9FYX: RNA polymerase II subunit D

Influenza A/H7N9 polymerase pre-cleavage cap-snatching complex. Determined by electron microscopy at 3.3 Å resolution. Released 16 Jul 2025.

Method
Electron microscopy
Resolution
3.3 Å
Organisms
Sus scrofa domesticus, synthetic construct, Influenza B virus
Chains
23
Atoms
56,176
Mol. weight
925.2 kDa
Ligands
ZN, G1G, MG, PO4
Released
16 Jul 2025

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

Secondary structure: helices and β-sheets

9FYX contains 322 α-helices and 388 β-strands across 17 chains. 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: 35 helices, 28 β-strands

ElementResiduesLengthSheet
α-helix2-76
α-helix11-2414
α-helix32-4817
β-strand53-54290
β-strand73-74290
β-strand76-78391
α-helix84-9815
β-strand109-111391
β-strand116-123891
α-helix127-13812
β-strand144-149691
β-strand154-156391
α-helix157-1593
α-helix165-18521
α-helix188-1914
α-helix210-2178
α-helix226-2349
α-helix241-2488
α-helix256-2572
β-strand258-259292
α-helix265-2717
β-strand275193
α-helix2761
β-strand287194
β-strand290-292394
α-helix303-3119
β-strand317-324894
α-helix331-35020
β-strand359-360294
α-helix364-3696
α-helix3761
β-strand377-378295
α-helix381-3833
β-strand391-392295
α-helix393-3942
α-helix396-3983
β-strand402193
α-helix405-41410
β-strand417196
β-strand421197
α-helix425-4317
α-helix434-45118
β-strand453196
α-helix454-47522
β-strand480-488994
β-strand490197
β-strand498-506994
β-strand517-5261094
α-helix530-5323
α-helix534-5374
β-strand541-5511194
β-strand556-5711694
α-helix572-5798
α-helix583-60321
α-helix608-6092
α-helix610-6145
β-strand619-624698
β-strand627-631598
α-helix633-64917
α-helix653-67321
β-strand679-680292
α-helix683-6919
α-helix698-71417
Chain A: 82 helices, 76 β-strands
ElementResiduesLengthSheet
α-helix141
β-strand15134
β-strand20-22335
β-strand25136
α-helix28-347
β-strand43137
β-strand47-48238
β-strand51-52238
α-helix531
β-strand56137
α-helix60-623
α-helix82-854
β-strand86-94939
α-helix97-993
α-helix100-10910
β-strand110140
β-strand117140
α-helix124-1329
α-helix137-14812
β-strand153141
β-strand187141
α-helix188-1892
β-strand190-194542
β-strand197-201542
β-strand213-216442
α-helix218-22710
α-helix230-2356
α-helix246-2483
β-strand250-255639
α-helix2561
β-strand265143
β-strand271143
α-helix272-2743
α-helix275-29521
α-helix301-31818
α-helix326-3272
β-strand329144
α-helix331-3333
α-helix3341
β-strand335144
α-helix3361
α-helix339-3424
α-helix350-3545
β-strand357-359345
β-strand362-369846
β-strand377-379346
β-strand381147
α-helix382-3876
β-strand389-393548
α-helix3941
α-helix399-40810
β-strand416-420548
β-strand426-428348
α-helix435-4384
β-strand445-449548
α-helix4501
β-strand455-459546
α-helix466-4683
β-strand469-474646
β-strand477147
β-strand482-484346
α-helix487-4893
β-strand500-504546
α-helix509-5146
α-helix515-5195
β-strand520146
α-helix522-5243
β-strand526-527249
β-strand532-533249
α-helix539-54810
β-strand554-555250
α-helix557-5659
α-helix5741
β-strand575112
α-helix576-5772
β-strand579-581313
β-strand585113
β-strand586-587250
α-helix588-5958
β-strand602-604351
β-strand628-631451
β-strand634-637451
α-helix642-6454
α-helix652-6598
α-helix662-68322
β-strand686152
α-helix689-6924
α-helix696-72126
α-helix726-7283
α-helix733-75927
α-helix765-7728
α-helix778-7858
β-strand789-790253
β-strand792-793254
β-strand796-797254
α-helix798-7992
β-strand822-823253
α-helix833-86836
β-strand872-873255
β-strand879-880255
β-strand886-888355
α-helix891-8933
β-strand896156
β-strand902-905457
α-helix913-9208
α-helix927-9337
β-strand934158
α-helix936-9449
α-helix946-96924
