9XD6: RNA-directed RNA polymerase L

Crimean-Congo hemorrhagic fever virus RNA polymerase in complex with the 3' vRNA. Determined by electron microscopy at 2.74 Å resolution. Released 6 May 2026.

Method
Electron microscopy
Resolution
2.74 Å
Organism
Crimean-Congo hemorrhagic fever virus strain IbAr10200
Chains
2
Atoms
12,295
Mol. weight
454.71 kDa
Ligands
ZN
Released
6 May 2026

Explore 9XD6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9XD6 contains 84 α-helices and 46 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 84 helices, 46 β-strands

ElementResiduesLengthSheet
α-helix931-94616
β-strand94711
β-strand95311
α-helix956-96611
β-strand971-97222
α-helix974-98613
α-helix988-9969
β-strand1003-100423
α-helix1009-102315
α-helix1029-104012
α-helix1045-105612
β-strand105714
α-helix1058-10603
α-helix1077-10804
α-helix1085-10873
α-helix1105-11106
α-helix1119-113820
β-strand1143-114535
β-strand115016
β-strand1151-115225
α-helix1175-118511
α-helix1197-120711
β-strand1219-122025
α-helix1222-123312
β-strand126217
β-strand126414
α-helix1267-127711
β-strand128318
α-helix1292-12954
α-helix1298-130811
α-helix1316-132712
β-strand133018
α-helix1331-134919
β-strand1357-136266
α-helix13631
β-strand1369-137466
β-strand1382-138766
β-strand1393-140086
α-helix1402-142524
α-helix1430-14345
α-helix1437-146226
α-helix1466-148015
α-helix1488-150114
α-helix1502-15065
α-helix1508-15136
α-helix1516-15238
α-helix1525-15306
α-helix1531-15333
β-strand1536-153723
α-helix1544-15463
β-strand155017
α-helix1553-157119
α-helix1573-15808
α-helix15911
β-strand159219
α-helix15931
β-strand160019
α-helix1604-16107
α-helix1613-16153
α-helix1631-165020
β-strand1754-175522
α-helix1759-177214
α-helix1781-179111
α-helix1792-17943
α-helix1797-18048
α-helix2296-23049
α-helix2318-233417
β-strand233913
β-strand2347-2358123
α-helix2368-237811
α-helix2383-239513
β-strand2400110
α-helix2401-24033
α-helix2448-24536
α-helix2454-24585
β-strand2466110
α-helix2479-250224
β-strand2507-251153
β-strand2518-2529123
α-helix2531-255828
β-strand2568-257033
β-strand2574-2576311
β-strand2579-2581311
β-strand2586-2587211
α-helix2590-25934
α-helix2596-25994
α-helix2606-262217
β-strand2623112
α-helix2627-264418
α-helix2646-26516
α-helix2653-26564
α-helix2661-26633
α-helix2672-26743
α-helix2679-269618
α-helix27021
β-strand2703113
α-helix2751-27533
α-helix2754-276310
α-helix2765-27684
α-helix2772-278211
α-helix2802-28043
α-helix2807-28159
α-helix2819-283517
β-strand2864114
α-helix2899-290911
α-helix2946-29527
β-strand2956-2959414
β-strand2991-2993314
α-helix2994-30029
β-strand3004-3009613
β-strand3027-3031513
β-strand3037-3042613
α-helix3043-305917
α-helix3063-307210
β-strand3078-3081415
β-strand3086-3089412
α-helix3094-30996
β-strand3101116
α-helix3105-31117
α-helix3117-31215
α-helix3132-31409
α-helix3143-316220
α-helix3167-318418
α-helix31861
β-strand3187116
α-helix3188-31892
α-helix3192-31943
β-strand3196-3199412
α-helix3209-32168
β-strand3221-3224415

