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- EMDB-80450: Cryo-EM structure of the Crimean-Congo hemorrhagic fever virus fu... -

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Basic information

Entry
Database: EMDB / ID: EMD-80450
TitleCryo-EM structure of the Crimean-Congo hemorrhagic fever virus full-length L protein RdRP elongation complex (EC14b form)
Map data
Sample
  • Complex: Crimean-Congo hemorrhagic fever virus RNA-dependent RNA polymerase elongation complex
    • Protein or peptide: RNA-directed RNA polymerase L
    • RNA: RNA (38-MER)
    • RNA: RNA (5'-R(*GP*GP*AP*UP*AP*UP*AP*AP*UP*CP*AP*AP*AP*A)-3')
    • RNA: RNA (5'-R(*UP*CP*UP*CP*AP*AP*AP*GP*AP*UP*AP*UP*CP*AP*AP*UP*CP*C)-3')
    • RNA: RNA (5'-R(*GP*GP*GP*A)-3')
  • Ligand: ZINC ION
  • Ligand: MANGANESE (II) ION
  • Ligand: water
Keywordsnegative-strand RNA virus / Crimean-Congo hemorrhagic fever virus / RNA-dependent RNA polymerase / elongation complex / VIRAL PROTEIN/RNA / 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-directed RNA polymerase L
Similarity search - Component
Biological speciesOrthonairovirus haemorrhagiae / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsJia H / Tang B / Gong P
Funding support China, 2 items
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, 2026-
Header (metadata) releaseAug 5, 2026-
Map releaseAug 5, 2026-
UpdateAug 5, 2026-
Current statusAug 5, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_80450.png

Downloads & links

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Map

FileDownload / File: emd_80450.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 360 pix.
= 342. Å		0.95 Å/pix.
x 360 pix.
= 342. Å		0.95 Å/pix.
x 360 pix.
= 342. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.105
Minimum - Maximum-0.28533658 - 0.64496005
Average (Standard dev.)0.0003932234 (±0.019707425)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 342.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_80450_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_80450_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 : Crimean-Congo hemorrhagic fever virus RNA-dependent RNA polymeras...

EntireName: Crimean-Congo hemorrhagic fever virus RNA-dependent RNA polymerase elongation complex
Components
  • Complex: Crimean-Congo hemorrhagic fever virus RNA-dependent RNA polymerase elongation complex
    • Protein or peptide: RNA-directed RNA polymerase L
    • RNA: RNA (38-MER)
    • RNA: RNA (5'-R(*GP*GP*AP*UP*AP*UP*AP*AP*UP*CP*AP*AP*AP*A)-3')
    • RNA: RNA (5'-R(*UP*CP*UP*CP*AP*AP*AP*GP*AP*UP*AP*UP*CP*AP*AP*UP*CP*C)-3')
    • RNA: RNA (5'-R(*GP*GP*GP*A)-3')
  • Ligand: ZINC ION
  • Ligand: MANGANESE (II) ION
  • Ligand: water

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Supramolecule #1: Crimean-Congo hemorrhagic fever virus RNA-dependent RNA polymeras...

SupramoleculeName: Crimean-Congo hemorrhagic fever virus RNA-dependent RNA polymerase elongation complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Orthonairovirus haemorrhagiae