β-strand976-979457
α-helix983-99311
β-strand1002158
α-helix1006-101914
α-helix1028-104821
α-helix1051-10566
α-helix1062-107918
β-strand1080156
α-helix1081-10822
α-helix1087-110115
α-helix1121-11299
β-strand1139-1142459
β-strand1143160
α-helix1146-11494
α-helix1152-116110
β-strand1162161
β-strand1164-1165262
α-helix1166-11694
β-strand1170-1177816
α-helix1181-11833
α-helix1190-11978
β-strand1210-1216716
α-helix1218-12236
α-helix1228-123912
β-strand1243-1247516
β-strand1256-1261616
α-helix1281-129515
β-strand1297-1299362
β-strand1301161
β-strand1307-1310459
α-helix1315-13173
β-strand1319-1322463
β-strand1328-1331463
β-strand1335-1338459
α-helix1343-13475
β-strand1352160
β-strand1358-1359259
α-helix1362-13687
α-helix1371-138818
α-helix1395-140511
α-helix1416-14194
α-helix1426-14327
α-helix1435-144511
β-strand1448-1449235
α-helix1454-14596
α-helix1462-14643
α-helix1467-14693
β-strand1471-147551
α-helix1477-14804
Chain b: 38 helices, 31 β-strands
ElementResiduesLengthSheet
β-strand2-3298
α-helix5-106
α-helix15-217
α-helix27-304
α-helix36-4813
β-strand54-57499
β-strand64-67499
α-helix72-743
α-helix85-9814
α-helix102-11615
β-strand1181100
α-helix119-1235
β-strand128-1303101
β-strand135-1373101
α-helix139-15214
β-strand1621100
α-helix163-17513
β-strand178-1858102
β-strand206-2138102
α-helix214-2229
β-strand223-2242103
β-strand225-2284104
β-strand240-2434104
α-helix246-26419
β-strand269192
α-helix275-29218
β-strand298-305892
β-strand3061105
α-helix309-3124
α-helix315-32511
α-helix331-34515
β-strand348-3503103
β-strand354-359695
β-strand364-369695
α-helix370-3723
α-helix378-3803
α-helix383-39210
α-helix393-3953
β-strand396-3972103
β-strand400-4023103
α-helix413-42513
α-helix429-4324
β-strand437-443792
β-strand446-453892
α-helix456-47318
β-strand4771105
β-strand483-486492
β-strand489-4924106
β-strand495-4984106
β-strand5011106
α-helix505-5084
α-helix519-53517
α-helix541-55919
α-helix573-58210
α-helix586-5883
α-helix591-5933
α-helix608-6114
α-helix618-6247
α-helix637-6393
β-strand642-6454107
β-strand653-6564107
β-strand667-6682108
α-helix669-6713
α-helix673-6764
α-helix680-69920
α-helix702-7054
β-strand7131109
α-helix714-73219
α-helix737-75620
Chain B: 52 helices, 83 β-strands
ElementResiduesLengthSheet
α-helix16-183
α-helix19-3618
α-helix41-499
α-helix50-545
α-helix55-617
α-helix63-642
β-strand67-68264
β-strand83-84264
β-strand87-93764
β-strand97-99365
β-strand105-107365
α-helix110-1167
β-strand121-1331364
β-strand139-1531564
α-helix168-1736
β-strand185-187366
β-strand190-193466
α-helix194-1952
β-strand196-200567
β-strand205-208468
β-strand215-223968
β-strand233-240868
β-strand256-259468
β-strand263169
β-strand267-268268
α-helix269-2757
α-helix281-2888
α-helix295-30713
α-helix314-32411
β-strand325169
α-helix332-34514
α-helix349-3513
α-helix358-37619
α-helix381-3844
α-helix388-3903
β-strand391-394467
α-helix396-42328
α-helix431-4344
α-helix437-45014
β-strand453170
β-strand463170
β-strand468-469266
α-helix470-4712
α-helix475-4828
β-strand484171
β-strand485-486267
α-helix503-5053
β-strand509172
β-strand525171
β-strand526172
β-strand531-532273
α-helix539-5479
β-strand551-552274
α-helix558-5614
β-strand565-569574
β-strand572-577674
α-helix580-59213
β-strand602-606574
β-strand611-615574
β-strand621-627773
β-strand628175
β-strand633175
α-helix637-6448
α-helix653-6586
β-strand662-666573
α-helix667-6704
β-strand675-676273
α-helix679-6824
β-strand695-696273
α-helix700-7034
α-helix706-7094
α-helix714-7163
β-strand717176
α-helix719-72810
β-strand732177
β-strand734121
β-strand747-751521
β-strand755119
β-strand759-760278