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
RNA-directed RNA polymerase LAprotein3945Crimean-Congo hemorrhagic fever virus strain IbAr10200Q6TQR6 (AlphaFold model)
RNA (5'-r(*gp*gp*gp*ap*up*up*gp*ap*up*ap*up*cp*up*up*up*gp*ap*gp*a)-3')CRNA19Crimean-Congo hemorrhagic fever virus strain IbAr10200
Sequence of entity 1 (A), FASTA
>9XD6_1 RNA-directed RNA polymerase L (chains A)
MDFLRSLDWTQVIAGQYVSNPRFNISDYFEIVRQPGDGNCFYHSIAELTMPNKTDHSYHY
IKRLTESAARKYYQEEPEARLVGLSLEDYLKRMLSDNEWGSTLEASMLAKEMGITIIIWT
VAASDEVEAGIKFGDGDVFTAVNLLHSGQTHFDALRILPQFETDTREALSLMDRVIAVDQ
LTSSSSDELQDYEDLALALTSAEESNRRSSLDEVTLSKKQAEILRQKASQLSKLVNKSQN
IPTRVGRVLDCMFNCKLCVEISADTLILRPESKEKIGEIMSLRQLGHKLLTRDKQIKQEF
SRMKLYVTKDLLDHLDVGGLLRAAFPGTGIERHMQLLHSEMILDICTVSLGVMLSTFLYG
SNNKNKKKFITNCLLSTALSGKKVYKVLGNLGNELLYKAPRKALATVCSALFGKQINKLQ
NCFRTISPVSLLALRNLDFDCLSVQDYNGMIENMSKLDNTDVEFNHREIADLNQLTSRLI
TLRKEKDTDLLKQWFPESDLTRRSIRNAANAEEFVISEFFKKKDIMKFISTSGRAMSAGK
IGNVLSYAHNLYLSKSSLNMTSEDISQLLIEIKRLYALQEDSEVEPIAIICDGIESNMKQ
LFAILPPDCARECEVLFDDIRNSPTHSTAWKHALRLKGTAYEGLFANCYGWQYIPEDIKP
SLTMLIQTLFPDKFEDFLDRTQLHPEFRDLTPDFSLTQKVHFKRNQIPSVENVQISIDAT
LPESVEAVPVTERKMFPLPETPLSEVHSIERIMENFTRLMHGGRLSTKKRDGDPAEQGNQ
QSITEHESSSISAFKDYGERGIVEENHMKFSGEDQLETRQLLLVEVGFQTDIDGKIRTDH
KKWKDILKLLELLGIKCSFIACADCSSTPPDRWWITEDRVRVLKNSVSFLFNKLSRNSPT
EVTDIVVGAISTQKVRSYLKAGTATKTPVSTKDVLETWEKMKEHILNRPTGLTLPTSLEQ
AMRKGLVEGVVISKEGSESCINMLKENLDRITDEFERTKFKHELTQNITTSEKMLLSWLS
EDIKSSRCGECLSNIKKAVDETANLSEKIELLAYNLQLTNHCSNCHPNGVNISNTSNVCK
RCPKIEVVSHCENKGFEDSNECLTDLDRLVRLTLPGKTEKERRVKRNVEYLIKLMMSMSG
IDCIKYPTGQLITHGRVSAKHNDGNLKDRSDDDQRLAEKIDTVRKELSESKLKDYSTYAR
GVISNSLKNLSRQGKSKCSVPRSWLEKVLFDLKVPTKDEEVLINIRNSLKARSEFVRNND
KLLIRSKEELKKCFDVQSFKLKKNKQPVPFQVDCILFKEVAAECMKRYIGTPYEGIVDTL
VSLINVLTRFTWFQEVVLYGKICETFLRCCTEFNRSGVKLVKIRHCNINLSVKLPSNKKE
NMLCCLYSGNMELLQGPFYLNRRQAVLGSSYLYIVITLYIQVLQQYRCLEVINSVSEKTL
QDIENHSMTLLEDSFREITFALEGRFEESYKIRTSRCRASGNFLNRSSRDHFISVVSGLN
LVYGFLIKDNLLANSQQQNKQLQMLRFGMLAGLSRLVCPNELGKKFSTSCRRIEDNIARL
YLQTSIYCSVRDVEDNVKHWKQRDLCPEVTIPCFTVYGTFVNSDRQLIFDIYNVHIYNKE
MDNFDEGCISVLEETAERHMLWELDLMNSLCSDEKKDTRTARLLLGCPNVRKAANREGKK
LLKLNSDTSTDTQSIASEVSDRRSYSSSKSRIRSIFGRYNSQKKPFELRSGLEVFNDPFN
DYQQAITDICQFSEYTPNKESILKDCLQIIRKNPSHTMGSFELIQAISEFGMSKFPPENI
DKARRDPKNWVSISEVTETTSIVASPRTHMMLKDCFKIILGTENKKIVKMLRGKLKKLGA
ISTNIEIGKRDCLDLLSTVDGLTDQQKENIVNGIFEPSKLSFYHWKELVKKNIDEVLLTE
DGNLIFCWLKTISSSVKGSLKKRLKFMNIHSPELMPENCLFSSEEFNELIKLKKLLLNEQ
QDEQELKQDLLISSWIKCITACKDFASINDKIQKFIYHLSEELYDIRLQHLELSKLKQEH
