9XEC: RNA-directed RNA polymerase L

Crimean-Congo hemorrhagic fever virus RNA polymerase containing a 9-bp RNA product. Determined by electron microscopy at 2.98 Å resolution. Released 6 May 2026.

Method
Electron microscopy
Resolution
2.98 Å
Organism
Crimean-Congo hemorrhagic fever virus strain IbAr10200
Chains
6
Atoms
26,146
Mol. weight
471.22 kDa
Ligands
ZN, 2KH, MN
Released
6 May 2026

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

Secondary structure: helices and β-sheets

9XEC contains 167 α-helices and 97 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: 167 helices, 97 β-strands

ElementResiduesLengthSheet
α-helix340-35516
α-helix400-41112
α-helix413-42311
α-helix428-4358
β-strand43811
α-helix448-45912
α-helix461-4633
α-helix467-48216
α-helix488-4936
β-strand50512
β-strand50712
α-helix511-52212
α-helix541-55212
α-helix564-57613
α-helix587-60115
α-helix609-62113
α-helix627-64721
α-helix651-6533
α-helix656-6583
α-helix662-6698
α-helix671-6733
α-helix674-6796
α-helix685-6895
β-strand694-69853
α-helix699-7002
α-helix7241
β-strand72514
α-helix7261
β-strand728-72925
α-helix742-7432
β-strand744-74633
α-helix749-76012
β-strand803-80533
β-strand821-82553
β-strand82816
α-helix832-84211
α-helix845-8539
β-strand857-86153
β-strand86416
α-helix877-8793
α-helix880-8834
α-helix884-8885
α-helix889-8935
α-helix900-91011
α-helix913-9175
α-helix931-94515
β-strand94717
β-strand95317
α-helix956-9627
α-helix963-9675
β-strand969-97245
α-helix974-98613
α-helix988-9958
β-strand1003-100428
α-helix1009-102315
α-helix1029-104012
α-helix1045-105612
α-helix1058-10603
α-helix1085-10873
α-helix1105-11106
α-helix1119-113517
β-strand115019
α-helix1182-11865
α-helix1197-120711
α-helix1210-12123
α-helix1222-123110
α-helix1238-125114
β-strand1262110
α-helix1267-128014
β-strand1283111
α-helix1298-130811
α-helix1316-132712
β-strand1330111
α-helix1331-134919
β-strand1357-1358212
β-strand135919
β-strand1361-1362213
α-helix13631
β-strand1369-1372413
β-strand1373-1374212
β-strand1382-1387613
β-strand1393113
β-strand1398-1400313
α-helix1402-142524
α-helix1430-14334
α-helix1437-146226
α-helix1466-148015
α-helix1488-150114
α-helix1502-15065
α-helix1508-15136
α-helix1516-152914
β-strand1536-153728
α-helix1544-15463
β-strand1550110
α-helix1553-157119
α-helix1573-15808
β-strand1592114
β-strand1600114
α-helix1604-16107
α-helix1613-16153
α-helix1624-164825
α-helix1660-16656
β-strand167014
β-strand1752-175545
α-helix1759-177214
α-helix1781-179010
α-helix1797-18048
β-strand1812115
α-helix1813-18153
β-strand1821-1825516
β-strand1829117
α-helix1832-185120
α-helix1869-18779
α-helix1884-189512
α-helix1905-19095
α-helix1913-19164
α-helix1923-19319
α-helix1932-19365
α-helix1937-19437
α-helix1944-19474
α-helix1963-197614
α-helix1988-200013
α-helix2005-20139
α-helix2016-203924
α-helix2046-206217
α-helix2065-207915
α-helix2138-215215
α-helix2158-21614
α-helix2199-220810
α-helix2212-22198
β-strand2231-2234416
α-helix2235-224612
β-strand2250115
α-helix2251-22599
β-strand2267-2272618
β-strand2281-2285518
β-strand2286116
α-helix2287-230519
β-strand231018
α-helix2317-233519
β-strand233918
β-strand2347-2357118
β-strand2359119
α-helix2368-237811
α-helix2383-239614
β-strand2400-2402318
α-helix2403-24042
α-helix2405-242117
α-helix2430-243910
α-helix2441-24444
α-helix2448-24569
β-strand2462117
β-strand2464-2466318
α-helix2478-250225
β-strand2507-251598
β-strand2518-2529128
α-helix2531-25399
α-helix2541-255717
β-strand2563119
β-strand2568-257038
β-strand2574-2575220
β-strand2579-2581320
β-strand2586-2588320
α-helix2596-25994
α-helix2606-262116
β-strand2623121
α-helix2627-264317
α-helix2646-26516
α-helix2661-26633
α-helix2681-269616
α-helix2751-27533
α-helix2754-276310
α-helix2771-27799
α-helix2803-28053
α-helix2807-28148
α-helix2819-283517
β-strand2837122
β-strand2860122
α-helix2864-28674
α-helix2870-288920
α-helix2891-28944
α-helix2899-29079
β-strand2914123
α-helix2917-292812
α-helix2933-29375
α-helix2945-29528
α-helix2994-30029
β-strand3006-3009424
β-strand3027-3031524
β-strand3037-3042624
α-helix3043-305917
α-helix3063-307311
β-strand3079-3081325
β-strand3086-3094921
α-helix3105-31139
α-helix3117-31204
β-strand3123123
α-helix3134-31396
α-helix3143-316018
α-helix3168-318821
β-strand3191-3199921
β-strand3205121
β-strand3208126
α-helix3209-32168
β-strand3221-3223325
β-strand3233126
α-helix3238-325114
α-helix3256-326712
β-strand3270127
α-helix3282-32854
β-strand3297127
α-helix3298-33047
α-helix3306-33083
α-helix3315-332612
α-helix3330-33323
α-helix3335-33373
β-strand3345-3346228
β-strand3355-3359528
β-strand3364-3369628
β-strand3374-3378528
α-helix3383-339614
α-helix3407-34159
β-strand3431-3433328
β-strand3434-3437429
β-strand3445-3448429
β-strand3457-3459328
β-strand3486130
β-strand3490-3491231
α-helix3504-35096
β-strand3531-3532231
β-strand3537130
α-helix3538-35392
β-strand3543132
α-helix3544-355512
α-helix3557-35648
β-strand358211
α-helix3586-35905
α-helix3592-35954
β-strand3599133
α-helix3607-362317
α-helix3628-36314
α-helix3637-36415
β-strand3649-3653534
β-strand3658-3662534
α-helix3678-36858
β-strand3689132
α-helix3693-36975
α-helix3701-372121
α-helix3725-373814
α-helix3742-37443
β-strand3751133
α-helix3755-37595
β-strand3765-3767335
β-strand3771-3778835
β-strand3781-3789935
α-helix3793-37953
α-helix3800-381718
α-helix3825-38295
β-strand3833-3838635
α-helix3840-38423
β-strand3845-3850635
α-helix3852-38543
α-helix3860-38678
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*up*ap*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)-3')DRNA9Crimean-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
>9XEC_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
>9XEC_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
>9XEC_3 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, E)
GGGAUUGAUAUCUUUGAGA
Sequence of entity 4 (D), FASTA
>9XEC_4 RNA (5'-R(P*UP*CP*UP*CP*AP*AP*AP*GP*A)-3') (chains D)
UCUCAAAGA
Sequence of entity 5 (F), FASTA
>9XEC_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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