α-helix764-7674
β-strand776-782779
β-strand783152
β-strand793-797579
α-helix798-8025
β-strand808-8171021
β-strand827-829380
β-strand848181
β-strand853182
β-strand854181
α-helix8551
β-strand859-860221
β-strand865-867382
β-strand869-872480
β-strand889-891380
α-helix8931
β-strand894-895282
α-helix896-8972
β-strand902-9111021
β-strand917-9271121
β-strand934-937479
β-strand942-949879
β-strand956183
β-strand965-967379
α-helix969-9713
β-strand977176
α-helix978-99316
β-strand997-998278
α-helix1008-10169
β-strand1025-1026279
β-strand1029183
α-helix10351
β-strand1036183
α-helix10371
β-strand1041-10501079
β-strand1051177
β-strand1060-1062346
β-strand1067184
β-strand1074184
α-helix1082-10832
β-strand1084-1086345
α-helix1088-109710
α-helix1100-11045
α-helix1105-11095
β-strand1113-1119734
α-helix11241
β-strand1125134
α-helix11261
β-strand1127-1129385
β-strand1134-1136385
β-strand1137186
β-strand1142186
β-strand1146-1152734
α-helix1153-116412
β-strand1167136
β-strand1170-1172335
Chain c: 38 helices, 42 β-strands
ElementResiduesLengthSheet
α-helix2-1211
α-helix14-229
β-strand241109
α-helix25-317
α-helix43-508
β-strand57-593108
α-helix63-664
β-strand701110
β-strand761110
β-strand78-825108
α-helix831
α-helix881
β-strand89-913108
α-helix93-10210
α-helix111-1144
α-helix116-12611
β-strand129-1357111
β-strand141-1488112
α-helix156-16712
α-helix170-1723
α-helix180-19213
α-helix200-21112
β-strand214-2207112
α-helix226-2294
α-helix232-2354
β-strand2361111
β-strand240-2456111
α-helix252-27120
α-helix276-28611
β-strand287-2893113
β-strand292-2932113
α-helix295-2984
α-helix306-3149
β-strand3191114
β-strand322-3254115
β-strand328-3358115
β-strand338-3458116
β-strand351-3588116
β-strand361-3666115
β-strand371-3777115
β-strand380-3867115
α-helix391-40515
α-helix408-4125
β-strand4211117
α-helix4261
β-strand4271117
α-helix428-4292
α-helix430-44011
α-helix443-4475
β-strand451-4533118
β-strand462-4632119
β-strand469-4702119
β-strand473-4753118
β-strand478-4803115
β-strand4941114
β-strand497-4982120
β-strand504-5052120
β-strand511-5133120
α-helix515-5173
β-strand529-5313113
α-helix542-55514
α-helix557-56610
α-helix568-5736
α-helix575-5773
α-helix578-5836
α-helix586-60520
α-helix612-6187
α-helix619-6224
α-helix625-6262
β-strand635-6406121
β-strand643-6486121
β-strand6531122
β-strand656-6594122
β-strand664-6674122
β-strand670-6745122
α-helix675-6773
β-strand694-6996123
α-helix712-7154
β-strand721-7255123
β-strand731-7366123
Chain C: 11 helices, 13 β-strands
ElementResiduesLengthSheet
β-strand8-14787
β-strand18-24787
α-helix28-4013
β-strand44-551222
α-helix61-699
β-strand72122
β-strand73188
β-strand99-106822
α-helix1121
β-strand113-116489
α-helix117-1193
β-strand121-122222
β-strand129188
α-helix130-1323
α-helix147-1482
β-strand149-153589
β-strand158-1681122
α-helix174-1763
β-strand179-185787
α-helix200-2023
α-helix204-2063
α-helix218-2203
β-strand229-235787
α-helix241-27030
Chain D: 9 helices, 1 β-strand
ElementResiduesLengthSheet
α-helix24-263
β-strand30-3121
α-helix34-4916
α-helix55-584
α-helix59-7012
α-helix77-8913
α-helix94-10310
α-helix108-1147
α-helix116-1183
α-helix124-13613
Chain E: 12 helices, 13 β-strands
ElementResiduesLengthSheet
α-helix4-2421
β-strand26-2722
α-helix30-334
α-helix37-448
β-strand4713
β-strand5213
α-helix55-584
β-strand60-6452
β-strand71-7552
β-strand81-8224
α-helix84-9714
β-strand101-10662
β-strand109-11024
α-helix112-1209
β-strand126-13162
α-helix132-1354
α-helix139-1413
β-strand147-15045
α-helix151-1522
α-helix153-16311
α-helix167-1693
β-strand172-17325
α-helix178-1836
β-strand190-19785
β-strand201-20995