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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: RNA-directed RNA polymerase
Source (natural)Organism: Orthonairovirus haemorrhagiae
Molecular weightTheoretical: 453.202312 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MWSHPQFEKG GGSGGGSGGG SWSHPQFEKG SSSHHHHHHH HGSSSNFLRN LDWTQVIAGQ YVSNPRFNIS DYFEIVRQPG DGNCFYHSI AELTMPNKTD HSYHNIKRLT ESAARKYYQE EPEAGLVGLS LEDYLKRMLS DNEWGSTLEA SMLAKEMGIT I IIWTVAAS ...String:
MWSHPQFEKG GGSGGGSGGG SWSHPQFEKG SSSHHHHHHH HGSSSNFLRN LDWTQVIAGQ YVSNPRFNIS DYFEIVRQPG DGNCFYHSI AELTMPNKTD HSYHNIKRLT ESAARKYYQE EPEAGLVGLS LEDYLKRMLS DNEWGSTLEA SMLAKEMGIT I IIWTVAAS DEVEAGIKFG DGDVFTAVNL LHSGQTHFDA LRILPQFEAD TRETLSLMDR VIAVDQLTSS SSDELQDYED LA LALTSAE ESYRRSSLDE VTLSKKQAEI LRQKASQLSK LVNKSQNIPT RVGRVLDCMF NCKLCVEISA DTLILRPESK EKI GEIMSL RQLGHKLLTR DKQIKQEFSR MKLYVTKDLL DHLDVGGLLR AAFPGTGIER HMQLLHSEMI LDICTVSLGV MLST FLYGS NNKNKKKFIT NCLLSTALSG KKVYKVLGNL GNELLYKAPR KALATVCSAL FGKQINKLQN CFRTISPVSL LALRN LDFD CLSVQDYNGM IENMSKLDNT DVEFNHREIA DLNQLTSRLI TLRKEKDTDL LKQWFPESDL TRRSTRNAAN AEEFVI SEF FKKKDIMKFI STSGRAMSAG KIGNVLSYAH NLYLSKSSLN MTSEDISQLL IEIKRLYALQ EDSEVEPIAI ICDGIES NM KQLFAILPPD CARECEVLFD DIRNSPTHST AWKHALRLKG TAYEGLFANC YGWQYIPEDI KPSLTMLIQT LFPDKFED F LDRTQLHPEF RDLTPDFSLT QKVHFKRNQI PSVENVQISI DATLPESVEA VPVTERKMFP LPETPLSEVH SIERIMENF TRLMHGGKLS AKKKDGDPAG QDSQQSTTEH ESTSISAFKD YGERGIVEEN HMRFSEEDQL ETRQLLLVEV GFQTDIDGKI RTDHKKWKD ILKLLELLGI KCSFIACADC SSTPPDRWWI SEDRVRVLKN SVSFLFNKLS RNSPTEVTDI VVGAISTQKV R SYLKAGTA TKTPVSTKDV LETWEKMKEH ILNRPTGLTL PTSLEQAMRK GLVEGVVISK EGSESCINML KENLDRITDE FE RTKFKHE LTQNITTSEK MLLSWLSEDI KSSRCGECLS SIKKTVDETA NLSEKIELLA YNLQLTNHCS NCHPNGLNIS NTS NVCKRC PKIEVVSHCE NKGFEDSNEC LTDLDRLVRL TLPGKTEKER RVKRNVEYLI KLMMSMSGID CIKYPTGQLI THGR VSAKH NDGNLKDRSD DDQRLAEKID AVRKELSESK LKDYSTYAKG VISNSLKNLS RQGKSKCSVP RSWLEKILFD LKVPT RDEE VLINIRNSLK ARSEFVRNND KLLIRSKEEL KKCFDVQSFK LKKNKQPVPF QVDCILFKEV AAECMKRYIG TPYEGI VDT LVSLINVLTR FTWFQEVVLY GKICETFLRC CTEFNRSGVK LVKIRHCDIN LSVKLPSNKK ENMLCCLYSS NMELLQG PF YLNRRQAVLG SSYLYIVITL YIQVLQQYRC LEVINSVNEK TLQDVENHSM TLLEDSFKEI TFALEGRFEE SYKIRTSR C RASGNFLNRS SRDHFISVVS GLNLVYGFLI KDNLLANSQQ QNKQLQMLRF GMLAGLSRLV CPNELGKKFS TSCRRIEDN IARLYLQTSI YCSVRDVEDN VKHWKQRDLC PEVTIPCFTV YGTFVNSDRQ LIFDIYNVHI YNKEMDNFDE GCISVLEETA ERHMLWELD LMNSLCSDEK RDTRTARLLL GCPNVRKAAN REGKKLLKLN SETSTDTQSI ASEVSDRRSY SSSKSRIRSI F GRYNSQKK PFELRSGLEV FNDPFNDYQQ AITDICQFSE YTPNKESILK DCLQIIRKNP SHTMGSFELI QAISEFGMSK FP PENIDKA RRDPKNWVSI SEVTETTSIV ASPRTHMMLK DCFKIILGTE NKKIVKMLRG KLKKLGAIST NIEIGKRDCL DLL STVDGL TDQQKENIVN GIFEPSKLSF YHWKELVRKN IDEVLLTEDG NLIFCWLKTI SSSVKGSLKK RLKFMNVHSP ELMP ENCLF SSEEFNELIK LKRLLLNEQQ DEQELKQDLL ISSWIKCITA CKDFASINDK IQKFIYHLSE ELYDIRLQHL ELSKL KQEH PSVSFTKEEV LIKRLEKNFL KQHNLEIMET VNLIFFAALS APWCLHYKAL ESYLVRHPEI LDCGSKEDCK LTLLDL SVS KLLVCLYQKD DEELTNSSSL KLGFLVKYAV TLFTSNGEPF SLSLNDGGLD LDLHKTTDEK LLHQTKIVFA KIGLSGN SY DFIWTTQMIA NSNFNVCKRL TGRSTGERLP RSVRSKVIYE MVKLVGETGM AILQQLAFAQ ALNYEHRFYA VLAPKAQL G GARDLLVQET GTKVMHATTE MFSRNLLKTT SDDGLTNPHL KETILNVGLD CLANMRNLDG KPISEGSNLV NFYKVICIS GDNTKWGPIH CCSFFSGMMQ QVLKNVPDWC SFYKLTFIKN LCRQVEIPAG SIKKILNVLR YRLCSKGGVE QHSEEDLRRL LTDNLDSWD GNDTVKFLVT TYISKGLMAL NSYNHMGQGI HHATSSVLTS LAAVLFEELA IFYLKRSLPQ TTVHVEHAGS S DDYAKCIV VTGILSKELY SQYDETFWKH ACRLKNFTAA VQRCCQMKDS AKTLVSDCFL EFYSEFMMGY RVTPAVIKFM FT GLINSSV TSPQSLMQAC QVSSQQAMYN SVPLVTNTAF TLLRQQIFFN HVEDFIRRYG ILTLGTLSPF GRLFVPTYSG LVS SAVALE DAEVIARAAQ TLQMNSVSIQ SSSLTTLDSL GRCRTSSTAE DSSSVSDTTA ASHDSGSSSS SFSFELNRPL SETE LQFIK ALSSLKSTQA CEVIQNRITG LYCNSNEGPL DRHNVIYSSR MADSCDWLKD GKRRGNLELA NRIQSVLCIL IAGYY RSFG GEGTEKQVKA SLNRDDNKII EDPMIQLIPE KLRRELERLG VSRMEVDELM PSISPDDTLA QLVAKKLISL NVSTEE YSA EVSRLKQTLT ARNVLHGLAG GIKELSLPIY TIFMKSYFFK DNVFLSLTDR WSTKHSTNYR DSCGKQLTGR IITKYTH WL DTFLGCSVSI NRHTTVKEPS LFNPNIRCVN LITFEDGLRE LSVIQSHLKV FENEFTNLNL QFSDPNRQKL RIVESRPA E SELEANRAVI VKTKLFSATE QVRLSNNPAV VMGYLLDESA ISEVKPTKVD FSNLLKDRFK IMQFFPSVFT LIKMLTDES SDSEKNGLSP DLQQVARYSN HLTLLSRMIQ QAKPTVTVFY MLKGNLMNTE PTVAELVSYG IKEGRFYRLS DTGIDASTYS VKYWKILHC ISAIGCLPLS QADKSSLLMS FLNWRVNMDI RTSDCPLSSH EASILSEFDG QVIANILASE LSSVKRDSER E GLTDLLDY LNSPTELLKK KPYLGTTCKF NTWGDSNRSG KFTYSSRSGE SIGIFIAGKL HIHLSSESVA LLCETERQVL SW MSKRRTE VITKEQHQLF LSLLPQSHEC LQKHKDGSAL SVIPDGSNPR LLKFVPLKKG LAVVKIKKQI LTVKKQVVFD AES EPRLQW GHGCLSIVYD ETDTQTTYHE NLLKVKHLVD CSTDRKKLLP QSVFSDSKVV LSRIKFKTEL LLNSLTLLHC FLKH APSDA IMEVESKSSL LHKYLKSGGV RQRNTEVLFR EKLNKVVIKD NLEQGVEEEI EFCNNLTKTV SENPLPLSCW SEVQN YIED IGFNNVLVNI DRNTVKSELL WKFTLDTNVS TTSTIKDVRT LVSYVSTETI PKFLLAFLLY EEVLMNLINQ CKAVKE LIN STGLSDFELE SLLTLCAFYF QNECSKRDGP RCSFAALLSL VHEDWQRIGK NILVRANNEL GDVSLKVNIV LVPLKDM SK PKPERVVMAR RSLNHALSLM FLDEMSLPEL KSLSVNCKMG NFEGQECFEF TILKDNSARL DYNKLIDHCV DMEKKREA V RAVEDLILML TGKAIKPSAV TQFVHEDEQC QEQISLDDLM ANDTVTDLPD REAEALRTGN LGFNWDSD

