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- EMDB-55399: Structure of Crimean Congo hemorrhagic fever virus (CCHFV) L prot... -

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Entry
Database: EMDB / ID: EMD-55399
TitleStructure of Crimean Congo hemorrhagic fever virus (CCHFV) L protein bound to 5' vRNA and nanobody 20096.
Map data
Sample
  • Complex: CCHFV-L protein bound to 5' vRNA and nanobody 20096.
    • Protein or peptide: Nanobody 20096
    • RNA: RNA (5'-R(P*UP*CP*UP*CP*AP*AP*AP*GP*AP*UP*AP*UP*A)-3')
    • Protein or peptide: RNA-directed RNA polymerase L
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: water
KeywordsRNA-dependent RNA polymerase / CCHF / CCHFV / CCHFV-L / Crimean Congo hemorrhagic fever virus / Bunyavirales / VIRAL PROTEIN
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-directed RNA polymerase L
Similarity search - Component
Biological speciesCrimean-Congo hemorrhagic fever virus strain IbAr10200 / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsKeown JR / Carrique L / Grimes JM
Funding support United Kingdom, 3 items
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 JR / Carrique L / Grimes JM
History
DepositionOct 17, 2025-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55399.png

Downloads & links

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Map

FileDownload / File: emd_55399.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 380 pix.
= 277.4 Å		0.73 Å/pix.
x 380 pix.
= 277.4 Å		0.73 Å/pix.
x 380 pix.
= 277.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.2792109 - 0.48875988
Average (Standard dev.)0.000092652444 (±0.013964884)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 277.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55399_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_55399_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_55399_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CCHFV-L protein bound to 5' vRNA and nanobody 20096.

EntireName: CCHFV-L protein bound to 5' vRNA and nanobody 20096.
Components
  • Complex: CCHFV-L protein bound to 5' vRNA and nanobody 20096.
    • Protein or peptide: Nanobody 20096
    • RNA: RNA (5'-R(P*UP*CP*UP*CP*AP*AP*AP*GP*AP*UP*AP*UP*A)-3')
    • Protein or peptide: RNA-directed RNA polymerase L
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: water

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Supramolecule #1: CCHFV-L protein bound to 5' vRNA and nanobody 20096.

SupramoleculeName: CCHFV-L protein bound to 5' vRNA and nanobody 20096. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Crimean-Congo hemorrhagic fever virus strain IbAr10200
Molecular weightTheoretical: 466 KDa

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Macromolecule #1: Nanobody 20096

MacromoleculeName: Nanobody 20096 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 14.180771 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
QVQLVESGGG LVQPGGSLRL SCAASGSIFS INAMGWYRQA PGRQRELVAA ITSGGITDYA GFVKGRFAIS RDNAKNTVYL QMNSLKPED TAVYYCNAYE LRPIQGARNY WGQGTQVTVS SHHHHHHEPE A

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Macromolecule #3: RNA-directed RNA polymerase L

