9XE9: RNA-directed RNA polymerase L

Crimean-Congo hemorrhagic fever virus RNA polymerase containing a 15-bp RNA product. Determined by electron microscopy at 2.81 Å resolution. Released 6 May 2026.

Method
Electron microscopy
Resolution
2.81 Å
Organism
Crimean-Congo hemorrhagic fever virus strain IbAr10200
Chains
6
Atoms
25,605
Mol. weight
473.18 kDa
Ligands
ZN, 2KH, MN
Released
6 May 2026

Explore 9XE9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9XE9 contains 180 α-helices and 94 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: 180 helices, 94 β-strands

ElementResiduesLengthSheet
α-helix428-4358
α-helix448-45912
α-helix467-48418
α-helix488-4903
α-helix491-4944
α-helix511-52212
α-helix541-55313
α-helix562-57918
α-helix587-60216
α-helix607-62115
α-helix626-64823
α-helix656-6583
α-helix662-6698
α-helix671-6733
α-helix674-6807
α-helix685-6895
β-strand694-69631
α-helix7241
β-strand72512
α-helix7261
β-strand728-72923
α-helix749-76012
β-strand801-80551
α-helix812-8165
β-strand821-82551
α-helix833-84210
α-helix845-8539
β-strand857-86261
α-helix870-8723
α-helix877-8837
α-helix884-8885
α-helix889-8968
α-helix900-91112
α-helix915-9184
α-helix931-94515
β-strand94714
α-helix9521
β-strand95314
α-helix954-9552
α-helix956-9627
α-helix963-9675
β-strand969-97243
α-helix974-98613
α-helix988-9969
β-strand1003-100425
α-helix1009-102315
α-helix1029-104113
α-helix1045-105511
β-strand105716
α-helix1058-10603
α-helix1077-10804
α-helix1085-10873
α-helix1105-11106
α-helix1119-113719
β-strand114317
β-strand114418
β-strand115019
β-strand115317
α-helix1179-11868
α-helix1197-120711
β-strand121918
α-helix1222-123110
α-helix1238-125316
β-strand1262110
β-strand126416
α-helix1267-127610
β-strand1283111
α-helix1292-12943
α-helix1298-130811
α-helix1316-132813
β-strand1330111
α-helix1331-134919
β-strand1357-136269
α-helix13631
β-strand1369-137469
β-strand1382-138769
β-strand1393-140089
α-helix1402-142524
α-helix1429-14335
α-helix1437-146226
α-helix1466-148015
α-helix1488-150114
α-helix1502-15065
α-helix1509-15135
α-helix1516-15238
α-helix1525-15306
α-helix1531-15333
β-strand1536-153725
α-helix1543-15464
β-strand1550110
α-helix1553-157018
α-helix1573-15808
α-helix15911
β-strand1592112
α-helix15931
β-strand1600112
α-helix1604-16107
α-helix1613-16153
α-helix1624-164825
α-helix1660-16656
β-strand167012
β-strand1752-175543
α-helix1761-177212
α-helix1781-179111
α-helix1792-17943
α-helix1797-18048
α-helix1807-18093
β-strand1812113
α-helix1813-18153
β-strand1821-1825514
β-strand1829115
α-helix1832-185221
α-helix1869-18768
α-helix1884-189512
α-helix1905-19095
α-helix1913-19175
α-helix1923-194422
α-helix1945-19473
α-helix1963-197614
α-helix1988-200114
α-helix2003-20053
α-helix2006-20138
α-helix2016-203924
α-helix2046-206217
α-helix2064-207815
α-helix2118-21214
α-helix2123-21264
α-helix2138-215316
α-helix2158-21625
α-helix2199-220810
α-helix2212-22187
β-strand2231-2234414
α-helix2235-224612
β-strand2250113
α-helix2251-22588
β-strand2268-2271416
β-strand2282-2285416
β-strand2286114
α-helix2287-230418
β-strand231015
α-helix2317-233418
β-strand2347-2356105
β-strand2359117
α-helix2362-23654
α-helix2368-237811
α-helix2383-239614
β-strand2401-2402216
α-helix2403-24042
α-helix2405-242218
α-helix2430-243910
α-helix2441-24444
α-helix2448-24569
α-helix2458-24603
β-strand2462115
β-strand2464-2465216
α-helix2479-250224
β-strand2507-251595
β-strand2518-2529125
α-helix2531-255727
β-strand2563117
β-strand2568-257035
β-strand2574-2575218
β-strand2580-2581218
β-strand2586-2587218
α-helix2591-25933
α-helix2596-25994
α-helix2606-262217
β-strand2623119
α-helix2627-264216
α-helix2643-26453
α-helix2646-265611
α-helix2661-26633
α-helix2672-26754
α-helix2679-269618
α-helix2751-27533
α-helix2754-276310
α-helix2771-278212
α-helix2807-28137
α-helix2817-283519
β-strand2837120
β-strand2860120
β-strand2864121
α-helix2865-28673
α-helix2870-288920
α-helix2890-28945
α-helix2899-29079
β-strand2914122
α-helix2917-292812
α-helix2933-29386
α-helix2945-29528
β-strand2958-2959221
β-strand2991-2992221
α-helix2994-30029
β-strand3006-3009423
β-strand3027-3031523
β-strand3037-3042623
α-helix3043-305917
α-helix3063-307210
β-strand3076-3081624
β-strand3086-3094919
α-helix3105-31139
α-helix3117-31204
β-strand3123122
α-helix3128-31303
α-helix3131-314010
α-helix3143-316220
α-helix3165-31673
α-helix3168-318619
β-strand3191-3199919
β-strand3205119
β-strand3208125
α-helix3210-32167
β-strand3221-3225524
β-strand3233125
α-helix3234-32352
α-helix3238-325013
α-helix3256-326712
β-strand3270126
α-helix3273-32753
α-helix3289-32924
β-strand3297126
α-helix3298-33047
α-helix3306-33083
α-helix3313-332513
α-helix3328-33303
α-helix3331-33344
β-strand3343-3346427
β-strand3355-3359527
β-strand3364-3369627
β-strand3374-3378527
α-helix3383-339715
α-helix3407-34159
β-strand3431-3437727
β-strand3445-3448427
β-strand3455-3459527
β-strand3466-3469428
α-helix3476-34783
β-strand3479-3482429
β-strand3486-3491629
β-strand3496-3499428
α-helix3504-351310
β-strand3531-3537729
α-helix3538-35392
α-helix3544-35518
α-helix3552-35565
α-helix3557-35648
α-helix3587-35937
α-helix3607-362317
α-helix3628-36303
α-helix3631-364111
β-strand3647-3650430
β-strand3661-3664430
α-helix3678-36869
α-helix3695-36995
α-helix3701-371717
α-helix3718-37225
α-helix3725-373814
α-helix3743-37442
α-helix3755-37595
β-strand3765-3767331
β-strand3771-3773331
β-strand3776-3778332
β-strand3781-3783332
β-strand3784-3789631
α-helix3793-37953
α-helix3800-381819
β-strand3819133
α-helix3825-38306
β-strand3833-3840831
β-strand3843-3850831
α-helix3852-38543
β-strand3858133
α-helix3860-38656
α-helix3874-388815

