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- EMDB-80707: Cryo-EM structure of Crimean-Congo hemorrhagic fever virus RNA po... -

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Basic information

Entry
Database: EMDB / ID: EMD-80707
TitleCryo-EM structure of Crimean-Congo hemorrhagic fever virus RNA polymerase in complex with the 5' vRNA promotor from the 5'/3' vRNA dual-promoter dataset
Map data
Sample
  • Complex: CCHFV RNA polymerase in complex with the 5' vRNA promoter
    • Protein or peptide: RNA-directed RNA polymerase L
    • RNA: 5' vRNA promoter
  • Ligand: ZINC ION
  • Ligand: MANGANESE (II) ION
  • Ligand: MAGNESIUM ION
Keywordspolymerase / RNA BINDING PROTEIN/RNA / RNA BINDING PROTEIN-RNA complex
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 / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / cysteine-type deubiquitinase activity / 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 speciesOrthonairovirus haemorrhagiae
Methodsingle particle reconstruction / cryo EM / Resolution: 3.03 Å
AuthorsMa J / Yang K / Wu H / Liu X / Liang Z
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structures of CCHFV polymerase reveal a stepwise initiation stabilization pathway and a dual-site inhibition mechanism
Authors: Yang K / Wu H / Liu X / Ma J
History
DepositionMay 4, 2026-
Header (metadata) releaseAug 19, 2026-
Map releaseAug 19, 2026-
UpdateAug 19, 2026-
Current statusAug 19, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_80707.png

Downloads & links

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Map

FileDownload / File: emd_80707.map.gz / Format: CCP4 / Size: 216 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 384 pix.
= 280.32 Å		0.73 Å/pix.
x 384 pix.
= 280.32 Å		0.73 Å/pix.
x 384 pix.
= 280.32 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.3109818 - 0.5613102
Average (Standard dev.)0.00047576646 (±0.014687777)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 280.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_80707_additional_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

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Half map: #2

Fileemd_80707_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_80707_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : CCHFV RNA polymerase in complex with the 5' vRNA promoter

EntireName: CCHFV RNA polymerase in complex with the 5' vRNA promoter
Components
  • Complex: CCHFV RNA polymerase in complex with the 5' vRNA promoter
    • Protein or peptide: RNA-directed RNA polymerase L
    • RNA: 5' vRNA promoter
  • Ligand: ZINC ION
  • Ligand: MANGANESE (II) ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: CCHFV RNA polymerase in complex with the 5' vRNA promoter

SupramoleculeName: CCHFV RNA polymerase in complex with the 5' vRNA promoter
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Orthonairovirus haemorrhagiae
Molecular weightTheoretical: 450 KDa

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Macromolecule #1: RNA-directed RNA polymerase L

