9YBN: RNA-directed RNA polymerase L

2.53A cryo-EM structure of RNA-directed RNA polymerase L of Crimean-Congo hemorrhagic fever virus (RNA bound). Determined by electron microscopy at 2.53 Å resolution. Released 4 Mar 2026.

Method
Electron microscopy
Resolution
2.53 Å
Organisms
Crimean-Congo hemorrhagic fever virus, Crimean-Congo hemorrhagic fever virus strain IbAr10200
Chains
3
Atoms
13,959
Mol. weight
463.94 kDa
Ligands
ZN
Released
4 Mar 2026

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

Secondary structure: helices and β-sheets

9YBN contains 99 α-helices and 54 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: 99 helices, 54 β-strands

ElementResiduesLengthSheet
α-helix931-94515
β-strand94711
β-strand95311
α-helix956-9638
α-helix964-9696
β-strand971-97222
α-helix974-98613
α-helix988-9969
β-strand1003-100423
α-helix1009-102618
α-helix1029-104113
α-helix1045-105612
β-strand105714
α-helix1077-10804
α-helix1085-10873
α-helix1101-11033
α-helix1104-11107
α-helix1119-113921
β-strand1143-114535
β-strand115016
β-strand1151-115335
α-helix1173-118614
α-helix1197-120812
β-strand1219-122025
α-helix1222-123110
α-helix1238-125316
β-strand126217
β-strand126414
α-helix1267-128014
β-strand128318
α-helix1298-130811
α-helix1316-132712
β-strand133018
α-helix1331-134919
α-helix13551
β-strand1357-136266
α-helix13631
β-strand1369-137466
β-strand1382-138766
β-strand1393-140086
α-helix1402-142524
α-helix1429-14335
α-helix1437-146226
α-helix1466-148015
α-helix1488-150114
α-helix1502-15065
α-helix1508-15125
α-helix1516-15238
α-helix1525-15306
α-helix1531-15333
β-strand1536-153723
α-helix1539-15424
α-helix1543-15464
β-strand155017
α-helix1553-157018
α-helix1573-15808
α-helix15911
β-strand159219
α-helix15931
β-strand160019
α-helix1604-16118
α-helix1613-16153
α-helix1624-165027
α-helix1659-16657
β-strand1754-175522
α-helix1759-177214
α-helix1781-179010
α-helix1791-17944
α-helix1797-18048
α-helix1807-18093
β-strand1829110
α-helix1832-185221
α-helix1869-187810
α-helix1884-189411
α-helix2250-225910
β-strand2267-2268211
β-strand2285111
α-helix2287-230418
β-strand231013
α-helix2317-233519
β-strand233913
β-strand2347-2356103
α-helix2368-237811
α-helix2383-239614
β-strand2399-2402411
α-helix2403-24042
α-helix2405-241814
α-helix2419-24213
α-helix2430-243910
α-helix2441-24444
α-helix2448-24569
α-helix2458-24603
β-strand2462110
β-strand2464-2467411
α-helix2477-250226
β-strand2507-251483
β-strand2519-2529113
α-helix2531-255828
β-strand2568-257033
β-strand2575-2576212
β-strand2579-2580212
β-strand2587112
α-helix2591-25944
α-helix2596-25994
α-helix2606-262116
β-strand2623113
α-helix2627-264418
α-helix2646-265611
α-helix2661-26633
α-helix2665-26673
α-helix2671-26755
α-helix2679-269618
α-helix27021
β-strand2703114
α-helix2704-27052
α-helix2751-27533
α-helix2754-276310
α-helix2765-27684
α-helix2771-278212
α-helix2807-28148
α-helix2817-283519
β-strand2837115
β-strand2860115
β-strand2864116
α-helix2865-28662
α-helix2899-291113
α-helix2945-295410
β-strand2958-2960316
β-strand2969116
β-strand2990-2992316
α-helix2994-300310
β-strand3005-3009514
β-strand3027-3031514
β-strand3037-3042614
α-helix3043-305917
α-helix3063-307210
β-strand3078-3081417
β-strand3086-3090513
α-helix3096-30994
β-strand3101118
α-helix3105-31139
α-helix3115-31206
α-helix3131-31388
α-helix3143-316119
α-helix3168-318215
α-helix31861
β-strand3187118
α-helix3188-31892
α-helix3192-31943
β-strand3195-3199513
α-helix3206-32072
α-helix3209-32168
β-strand3221-3224417

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
RNA-directed RNA polymerase LAprotein3945Crimean-Congo hemorrhagic fever virusQ6TQR6 (AlphaFold model)
RNA (5'-r(p*up*cp*up*cp*ap*ap*ap*gp*ap*ap*ap*up*ap*cp*up*up*gp*cp*gp*gp*cp*ap*cp*g)-3')BRNA24Crimean-Congo hemorrhagic fever virus strain IbAr10200
RNA (5'-r(*cp*gp*up*gp*cp*cp*gp*cp*cp*ap*cp*up*ap*up*ap*up*cp*up*up*up*gp*ap*gp*a)-3')CRNA24Crimean-Congo hemorrhagic fever virus strain IbAr10200
Sequence of entity 1 (A), FASTA
>9YBN_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
>9YBN_2 RNA (5'-R(P*UP*CP*UP*CP*AP*AP*AP*GP*AP*AP*AP*UP*AP*CP*UP*UP*GP*CP*GP*GP*CP*AP*CP*G)-3') (chains B)
UCUCAAAGAAAUACUUGCGGCACG
Sequence of entity 3 (C), FASTA
>9YBN_3 RNA (5'-R(*CP*GP*UP*GP*CP*CP*GP*CP*CP*AP*CP*UP*AP*UP*AP*UP*CP*UP*UP*UP*GP*AP*GP*A)-3') (chains C)
CGUGCCGCCACUAUAUCUUUGAGA

Ligands and cofactors

IDNameFormulaCopies
ZNZinc ionZn2

Primary citation

Structure of Crimean-Congo haemorrhagic fever virus RNA polymerase. Wang, D., Yang, G., Liu, B. Nat Microbiol (2026) 11:1711-1721. DOI 10.1038/s41564-026-02319-1 · PubMed

Other PDB entries of the same protein (UniProt Q6TQR6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

About this viewer

MolViewer shows 9YBN directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.