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(p*gp*gp*gp*ap*up*up*gp*gp*up*gp*up*cp*up*up*up*gp*ap*gp*a)-3')C, ERNA19Crimean-Congo hemorrhagic fever virus strain IbAr10200
RNA (5'-r(*up*cp*up*cp*ap*ap*ap*gp*ap*cp*ap*cp*cp*ap*a)-3')DRNA15Crimean-Congo hemorrhagic fever virus strain IbAr10200
RNA (5'-r(p*up*cp*u)-3')FRNA3Crimean-Congo hemorrhagic fever virus strain IbAr10200
Sequence of entity 1 (A), FASTA
>9XE9_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
>9XE9_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
>9XE9_3 RNA (5'-R(P*GP*GP*GP*AP*UP*UP*GP*GP*UP*GP*UP*CP*UP*UP*UP*GP*AP*GP*A)-3') (chains C, E)
GGGAUUGGUGUCUUUGAGA
Sequence of entity 4 (D), FASTA
>9XE9_4 RNA (5'-R(*UP*CP*UP*CP*AP*AP*AP*GP*AP*CP*AP*CP*CP*AP*A)-3') (chains D)
UCUCAAAGACACCAA
Sequence of entity 5 (F), FASTA
>9XE9_5 RNA (5'-R(P*UP*CP*U)-3') (chains F)
UCU

Ligands and cofactors

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

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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