9XE6: RNA-directed RNA polymerase L

Crimean-Congo hemorrhagic fever virus RNA polymerase containing a 10-bp RNA product and incorporated 2FC. Determined by electron microscopy at 3.09 Å resolution. Released 6 May 2026.

Method
Electron microscopy
Resolution
3.09 Å
Organism
Crimean-Congo hemorrhagic fever virus strain IbAr10200
Chains
6
Atoms
26,455
Mol. weight
471.91 kDa
Ligands
ZN, MN, 2KH
Released
6 May 2026

Explore 9XE6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9XE6 contains 187 α-helices and 95 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: 187 helices, 95 β-strands

ElementResiduesLengthSheet
α-helix317-3248
α-helix330-3323
α-helix339-35113
α-helix402-41110
α-helix413-42412
α-helix428-4358
β-strand43811
α-helix446-45813
α-helix467-48418
α-helix488-4936
α-helix511-52212
α-helix541-55313
α-helix565-57915
α-helix587-60317
α-helix607-62115
α-helix627-64822
α-helix656-6583
α-helix662-6698
α-helix671-6733
α-helix674-6807
α-helix685-6895
β-strand694-69742
α-helix7241
β-strand72513
α-helix7261
β-strand728-72924
α-helix737-7393
α-helix742-7432
β-strand744-74522
α-helix749-76012
β-strand801-80552
α-helix812-8165
β-strand821-82552
α-helix833-84210
α-helix845-8539
β-strand857-86262
α-helix870-8723
α-helix877-8837
α-helix884-8885
α-helix889-8968
α-helix900-91011
α-helix913-9164
α-helix931-94515
β-strand94715
α-helix9521
β-strand95315
α-helix954-9552
α-helix956-9627
α-helix963-9675
β-strand970-97234
α-helix974-98613
α-helix988-9958
β-strand1003-100426
α-helix1009-102315
α-helix1029-104113
α-helix1045-105410
α-helix1058-10603
α-helix1077-10815
α-helix1085-10873
α-helix1105-11106
α-helix1119-113719
β-strand1143-114537
β-strand115018
β-strand1151-115337
α-helix1179-11835
α-helix1197-120711
α-helix1210-12123
β-strand122017
α-helix1222-12287
α-helix1238-125316
β-strand126219
α-helix1267-128014
β-strand1283110
α-helix1292-12943
α-helix1298-130811
α-helix1316-132712
β-strand1330110
α-helix1331-134919
β-strand1357-136268
α-helix13631
β-strand1369-137468
β-strand1382-138768
β-strand1393-140088
α-helix1402-142524
α-helix1430-14334
α-helix1437-146226
α-helix1466-148015
α-helix1488-150114
α-helix1502-15065
α-helix1509-15135
α-helix1516-15238
α-helix1525-15306
β-strand1536-153726
α-helix1543-15464
β-strand155019
α-helix1553-157018
α-helix1573-15808
α-helix15911
β-strand1592111
α-helix15931
β-strand1600111
α-helix1604-16107
α-helix1613-16153
α-helix1624-165027
α-helix1660-16656
β-strand167013
β-strand1753-175534
α-helix1761-177212
α-helix1781-179111
α-helix1792-17943
α-helix1797-18048
α-helix1807-18093
β-strand1812112
α-helix1813-18153
β-strand1821-1825513
β-strand1829114
α-helix1832-185120
α-helix1869-18779
α-helix1884-189512
α-helix1905-19095
α-helix1913-19164
α-helix1923-193614
α-helix1938-19436
α-helix1944-19474
α-helix1963-197614
α-helix1988-200114
α-helix2003-20053
α-helix2008-20103
α-helix2012-20143
α-helix2016-203924
α-helix2046-206217
α-helix2064-207815
α-helix2082-20843
α-helix2118-21236
α-helix2138-215417
α-helix2158-21614
α-helix2199-220810
α-helix2212-22187
β-strand2231-2234413
α-helix2235-224612
β-strand2250112
α-helix2251-22599
β-strand2268-2272515
β-strand2281-2285515
β-strand2286113
α-helix2287-230418
β-strand231016
α-helix2317-233418
β-strand233916
β-strand2347-2357116
β-strand2359116
α-helix2362-23654
α-helix2368-237811
α-helix2383-239715
β-strand2401-2402215
α-helix2403-24042
α-helix2405-242117
α-helix2430-243910
α-helix2442-24443
α-helix2448-24569
α-helix2458-24603
β-strand2462114
β-strand2464-2465215
α-helix2478-250225
β-strand2507-251596
β-strand2518-2529126
α-helix2531-255727
α-helix25621
β-strand2563116
α-helix25641
β-strand2568-257036
β-strand2574-2576317
β-strand2579-2581317
β-strand2586-2588317
α-helix2590-25934
α-helix2596-25994
α-helix2606-262116
β-strand2623118
α-helix2627-264216
α-helix2643-26453
α-helix2646-265611
α-helix2661-26633
α-helix2671-26755
α-helix2679-269618
α-helix2751-27533
α-helix2754-276310
α-helix2771-278212
α-helix2807-28159
α-helix2817-283317
β-strand2837119
β-strand2860119
α-helix2861-28622
β-strand2864120
α-helix2870-288819
α-helix2899-29079
β-strand2914121
α-helix2917-292812
α-helix2933-29375
α-helix2945-29528
β-strand2956-2959420
β-strand2991-2993320
α-helix2994-30029
β-strand3006-3009422
β-strand3028-3031422
β-strand3037-3042622
α-helix3043-305917
α-helix3063-307210
β-strand3079-3081323
β-strand3086-3094918
α-helix3105-31139
α-helix3117-31204
β-strand3123121
α-helix3128-31303
α-helix3134-31396
α-helix3143-316220
α-helix3165-31673
α-helix3168-318619
β-strand3191-3199918
β-strand3205118
β-strand3208124
α-helix3210-32167
β-strand3221-3223323
β-strand3233124
α-helix3234-32352
α-helix3238-325013
α-helix3256-326712
β-strand3270-3271225
α-helix3273-32753
α-helix3286-32927
β-strand3296-3297225
α-helix3298-33047
α-helix3305-33084
α-helix3313-332513
α-helix3328-33336
β-strand3343-3346426
β-strand3355-3359526
β-strand3364-3369626
β-strand3374-3378526
α-helix3383-339715
α-helix3407-341610
β-strand3431-3437726
β-strand3445-3448426
β-strand3455-3459526
β-strand3466-3468327
β-strand3478-3481428
β-strand3486-3491628
β-strand3497-3499327
α-helix3504-351411
β-strand3531-3537728
α-helix3538-35392
α-helix3544-35518
α-helix3552-35565
α-helix3557-356610
α-helix3570-35789
β-strand358211
α-helix3587-35915
α-helix3607-362317
α-helix3628-36303
α-helix3631-36399
β-strand3647-3650429
β-strand3661-3664429
α-helix3678-36869
α-helix3695-36973
α-helix3701-371717
α-helix3718-37225
α-helix3725-373814
α-helix3743-37442
α-helix3755-37595
β-strand3765-3767330
β-strand3771-3773330
β-strand3776-3778331
β-strand3781-3783331
β-strand3784-3789630
α-helix3793-37953
α-helix3800-381819
β-strand3819132
α-helix3825-38306
β-strand3833-3840830
β-strand3843-3850830
β-strand3858132
α-helix3860-38656
α-helix3874-388714