9 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
RNA polymerase II subunit DDprotein184Sus scrofa domesticusA0A287ADR4 (AlphaFold model)
DNA-directed RNA polymerase II subunit EEprotein210Sus scrofa domesticusI3LSI7 (AlphaFold model)
DNA-directed RNA polymerases I, II, and III subunit RPABC2Fprotein127Sus scrofa domesticusA0A4X1VEK9 (AlphaFold model)
DNA-directed RNA polymerase subunitGprotein171Sus scrofa domesticusA0A4X1VKG7 (AlphaFold model)
DNA-directed RNA polymerases I, II, and III subunit RPABC3Hprotein150Sus scrofa domesticusI3LCB2
DNA-directed RNA polymerase II subunit RPB9Iprotein125Sus scrofa domesticusP60899
DNA-directed RNA polymerases I, II, and III subunit RPABC5Jprotein67Sus scrofa domesticusA0A4X1VYD0
DNA-directed RNA polymerase II subunit RPB11-aKprotein117Sus scrofa domesticusF1RKE4
RNA polymerase II, I and III subunit KLprotein58Sus scrofa domesticusA0A4X1TRS6
non-template DNA (43-mer)NDNA43synthetic construct
cap(1)-RNA (35-MER)PRNA35Influenza B virus
Template DNA (43-MER)TDNA43synthetic construct

