mMsodium chlorideNaCl1
31 mMdithiothreitolDTT1
45 %GlycerolGlycerol1
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2600 nm / Nominal defocus min: 1400 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4particle selection
2Topaz1.5particle selection
3EPU3.7image acquisition
5cryoSPARC4CTF correction
8UCSF ChimeraX1.1model fitting
9Coot0.9.8.95model fitting
11cryoSPARC4initial Euler assignment
12cryoSPARC4final Euler assignment
13cryoSPARC4classification
14cryoSPARC43D reconstruction
15PHENIX1.19.2model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 52000 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 52.7 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 60.36 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.005314803
ELECTRON MICROSCOPYf_angle_d0.548420021
ELECTRON MICROSCOPYf_chiral_restr0.04132307
ELECTRON MICROSCOPYf_plane_restr0.00452495
ELECTRON MICROSCOPYf_dihedral_angle_d6.13442082

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