MacromoleculeName: RNA-directed RNA polymerase L / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: ubiquitinyl hydrolase 1
Source (natural)Organism: Crimean-Congo hemorrhagic fever virus strain IbAr10200
Molecular weightTheoretical: 453.487 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MWSHPQFEKG GGSGGGSGGS SAWSHPQFEK HHHHHHHHEN LYFQGMDFLR SLDWTQVIAG QYVSNPRFNI SDYFEIVRQP GDGNCFYHS IAELTMPNKT DHSYHYIKRL TESAARKYYQ EEPEARLVGL SLEDYLKRML SDNEWGSTLE ASMLAKEMGI T IIIWTVAA ...String:
MWSHPQFEKG GGSGGGSGGS SAWSHPQFEK HHHHHHHHEN LYFQGMDFLR SLDWTQVIAG QYVSNPRFNI SDYFEIVRQP GDGNCFYHS IAELTMPNKT DHSYHYIKRL TESAARKYYQ EEPEARLVGL SLEDYLKRML SDNEWGSTLE ASMLAKEMGI T IIIWTVAA SDEVEAGIKF GDGDVFTAVN LLHSGQTHFD ALRILPQFET DTREALSLMD RVIAVDQLTS SSSDELQDYE DL ALALTSA EESNRRSSLD EVTLSKKQAE ILRQKASQLS KLVNKSQNIP TRVGRVLDCM FNCKLCVEIS ADTLILRPES KEK IGEIMS LRQLGHKLLT RDKQIKQEFS RMKLYVTKDL LDHLDVGGLL RAAFPGTGIE RHMQLLHSEM ILDICTVSLG VMLS TFLYG SNNKNKKKFI TNCLLSTALS GKKVYKVLGN LGNELLYKAP RKALATVCSA LFGKQINKLQ NCFRTISPVS LLALR NLDF DCLSVQDYNG MIENMSKLDN TDVEFNHREI ADLNQLTSRL ITLRKEKDTD LLKQWFPESD LTRRSIRNAA NAEEFV ISE FFKKKDIMKF ISTSGRAMSA GKIGNVLSYA HNLYLSKSSL NMTSEDISQL LIEIKRLYAL QEDSEVEPIA IICDGIE SN MKQLFAILPP DCARECEVLF DDIRNSPTHS TAWKHALRLK GTAYEGLFAN CYGWQYIPED IKPSLTMLIQ TLFPDKFE D FLDRTQLHPE FRDLTPDFSL TQKVHFKRNQ IPSVENVQIS IDATLPESVE AVPVTERKMF PLPETPLSEV HSIERIMEN FTRLMHGGRL STKKRDGDPA EQGNQQSITE HESSSISAFK DYGERGIVEE NHMKFSGEDQ LETRQLLLVE VGFQTDIDGK IRTDHKKWK DILKLLELLG IKCSFIACAD CSSTPPDRWW ITEDRVRVLK NSVSFLFNKL SRNSPTEVTD IVVGAISTQK V RSYLKAGT ATKTPVSTKD VLETWEKMKE HILNRPTGLT LPTSLEQAMR KGLVEGVVIS KEGSESCINM LKENLDRITD EF ERTKFKH ELTQNITTSE KMLLSWLSED IKSSRCGECL SNIKKAVDET ANLSGKIELL AYNLQLTNHC SNCHPNGVNI SNT SNVCKR CPKIEVVSHC ENKGFEDSNE CLTDLDRLVR LTLPGKTEKE RRVKRNVEYL IKLMMSMSGI DCIKYPTGQL ITHG RVSAK HNDGNLKDRS DDDQRLAEKI DTVRKELSES KLKDYSTYAR GVISNSLKNL SRQGKSKCSV PRSWLEKVLF DLKVP TKDE EVLINIRNSL KARSEFVRNN DKLLIRSKEE LKKCFDVQSF KLKKNKQPVP FQVDCILFKE VAAECMKRYI GTPYEG IVD TLVSLINVLT RFTWFQEVVL YGKICETFLR CCTEFNRSGV KLVKIRHCNI NLSVKLPSNK KENMLCCLYS GNMELLQ GP FYLNRRQAVL GSSYLYIVIT LYIQVLQQYR CLEVINSVSE KTLQDIENHS MTLLEDSFRE ITFALEGRFE ESYKIRTS R CRASGNFLNR SSRDHFISVV SGLNLVYGFL IKDNLLANSQ QQNKQLQMLR FGMLAGLSRL VCPNELGKKF STSCRRIED NIARLYLQTS IYCSVRDVED NVKHWKQRDL CPEVTIPCFT VYGTFVNSDR QLIFDIYNVH IYNKEMDNFD EGCISVLEET AERHMLWEL DLMNSLCSDE KKDTRPARLL LGCPNVRKAA TREGKKLLKL NSDTSTDTQS IASEVSDRRS YSSSKSRIRS I FGRYNSQK KPFELRSGLE VFNDPFNDYQ QAITDICQFS EYTPNKESIL KDCLQIIRKN PSHTMGSFEL IQAISEFGMS KF PPENIDK ARRDPKNWVS ISEVTETTSI VASPRTHMML KDCFKIILGT ENKKIVKMLR GKLKKLGAIS TNIEIGKRDC LDL LSTVDG LTDQQKENIV NGIFEPSKLS FYHWKELVKK NIDEVLLTED GNLIFCWLKT ISSSVKGSLK KRLKFMNIHS PELM PENCL FSSEEFNELI KLKKLLLNEQ QDEQELKQDL LISSWIKCIT ACKDFASIND KIQKFIYHLS EELYDIRLQH LELSK LKQE HPSVSFTKEE VLIKRLEKNF LKQHNLEIME TVNLVFFAAL SAPWCLHYKA LESYLVRHPE ILDCGSKEDC KLTLLD LSV SKLLVCLYQK DDEELINSSS LKLGFLVKYV VTLFTSNGEP FSLSLNDGGL DLDLHKTTDE KLLHQTKIVF AKIGLSG NS YDFIWTTQMI ANSNFNVCKR LTGRSTGERL PRSVRSKVIY EMVKLVGETG MAILQQLAFA QALNYEHRFY AVLAPKAQ L GGARDLLVQE TGTKVMHATT EMFSRNLLKT TSDDGLTNPH LKETILNVGL