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
RNA-directed RNA polymerase LAprotein3945Crimean-Congo hemorrhagic fever virus strain IbAr10200Q6TQR6 (AlphaFold model)
RNA (5'-r(*up*up*cp*cp*ap*ap*ap*ap*ap*ap*ap*up*cp*gp*up*up*cp*cp*c)-3')BRNA19Crimean-Congo hemorrhagic fever virus strain IbAr10200
RNA (5'-r(*gp*gp*gp*ap*up*up*gp*ap*ap*gp*up*cp*up*up*up*gp*ap*gp*a)-3')C, ERNA19Crimean-Congo hemorrhagic fever virus strain IbAr10200
RNA (5'-r(p*up*cp*up*cp*ap*ap*ap*gp*a)-d(p*(cfz))-3')DRNA10Crimean-Congo hemorrhagic fever virus strain IbAr10200
RNA (5'-r(p*up*cp*up*c)-3')FRNA4Crimean-Congo hemorrhagic fever virus strain IbAr10200
Sequence of entity 1 (A), FASTA
>9XE6_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 (B), FASTA
>9XE6_2 RNA (5'-R(*UP*UP*CP*CP*AP*AP*AP*AP*AP*AP*AP*UP*CP*GP*UP*UP*CP*CP*C)-3') (chains B)
UUCCAAAAAAAUCGUUCCC
Sequence of entity 3 (C, E), FASTA
>9XE6_3 RNA (5'-R(*GP*GP*GP*AP*UP*UP*GP*AP*AP*GP*UP*CP*UP*UP*UP*GP*AP*GP*A)-3') (chains C, E)
GGGAUUGAAGUCUUUGAGA
Sequence of entity 4 (D), FASTA
>9XE6_4 RNA (5'-R(P*UP*CP*UP*CP*AP*AP*AP*GP*A)-D(P*(CFZ))-3') (chains D)
UCUCAAAGAX
Sequence of entity 5 (F), FASTA
>9XE6_5 RNA (5'-R(P*UP*CP*UP*C)-3') (chains F)
UCUC

Ligands and cofactors

IDNameFormulaCopies
ZNZinc ionZn1
MNManganese (II) ionMn4
2KH5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridineC9 H16 N3 O14 P31

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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