PSVSFTKEEVLIKRLEKNFLKQHNLEIMETVNLVFFAALSAPWCLHYKALESYLVRHPEI
LDCGSKEDCKLTLLDLSVSKLLVCLYQKDDEELINSSSLKLGFLVKYVVTLFTSNGEPFS
LSLNDGGLDLDLHKTTDEKLLHQTKIVFAKIGLSGNSYDFIWTTQMIANSNFNVCKRLTG
RSTGERLPRSVRSKVIYEMVKLVGETGMAILQQLAFAQALNYEHRFYAVLAPKAQLGGAR
DLLVQETGTKVMHATTEMFSRNLLKTTSDDGLTNPHLKETILNVGLDCLANMRNLDGKPI
SEGSNLVNFYKVICISGDNTKWGPIHCCSFFSGMMQQVLKNVPDWCSFYKLTFIKNLCRQ
VEIPAGSIKKILNVLRYRLCSKGGVEQHSEEDLRRLLTDNLDSWDGNDTVKFLVTTYISK
GLMALNSYNHMGQGIHHATSSVLTSLAAVLFEELAIFYLKRSLPQTTVHVEHAGSSDDYA
KCIVVTGILSKELYSQYDETFWKHACRLKNFTAAVQRCCQMKDSAKTLVSDCFLEFYSEF
MMGYRVTPAVIKFMFTGLINSSVTSPQSLMQACQVSSQQAMYNSVPLVTNTAFTLLRQQI
FFNHVEDFIRRYGILTLGTLSPFGRLFVPTYSGLVSSAVALEDAEVIARAAQTLQMNSVS
IQSSSLTTLDSLGRSRTSSTAEDSSSVSDTTAASHDSGSSSSSFSFELNRPLSETELQFI
KALSSLKSTQACEVIQNRITGLYCNSNEGPLDRHNVIYSSRMADSCDWLKDGKRRGNLEL
ANRIQSVLCILIAGYYRSFGGEGTEKQVKASLNRDDNKIIEDPMIQLIPEKLRRELERLG
VSRMEVDELMPSISPDDTLAQLVAKKLISLNVSTEEYSAEVSRLKQTLTARNVLHGLAGG
IKELSLPIYTIFMKSYFFKDNVFLSLTDRWSTKHSTNYRDSCGKQLKGRIITKYTHWLDT
FLGCSVSINRHTTVKEPSLFNPNIRCVNLITFEDGLRELSVIQSHLKVFENEFTNLNLQF
SDPNRQKLRIVESRPAESELEANRAVIVKTKLFSATEQVRLSNNPAVVMGYLLDESAISE
VKPTKVDFSNLLKDRFKIMQFFPSVFTLIKMLTDESSDSEKSGLSPDLQQVARYSNHLTL
LSRMIQQAKPTVTVFYMLKGNLMNTEPTVAELVSYGIKEGRFFRLSDTGVDASTYSVKYW
KILHCISAIGCLPLSQADKSSLLMSFLNWRVNMDIRTSDCPLSSHEASILSEFDGQVIAN
ILASELSSVKRDSEREGLTDLLDYLNSPTELLKKKPYLGTTCKFNTWGDSNRSGKFTYSS
RSGESIGIFIAGKLHIHLSSESVALLCETERQVLSWMSKRRTEVITKEQHQLFLSLLPQS
HECLQKHKDGSALSVIPDSSNPRLLKFVPLKKGLAVVKIKKQILTVKKQVVFDAESEPRL
QWGHGCLSIVYDETDTQTTYHENLLKVKHLVDCSTDRKKLLPQSVFSDSKVVLSRIKFKT
ELLLNSLTLLHCFLKHAPSDAIMEVESKSSLLHKYLKSGGVRQRNTEVLFREKLNKVVIK
DNLEQGVEEEIEFCNNLTKTVSENPLPLSCWSEVQNYIEDIGFNNVLVNIDRNTVKSELL
WKFTLDTNVSTTSTIKDVRTLVSYVSTETIPKFLLAFLLYEEVLMNLINQCKAVKELINS
TGLSDLELESLLTLCAFYFQSECSKRDGPRCSFAALLSLIHEDWQRIGKNILVRANNELG
DVSLKVNIVLVPLKDMSKPKSERVVMARRSLNHALSLMFLDEMSLPELKSLSVNCKMGNF
EGQECFEFTILKDNSARLDYNKLIDHCVDMEKKREAVRAVEDLILMLTGRAVKPSAVTQF
VHGDEQCQEQISLDDLMANDTVTDFPDREAEALKTGNLGFNWDSD
Sequence of entity 2 (C), FASTA
>9XD6_2 RNA (5'-R(*GP*GP*GP*AP*UP*UP*GP*AP*UP*AP*UP*CP*UP*UP*UP*GP*AP*GP*A)-3') (chains C)
GGGAUUGAUAUCUUUGAGA

Ligands and cofactors

IDNameFormulaCopies
ZNZinc ionZn1

Primary citation

Structures and inhibition of the Crimean-Congo haemorrhagic fever virus polymerase. Xue, L., Gui, J., Pan, H. et al. Nature (2026). DOI 10.1038/s41586-026-10701-6 · PubMed

Other PDB entries of the same protein (UniProt Q6TQR6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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