UniProtKB: RNA-directed RNA polymerase L

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Macromolecule #2: RNA (38-MER)

MacromoleculeName: RNA (38-MER) / type: rna / ID: 2 / Number of copies: 2
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 12.117196 KDa
SequenceString:
GGGAGAUGAA AAUCUCCAAC UUUUGAUUAU AUCCUUAA

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

MacromoleculeName: RNA (5'-R(*GP*GP*AP*UP*AP*UP*AP*AP*UP*CP*AP*AP*AP*A)-3')
type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 4.50278 KDa
SequenceString:
GGAUAUAAUC AAAA

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Macromolecule #4: RNA (5'-R(*UP*CP*UP*CP*AP*AP*AP*GP*AP*UP*AP*UP*CP*AP*AP*UP*CP*C)-3')

MacromoleculeName: RNA (5'-R(*UP*CP*UP*CP*AP*AP*AP*GP*AP*UP*AP*UP*CP*AP*AP*UP*CP*C)-3')
type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 5.661427 KDa
SequenceString:
UCUCAAAGAU AUCAAUCC

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Macromolecule #5: RNA (5'-R(*GP*GP*GP*A)-3')

MacromoleculeName: RNA (5'-R(*GP*GP*GP*A)-3') / type: rna / ID: 5 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 1.319866 KDa
SequenceString:
GGGA

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Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 3 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #7: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 7 / Number of copies: 3 / Formula: MN
Molecular weightTheoretical: 54.938 Da

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Macromolecule #8: water

MacromoleculeName: water / type: ligand / ID: 8 / Number of copies: 3 / 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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 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: 0.5 µm

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.6.2) / Number images used: 84438
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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