9XE7: RNA-directed RNA polymerase L

Crimean-Congo hemorrhagic fever virus RNA polymerase containing a 10-bp RNA product and incorporated cytidine. Determined by electron microscopy at 3.02 Å resolution. Released 6 May 2026.

Method
Electron microscopy
Resolution
3.02 Å
Organism
Crimean-Congo hemorrhagic fever virus strain IbAr10200
Chains
6
Atoms
26,422
Mol. weight
471.9 kDa
Ligands
ZN, MN, 2KH
Released
6 May 2026

Explore 9XE7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9XE7 contains 181 α-helices and 96 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: 181 helices, 96 β-strands

ElementResiduesLengthSheet
α-helix317-3248
α-helix330-3334
α-helix339-35012
α-helix402-41110
α-helix413-42412
α-helix428-4358
β-strand437-43821
α-helix446-45813
α-helix467-48418
α-helix490-4934
α-helix512-52211
α-helix541-55212
α-helix564-58017
α-helix587-60317
α-helix607-62115
α-helix626-64823
α-helix656-6583
α-helix662-6698
α-helix671-6733
α-helix674-6796
α-helix685-6895
β-strand694-69632
α-helix7241
β-strand72513
α-helix7261
β-strand728-72924
α-helix737-7393
α-helix742-7432
α-helix749-76012
β-strand801-80552
α-helix813-8153
β-strand821-82552
α-helix833-84210
α-helix845-8539
β-strand857-86262
α-helix870-8723
α-helix877-8837
α-helix884-8885
α-helix889-8957
α-helix900-91011
α-helix913-9164
α-helix924-9263
α-helix931-94515
β-strand947-94825
β-strand952-95325
α-helix954-9552
α-helix956-9627
α-helix963-9675
β-strand970-97234
α-helix974-98613
α-helix988-9969
β-strand1003-100426
α-helix1009-102315
α-helix1029-104113
α-helix1045-105410
α-helix1058-10603
α-helix1077-10804
α-helix1085-10873
α-helix1105-11106
α-helix1119-113719
β-strand1143-114427
β-strand115018
β-strand115317
α-helix1179-11868
α-helix1197-120711
β-strand1219-122027
α-helix1222-123110
α-helix1238-125316
β-strand126219
α-helix1267-127610
β-strand1283110
α-helix1292-12943
α-helix1298-130811
α-helix1316-132712
β-strand1330110
α-helix1331-134919
β-strand1357-1358211
β-strand135918
β-strand1361-1362212
α-helix13631
β-strand1369-1372412
β-strand1373-1374211
β-strand1382-1387612
β-strand1393-1400812
α-helix1403-142523
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-strand1536-153726
α-helix1544-15463
β-strand155019
α-helix1553-157018
α-helix1573-15808
α-helix15911
β-strand1592113
α-helix15931
β-strand1600113
α-helix1604-16107
α-helix1613-16153
α-helix1624-164825
α-helix1660-16656
β-strand167013
β-strand1732-1737614
α-helix1738-17403
β-strand1743-1748614
β-strand1753-175534
α-helix1761-177212
α-helix1781-179010
α-helix1791-17944
α-helix1797-18048
α-helix1807-18093
β-strand1812115
α-helix1813-18153
β-strand1821-1825516
β-strand1829117
α-helix1832-185120
α-helix1869-18768
α-helix1884-189512
α-helix1913-19164
α-helix1923-194321
α-helix1963-197614
α-helix1989-200113
α-helix2006-20094
α-helix2012-20143
α-helix2016-203924
α-helix2046-206217
α-helix2064-207916
α-helix2082-20843
α-helix2118-21225
α-helix2138-215417
α-helix2158-21625
α-helix2199-220810
α-helix2213-22186
β-strand2231-2234416
α-helix2235-224612
β-strand2250115
α-helix2251-22599
β-strand2268-2272518
β-strand2281-2285518
β-strand2286116
α-helix2287-230418
α-helix2317-233418
β-strand233916
β-strand2347-2356106
β-strand2359119
α-helix2362-23654
α-helix2368-237811
α-helix2383-239614
β-strand2399-2402418
α-helix2403-24042
α-helix2405-242016
α-helix2430-243910
α-helix2441-24444
α-helix2448-24569
α-helix2458-24603
β-strand2462117
β-strand2464-2467418
α-helix2477-250125
β-strand2507-251596
β-strand2518-2529126
α-helix2531-255727
β-strand2563119
β-strand2568-257036
β-strand2574-2575220
β-strand2579-2581320
β-strand2586-2588320
α-helix2590-25934
α-helix2596-25994
α-helix2606-262116
β-strand2623121
α-helix2627-264216
α-helix2646-265611
α-helix2661-26633
α-helix2671-26744
α-helix2680-269617
α-helix2751-27533
α-helix2754-276310
α-helix2771-278212
α-helix2807-28159
α-helix2817-283519
β-strand2837122
β-strand2860122
β-strand2864123
α-helix2870-288920
α-helix2891-28944
α-helix2899-29079
β-strand2914124
α-helix2917-292812
α-helix2933-29386
α-helix2945-29528
β-strand2958-2959223
β-strand2991-2992223
α-helix2994-30029
β-strand3006-3009425
β-strand3027-3031525
β-strand3037-3042625
α-helix3043-305917
α-helix3063-307210
β-strand3079-3081326
β-strand3086-3094921
α-helix3105-31139
α-helix3117-31204
β-strand3123124
α-helix3131-31399
α-helix3143-316220
α-helix3170-318617
β-strand3191-3199921
β-strand3205121
β-strand3208127
α-helix3210-32167
β-strand3221-3223326
β-strand3233127
α-helix3234-32352
α-helix3238-325013
α-helix3256-326712
β-strand3270128
α-helix3273-32753
β-strand3297128
α-helix3298-33047
α-helix3306-33083
α-helix3312-332514
α-helix3331-33344
β-strand3345-3346229
β-strand3355-3359529
β-strand3364-3369629
β-strand3374-3378529
α-helix3383-339715
α-helix3407-34159
α-helix3420-34223
β-strand3431-3437729
β-strand3445-3448429
β-strand3455-3459529
β-strand3466-3468330
α-helix3476-34772
β-strand3478-3480331
β-strand3486-3491631
β-strand3497-3499330
α-helix3504-35129
β-strand3531-3537731
α-helix3538-35392
α-helix3544-355411
α-helix3556-356813
α-helix3570-35789
β-strand3582-358321
α-helix3588-35936
α-helix3607-362317
α-helix3628-36303
α-helix3631-364111
β-strand3647-3650432
β-strand3661-3664432
α-helix3678-36869
α-helix3695-36984
α-helix3701-372121
α-helix3725-373814
α-helix3739-37413
α-helix3743-37442
α-helix3753-37597
β-strand3765-3767333
β-strand3771-3776633
β-strand3783-3789733
α-helix3793-37953
α-helix3800-381819
β-strand3819134
α-helix3825-38306
β-strand3833-3840833
β-strand3843-3849733
α-helix3850-38512
α-helix3852-38543
β-strand3858134
α-helix3860-38656
α-helix3870-388718

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(*up*cp*up*cp*ap*ap*ap*gp*ap*c)-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
>9XE7_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
>9XE7_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
>9XE7_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
>9XE7_4 RNA (5'-R(*UP*CP*UP*CP*AP*AP*AP*GP*AP*C)-3') (chains D)
UCUCAAAGAC
Sequence of entity 5 (F), FASTA
>9XE7_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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