9XD5: RNA-directed RNA polymerase L

Crimean-Congo hemorrhagic fever virus RNA polymerase in complex with the 5' vRNA. Determined by electron microscopy at 2.72 Å resolution. Released 6 May 2026.

Method
Electron microscopy
Resolution
2.72 Å
Organism
Crimean-Congo hemorrhagic fever virus strain IbAr10200
Chains
2
Atoms
12,810
Mol. weight
454.58 kDa
Ligands
ZN
Released
6 May 2026

Explore 9XD5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9XD5 contains 94 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: 94 helices, 46 β-strands

ElementResiduesLengthSheet
α-helix931-94010
α-helix943-9464
β-strand94711
β-strand95311
α-helix954-9552
α-helix956-9638
α-helix964-9685
β-strand971-97222
α-helix974-98613
α-helix988-9969
β-strand1003-100423
α-helix1007-102317
α-helix1030-104011
α-helix1045-105511
α-helix1085-10873
α-helix1105-11106
α-helix1119-113921
β-strand1143-114534
β-strand115015
β-strand1151-115334
α-helix1170-118112
α-helix1183-11864
α-helix1192-11954
α-helix1200-12034
β-strand1219-122024
α-helix1222-123110
α-helix1238-125316
β-strand126216
α-helix1267-128014
β-strand128317
α-helix1292-12954
α-helix1298-13069
α-helix1316-132712
β-strand133017
α-helix1331-135121
β-strand1357-136265
α-helix13631
β-strand1369-137465
β-strand1382-138765
β-strand1393-140085
α-helix1402-14087
α-helix1411-142515
α-helix1430-14334
α-helix1437-146226
α-helix1466-148015
α-helix1488-150114
α-helix1502-15065
α-helix1508-15114
α-helix1516-15238
α-helix1525-15295
α-helix1531-15333
β-strand1536-153723
α-helix1539-15424
α-helix1543-15464
β-strand155016
α-helix1553-156917
α-helix1573-15808
α-helix15911
β-strand159218
α-helix15931
β-strand160018
α-helix1606-16116
α-helix1613-16153
α-helix1630-164415
α-helix1662-16654
β-strand1754-175522
α-helix1759-177113
α-helix1781-179111
α-helix1797-18059
α-helix1838-185114
α-helix2296-23049
β-strand231019
α-helix2317-233418
β-strand233913
β-strand2347-2356103
α-helix2359-23602
α-helix2368-237811
α-helix2383-239614
β-strand2399-2400210
α-helix2402-24043
α-helix2405-241814
α-helix2430-24334
α-helix2436-24394
α-helix2441-24444
α-helix2448-24569
α-helix2458-24603
β-strand2466-2467210
α-helix2477-250226
β-strand2507-251153
β-strand251419
β-strand2520-2529103
α-helix2531-25399
α-helix2541-255717
β-strand2568-257033
β-strand2574-2576311
β-strand2579-2581311
β-strand2586-2587211
α-helix2590-25934
α-helix2596-25994
α-helix2608-262215
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-helix27041
α-helix2751-27533
α-helix2754-276310
α-helix2765-27684
α-helix2771-278212
α-helix2807-28159
α-helix2819-283517
β-strand2837114
β-strand2860114
β-strand2864115
α-helix2899-290911
α-helix2950-29534
β-strand2958-2960315
β-strand2990-2992315
α-helix2994-30029
β-strand3005-3009513
β-strand3028-3031413
β-strand3037-3042613
α-helix3043-305917
α-helix3063-307210
β-strand3078-3081416
β-strand3086-3089412
α-helix3095-30995
α-helix3105-31117
α-helix3117-31193
α-helix3131-314010
α-helix3143-315614
α-helix3170-318415
β-strand3196-3199412
α-helix3209-32168
β-strand3221-3224416

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
RNA-directed RNA polymerase LAprotein3945Crimean-Congo hemorrhagic fever virus strain IbAr10200Q6TQR6 (AlphaFold model)
RNA (5'-r(*up*cp*up*cp*ap*ap*ap*gp*ap*ap*ap*up*cp*gp*up*up*cp*cp*c)-3')CRNA19Crimean-Congo hemorrhagic fever virus strain IbAr10200
Sequence of entity 1 (A), FASTA
>9XD5_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
>9XD5_2 RNA (5'-R(*UP*CP*UP*CP*AP*AP*AP*GP*AP*AP*AP*UP*CP*GP*UP*UP*CP*CP*C)-3') (chains C)
UCUCAAAGAAAUCGUUCCC

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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