DCLANMRNLD GKPISEGSNL VNFYKVICI SGDNTKWGPI HCCSFFSGMM QQVLKNVPDW CSFYKLTFIK NLCRQVEIPA GSIKKILNVL RYRLCSKGGV EQHSEEDLRR LLTDNLDSW DGNDTVKFLV TTYISKGLMA LNSYNHMGQG IHHATSSVLT SLAAVLFEEL AIFYLKRSLP QTTVHVEHAG S SDDYAKCI VVTGILSKEL YSQYDETFWK HACRLKNFTA AVQRCCQMKD SAKTLVSDCF LEFYSEFMMG YRVTPAVIKF MF TGLINSS VTSPQSLMQA CQVSSQQAMY NSVPLVTNTA FTLLRQQIFF NHVEDFIRRY GILTLGTLSP FGRLFVPTYS GLV SSAVAL EDAEVIARAA QTLQMNSVSI QSSSLTTLDS LGRSRTSSTA EDSSSVSDTT AASHDSGSSS SSFSFELNRP LSET ELQFI KALSSLKSTQ ACEVIQNRIT GLYCNSNEGP LDRHNVIYSS RMADSCDWLK DGKRRGNLEL ANRIQSVLCI LIAGY YRSF GGEGTEKQVK ASLNRDDNKI IEDPMIQLIP EKLRRELERL GVSRMEVDEL MPSISPDDTL AQLVAKKLIS LNVSTE EYS AEVSRLKQTL TARNVLHGLA GGIKELSLPI YTIFMKSYFF KDNVFLSLTD RWSTKHSTNY RDSCGKQLKG RIITKYT HW LDTFLGCSVS INRHTTVKEP SLFNPNIRCV NLITFEDGLR ELSVIQSHLK VFENEFTNLN LQFSDPNRQK LRIVESRP A ESELEANRAV IVKTKLFSAT EQVRLSNNPA VVMGYLLDES AISEVKPTKV DFSNLLKDRF KIMQFFPSVF TLIKMLTDE SSDSEKSGLS PDLQQVARYS NHLTLLSRMI QQAKPTVTVF YMLKGNLMNT EPTVAELVSY GIKEGRFFRL SDTGVDASTY SVKYWKILH CISAIGCLPL SQADKSSLLM SFLNWRVNMD IRTSDCPLSS HEASILSEFD GQVIANILAS ELSSVKRDSE R EGLTDLLD YLNSPTELLK KKPYLGTTCK FNTWGDSNRS GKFTYSSRSG ESIGIFIAGK LHIHLSSESV ALLCETERQV LS WMSKRRT EVITKEQHQL FLSLLPQSHE CLQKHKDGSA LSVIPDSSNP RLLKFVPLKK GLAVVKIKKQ ILTVKKQVVF DAE SEPRLQ WGHGCLSIVY DETDTQTTYH ENLLKVKHLV DCSTDRKKLL PQSVFSDSKV VLSRIKFKTE LLLNSLTLLH CFLK HAPSD AIMEVESKSS LLHKYLKSGG VRQRNTEVLF REKLNKVVIK DNLEQGVEEE IEFCNNLTKT VSENPLPLSC WSEVQ NYIE DIGFNNVLVN IDRNTVKSEL LWKFTLDTNV STTSTIKDVR TLVSYVSTET IPKFLLAFLL YEEVLMNLIN QCKAVK ELI NSTGLSDLEL ESLLTLCAFY FQSECSKRDG PRCSFAALLS LIHEDWQRIG KNILVRANNE LGDVSLKVNI VLVPLKD MS KPKSERVVMA RRSLNHALSL MFLDEMSLPE LKSLSVNCKM GNFEGQECFE FTILKDNSAR LDYNKLIDHC VDMEKKRE A VRAVEDLILM LTGRAVKPSA VTQFVHGDEQ CQEQISLDDL MANDTVTDFP DREAEALKTG NLGFNWDSD

UniProtKB: RNA-directed RNA polymerase L

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Macromolecule #2: RNA (5'-R(P*UP*CP*UP*CP*AP*AP*AP*GP*AP*UP*AP*UP*A)-3')

MacromoleculeName: RNA (5'-R(P*UP*CP*UP*CP*AP*AP*AP*GP*AP*UP*AP*UP*A)-3')
type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Crimean-Congo hemorrhagic fever virus strain IbAr10200
Molecular weightTheoretical: 5.090103 KDa
SequenceString:
UCUCAAAGAU AUAGCA

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 293 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMHEPES2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid
500.0 mMNaClsodium chloride
1.0 mMDTTdithiothreitol
5.0 %GlycerolGlycerol
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.4000000000000001 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Alphafold3 model
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0) / Number images used: 52000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.0)
Final 3D classificationNumber classes: 8 / Software - Name: cryoSPARC (ver. 4.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 52.7 / Target criteria: Cross-correlation coefficient
Output model

PDB-9t0e:
Structure of Crimean Congo hemorrhagic fever virus (CCHFV) L protein bound to 5' vRNA and nanobody 20096.

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