MacromoleculeName: RNA-directed RNA polymerase L / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: ubiquitinyl hydrolase 1
Source (natural)Organism: Orthonairovirus haemorrhagiae
Molecular weightTheoretical: 451.547625 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDFLRSLDWT QVIAGQYVSN PRFNISDYFE IVRQPGDGNC FYHSIAELTM PNKTDHSYHY IKRLTESAAR KYYQEEPEAR LVGLSLEDY LKRMLSDNEW GSTLEASMLA KEMGITIIIW TVAASDEVEA GIKFGDGDVF TAVNLLHSGQ THFDALRILP Q FETDTREA ...String:
MDFLRSLDWT QVIAGQYVSN PRFNISDYFE IVRQPGDGNC FYHSIAELTM PNKTDHSYHY IKRLTESAAR KYYQEEPEAR LVGLSLEDY LKRMLSDNEW GSTLEASMLA KEMGITIIIW TVAASDEVEA GIKFGDGDVF TAVNLLHSGQ THFDALRILP Q FETDTREA LSLMDRVIAV DQLTSSSSDE LQDYEDLALA LTSAEESNRR SSLDEVTLSK KQAEILRQKA SQLSKLVNKS QN IPTRVGR VLDCMFNCKL CVEISADTLI LRPESKEKIG EIMSLRQLGH KLLTRDKQIK QEFSRMKLYV TKDLLDHLDV GGL LRAAFP GTGIERHMQL LHSEMILDIC TVSLGVMLST FLYGSNNKNK KKFITNCLLS TALSGKKVYK VLGNLGNELL YKAP RKALA TVCSALFGKQ INKLQNCFRT ISPVSLLALR NLDFDCLSVQ DYNGMIENMS KLDNTDVEFN HREIADLNQL TSRLI TLRK EKDTDLLKQW FPESDLTRRS IRNAANAEEF VISEFFKKKD IMKFISTSGR AMSAGKIGNV LSYAHNLYLS KSSLNM TSE DISQLLIEIK RLYALQEDSE VEPIAIICDG IESNMKQLFA ILPPDCAREC EVLFDDIRNS PTHSTAWKHA LRLKGTA YE GLFANCYGWQ YIPEDIKPSL TMLIQTLFPD KFEDFLDRTQ LHPEFRDLTP DFSLTQKVHF KRNQIPSVEN VQISIDAT L PESVEAVPVT ERKMFPLPET PLSEVHSIER IMENFTRLMH GGRLSTKKRD GDPAEQGNQQ SITEHESSSI SAFKDYGER GIVEENHMKF SGEDQLETRQ LLLVEVGFQT DIDGKIRTDH KKWKDILKLL ELLGIKCSFI ACADCSSTPP DRWWITEDRV RVLKNSVSF LFNKLSRNSP TEVTDIVVGA ISTQKVRSYL KAGTATKTPV STKDVLETWE KMKEHILNRP TGLTLPTSLE Q AMRKGLVE GVVISKEGSE SCINMLKENL DRITDEFERT KFKHELTQNI TTSEKMLLSW LSEDIKSSRC GECLSNIKKA VD ETANLSE KIELLAYNLQ LTNHCSNCHP NGVNISNTSN VCKRCPKIEV VSHCENKGFE DSNECLTDLD RLVRLTLPGK TEK ERRVKR NVEYLIKLMM SMSGIDCIKY PTGQLITHGR VSAKHNDGNL KDRSDDDQRL AEKIDTVRKE LSESKLKDYS TYAR GVISN SLKNLSRQGK SKCSVPRSWL EKVLFDLKVP TKDEEVLINI RNSLKARSEF VRNNDKLLIR SKEELKKCFD VQSFK LKKN KQPVPFQVDC ILFKEVAAEC MKRYIGTPYE GIVDTLVSLI NVLTRFTWFQ EVVLYGKICE TFLRCCTEFN RSGVKL VKI RHCNINLSVK LPSNKKENML CCLYSGNMEL LQGPFYLNRR QAVLGSSYLY IVITLYIQVL QQYRCLEVIN SVSEKTL QD IENHSMTLLE DSFREITFAL EGRFEESYKI RTSRCRASGN FLNRSSRDHF ISVVSGLNLV YGFLIKDNLL ANSQQQNK Q LQMLRFGMLA GLSRLVCPNE LGKKFSTSCR RIEDNIARLY LQTSIYCSVR DVEDNVKHWK QRDLCPEVTI PCFTVYGTF VNSDRQLIFD IYNVHIYNKE MDNFDEGCIS VLEETAERHM LWELDLMNSL CSDEKKDTRT ARLLLGCPNV RKAANREGKK LLKLNSDTS TDTQSIASEV SDRRSYSSSK SRIRSIFGRY NSQKKPFELR SGLEVFNDPF NDYQQAITDI CQFSEYTPNK E SILKDCLQ IIRKNPSHTM GSFELIQAIS EFGMSKFPPE NIDKARRDPK NWVSISEVTE TTSIVASPRT HMMLKDCFKI IL GTENKKI VKMLRGKLKK LGAISTNIEI GKRDCLDLLS TVDGLTDQQK ENIVNGIFEP SKLSFYHWKE LVKKNIDEVL LTE DGNLIF CWLKTISSSV KGSLKKRLKF MNIHSPELMP ENCLFSSEEF NELIKLKKLL LNEQQDEQEL KQDLLISSWI KCIT ACKDF ASINDKIQKF IYHLSEELYD IRLQHLELSK LKQEHPSVSF TKEEVLIKRL EKNFLKQHNL EIMETVNLVF FAALS APWC LHYKALESYL VRHPEILDCG SKEDCKLTLL DLSVSKLLVC LYQKDDEELI NSSSLKLGFL VKYVVTLFTS NGEPFS LSL NDGGLDLDLH KTTDEKLLHQ TKIVFAKIGL SGNSYDFIWT TQMIANSNFN VCKRLTGRST GERLPRSVRS KVIYEMV KL