11 more molecules are not listed.

Sequence of entity 1 (D), FASTA
>9FYX_1 RNA polymerase II subunit D (chains D)
MWGPAQPYSDSALSPKPRPFRAVFRGSALPFPAVRVEVRGRSMAAGGSDPRAGDVEEDAS
QLIFPKEFETAETLLNSEVHMLLEHRKQQNESAEDEQELSEVFMKTLNYTARFSRFKNRE
TIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEGRFEDEELQQILDDIQTKR
SFQY
Sequence of entity 2 (E), FASTA
>9FYX_2 DNA-directed RNA polymerase II subunit E (chains E)
MDDEEETYRLWKIRKTIMQLCHDRGYLVTQDELDQTLEEFKAQFGDKPSEGRPRRTDLTV
LVAHNDDPTDQMFVFFPEEPKVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVD
MAPKYILEQFLQQELLINITEHELVPEHVVMTKEEVTELLARYKLRENQLPRIQAGDPVA
RYFGIKRGQVVKIIRPSETAGRYITYRLVQ
Sequence of entity 3 (F), FASTA
>9FYX_3 DNA-directed RNA polymerases I, II, and III subunit RPABC2 (chains F)
MSDNEDNFDGDDFDDVEEDEGLDDLENAEEEGQENVEILPSGERPQANQKRITTPYMTKY
ERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDWGV
DELIISD
Sequence of entity 4 (G), FASTA
>9FYX_4 DNA-directed RNA polymerase subunit (chains G)
MFYHISLEHEILLHPRYFGPNLLNTVKQKLFTEVEGTCTGKYGFVIAVTTIDNIGAGVIQ
PGRGFVLYPVKYKAIVFRPFKGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFD
PNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDKNDIFAIGSLMDDYLGLV
Sequence of entity 5 (H), FASTA
>9FYX_5 DNA-directed RNA polymerases I, II, and III subunit RPABC3 (chains H)
MAGILFEDIFDVKDIDPEGKKFDRVSRLHCESESFKMDLILDVNIQIYPVDLGDKFRLVI
ASTLYEDGTLDDGEYNPTDDRPSRADQFEYVMYGKVYRIEGDETSTEAATRLSAYVSYGG
LLMRLQGDANNLHGFEVDSRVYLLMKKLAF
Sequence of entity 6 (I), FASTA
>9FYX_6 DNA-directed RNA polymerase II subunit RPB9 (chains I)
MEPDGTYEPGFVGIRFCQECNNMLYPKEDKENRILLYACRNCDYQQEADNSCIYVNKITH
EVDELTQIIADVSQDPTLPRTEDHPCQKCGHKEAVFFQSHSARAEDAMRLYYVCTAPHCG
HRWTE
Sequence of entity 7 (J), FASTA
>9FYX_7 DNA-directed RNA polymerases I, II, and III subunit RPABC5 (chains J)
MIIPVRCFTCGKIVGNKWEAYLGLLQAEYTEGDALDALGLKRYCCRRMLLAHVDLIEKLL
NYAPLEK
Sequence of entity 8 (K), FASTA
>9FYX_8 DNA-directed RNA polymerase II subunit RPB11-a (chains K)
MNAPPAFESFLLFEGEKKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAG
YKVPHPLEHKIIIRVQTTPDYSPQEAFTNAITDLISELSLLEERFRVAIKDKQEGIE
Sequence of entity 9 (L), FASTA
>9FYX_9 RNA polymerase II, I and III subunit K (chains L)
MDTQKDVQPPKQQPMIYICGECHTENEIKSRDPIRCRECGYRIMYKKRTKRLVVFDAR
Sequence of entity 10 (N), FASTA
>9FYX_10 non-template DNA (43-mer) (chains N)
GGCAGTACTAGTATTCTAGTATTGAAAGTACTTGAGCTTGATC
Sequence of entity 11 (P), FASTA
>9FYX_11 cap(1)-RNA (35-MER) (chains P)
GAAGCGAGAAGAACACAGACAGCAGAAGACCAGGC
Sequence of entity 12 (T), FASTA
>9FYX_12 Template DNA (43-MER) (chains T)
GATCAAGCTCAAGTACTTAAGCCTGGTCTATACTAGTACTGCC

Ligands and cofactors

IDNameFormulaCopies
ZNZinc ionZn9
G1G7-methyl-guanosine-5'-triphosphate-5'-(2'-O-methyl)-guanosineC22 H32 N10 O18 P31
MGMagnesium ionMg2
PO4Phosphate ionO4 P2

Primary citation

Mechanism of co-transcriptional cap snatching by influenza polymerase. Rotsch, A.H., Li, D., Dupont, M. et al. Nature (2026) 652:1281-1288. DOI 10.1038/s41586-026-10189-0 · PubMed

Other PDB entries of the same protein (UniProt A0A287ADR4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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