VGETGMAILQ QLAFAQALNY EHRFYAVLAP KAQLGGARDL LVQETGTKVM HATTEMFSRN LLKTTSDDGL TNPHLKET I LNVGLDCLAN MRNLDGKPIS EGSNLVNFYK VICISGDNTK WGPIHCCSFF SGMMQQVLKN VPDWCSFYKL TFIKNLCRQ VEIPAGSIKK ILNVLRYRLC SKGGVEQHSE EDLRRLLTDN LDSWDGNDTV KFLVTTYISK GLMALNSYNH MGQGIHHATS SVLTSLAAV LFEELAIFYL KRSLPQTTVH VEHAGSSDDY AKCIVVTGIL SKELYSQYDE TFWKHACRLK NFTAAVQRCC Q MKDSAKTL VSDCFLEFYS EFMMGYRVTP AVIKFMFTGL INSSVTSPQS LMQACQVSSQ QAMYNSVPLV TNTAFTLLRQ QI FFNHVED FIRRYGILTL GTLSPFGRLF VPTYSGLVSS AVALEDAEVI ARAAQTLQMN SVSIQSSSLT TLDSLGRSRT SST AEDSSS VSDTTAASHD SGSSSSSFSF ELNRPLSETE LQFIKALSSL KSTQACEVIQ NRITGLYCNS NEGPLDRHNV IYSS RMADS CDWLKDGKRR GNLELANRIQ SVLCILIAGY YRSFGGEGTE KQVKASLNRD DNKIIEDPMI QLIPEKLRRE LERLG VSRM EVDELMPSIS PDDTLAQLVA KKLISLNVST EEYSAEVSRL KQTLTARNVL HGLAGGIKEL SLPIYTIFMK SYFFKD NVF LSLTDRWSTK HSTNYRDSCG KQLKGRIITK YTHWLDTFLG CSVSINRHTT VKEPSLFNPN IRCVNLITFE DGLRELS VI QSHLKVFENE FTNLNLQFSD PNRQKLRIVE SRPAESELEA NRAVIVKTKL FSATEQVRLS NNPAVVMGYL LDESAISE V KPTKVDFSNL LKDRFKIMQF FPSVFTLIKM LTDESSDSEK SGLSPDLQQV ARYSNHLTLL SRMIQQAKPT VTVFYMLKG NLMNTEPTVA ELVSYGIKEG RFFRLSDTGV DASTYSVKYW KILHCISAIG CLPLSQADKS SLLMSFLNWR VNMDIRTSDC PLSSHEASI LSEFDGQVIA NILASELSSV KRDSEREGLT DLLDYLNSPT ELLKKKPYLG TTCKFNTWGD SNRSGKFTYS S RSGESIGI FIAGKLHIHL SSESVALLCE TERQVLSWMS KRRTEVITKE QHQLFLSLLP QSHECLQKHK DGSALSVIPD SS NPRLLKF VPLKKGLAVV KIKKQILTVK KQVVFDAESE PRLQWGHGCL SIVYDETDTQ TTYHENLLKV KHLVDCSTDR KKL LPQSVF SDSKVVLSRI KFKTELLLNS LTLLHCFLKH APSDAIMEVE SKSSLLHKYL KSGGVRQRNT EVLFREKLNK VVIK DNLEQ GVEEEIEFCN NLTKTVSENP LPLSCWSEVQ NYIEDIGFNN VLVNIDRNTV KSELLWKFTL DTNVSTTSTI KDVRT LVSY VSTETIPKFL LAFLLYEEVL MNLINQCKAV KELINSTGLS DLELESLLTL CAFYFQSECS KRDGPRCSFA ALLSLI HED WQRIGKNILV RANNELGDVS LKVNIVLVPL KDMSKPKSER VVMARRSLNH ALSLMFLDEM SLPELKSLSV NCKMGNF EG QECFEFTILK DNSARLDYNK LIDHCVDMEK KREAVRAVED LILMLTGRAV KPSAVTQFVH GDEQCQEQIS LDDLMAND T VTDFPDREAE ALKTGNLGFN WDSDWSHPQF EKGSSGGSSG SSGGAWSHPQ FEK

UniProtKB: RNA-directed RNA polymerase L

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Macromolecule #2: 5' vRNA promoter

MacromoleculeName: 5' vRNA promoter / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Orthonairovirus haemorrhagiae
Molecular weightTheoretical: 4.737857 KDa
SequenceString:
UCUCAAAGAU AUCGU

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #4: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MN
Molecular weightTheoretical: 54.938 Da

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
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 opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 33620
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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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
Output model

PDB-26ka:
Cryo-EM structure of Crimean-Congo hemorrhagic fever virus RNA polymerase in complex with the 5' vRNA promotor from the 5'/3' vRNA dual-promoter dataset

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