9EH1: DNA-directed RNA polymerase subunit

RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, 20 bp upstream. Determined by electron microscopy at 3.1 Å resolution. Released 18 Dec 2024.

Method
Electron microscopy
Resolution
3.1 Å
Organisms
Sus scrofa, Homo sapiens, synthetic construct
Chains
35
Atoms
72,243
Mol. weight
1180.54 kDa
Ligands
MG, ZN
Released
18 Dec 2024

Explore 9EH1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9EH1 contains 386 α-helices and 426 β-strands across 32 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: 5 helices, 4 β-strands

ElementResiduesLengthSheet
β-strand36132
β-strand37133
α-helix41-422
α-helix45-5612
α-helix64-7512
β-strand83-84234
α-helix86-11328
β-strand118-119235
α-helix121-13111
Chain A: 78 helices, 71 β-strands
ElementResiduesLengthSheet
β-strand1511
β-strand21-2222
α-helix28-347
β-strand4313
β-strand4914
β-strand5114
β-strand5613
α-helix83-853
β-strand8815
β-strand9416
α-helix100-10910
α-helix1111
α-helix120-1223
α-helix124-1329
α-helix137-14711
β-strand192-19327
β-strand198-19927
β-strand215-21627
α-helix218-22710
α-helix230-2367
β-strand25016
β-strand25315
α-helix254-2563
α-helix258-2603
α-helix262-2632
β-strand26418
α-helix2651
β-strand27218
α-helix273-2742
α-helix275-29218
α-helix293-2975
α-helix302-31817
α-helix326-3283
β-strand32919
β-strand33519
α-helix339-3435
α-helix350-3545
β-strand357-358210
β-strand362-365411
β-strand367-369312
β-strand377-380411
α-helix382-3876
β-strand389-393513
α-helix399-40810
β-strand416-420513
β-strand426-428313
α-helix429-4313
α-helix435-4384
β-strand445-449513
α-helix4501
β-strand455-460611
β-strand469-476811
β-strand482-484312
α-helix486-4883
α-helix489-4924
β-strand501-504411
α-helix509-51810
α-helix522-5243
β-strand526-527214
β-strand532-533214
α-helix540-5489
β-strand554-556315
α-helix557-5659
α-helix574-5774
β-strand579-581315
β-strand585-587315
α-helix588-5958
β-strand602-604316
β-strand628-631416
β-strand634-637416
α-helix642-6454
α-helix652-6598
α-helix662-68322
β-strand686117
α-helix689-6913
α-helix698-72124
α-helix726-7283
α-helix733-75826
α-helix765-7728
α-helix778-7847
β-strand789118
β-strand793119
β-strand796119
β-strand802120
β-strand805120
α-helix8111
α-helix817-8204
β-strand823118
α-helix833-86735
β-strand872-874321
β-strand878-880321
β-strand886-888321
α-helix891-8933
β-strand896122
β-strand902-905423
α-helix913-9208
α-helix927-9337
β-strand934124
α-helix936-9449
α-helix946-96924
β-strand976-979423
α-helix983-99412
α-helix10011
β-strand1002124
α-helix1006-101914
α-helix1028-103710
α-helix1040-10489
α-helix1051-10533
α-helix1054-10585
α-helix1062-107817
β-strand1080122
α-helix1081-10822
α-helix1087-110115
α-helix1121-11288
β-strand1140-1142325
β-strand1143126
α-helix1146-11483
α-helix1152-116110
β-strand1164127
α-helix1166-11694
β-strand1170-1176728
α-helix1191-11944
β-strand1211-1216628
α-helix1218-12247
α-helix1228-123811
β-strand1243129
β-strand1255128
β-strand1259128
β-strand1261129
α-helix1281-129414
β-strand1299127
β-strand1308-1309225
β-strand1319130
β-strand1331130
β-strand1335-1337325
α-helix1344-13485
β-strand1352126
β-strand1358125
α-helix1362-13687
α-helix1371-138717
α-helix1395-140511
α-helix1416-14194
α-helix1426-14327
α-helix1435-144511
β-strand1448-144922
α-helix1454-14596
β-strand1471-1475531
α-helix1479-14813
α-helix1534-15374
Chain b: 4 helices, 3 β-strands
ElementResiduesLengthSheet
α-helix25-284
α-helix31-4111
β-strand45-46235
α-helix50-7526
β-strand80-81234
α-helix83-9311
β-strand96-98358
Chain B: 48 helices, 76 β-strands
ElementResiduesLengthSheet
α-helix22-3615
α-helix41-499
α-helix50-545
α-helix55-617
β-strand83-84236
β-strand87-93737
α-helix110-1156
β-strand121-129937
β-strand131-134436
β-strand138-141436
β-strand144-1531037
α-helix168-1736
β-strand185-187338
β-strand190-194538
β-strand196-200539
α-helix2011
β-strand205140
β-strand208140
β-strand215-223940
α-helix231-2322
β-strand233-240840
β-strand256140
β-strand258141
β-strand259140
β-strand263142
β-strand267141
α-helix269-2757
α-helix281-2888
α-helix295-30713
α-helix314-32310
β-strand325142
α-helix332-34514
α-helix358-37720
α-helix381-3844
α-helix388-3903
β-strand391-394439
α-helix396-42429
α-helix427-4293
α-helix431-4344
α-helix440-45011
β-strand453143
α-helix459-4613
β-strand463143
β-strand467-469338
α-helix475-4828
β-strand484-486339
α-helix4901
β-strand509144
β-strand523-525339
β-strand526144
β-strand531-532245
α-helix539-5479
β-strand551146
α-helix558-5603
β-strand565-569546
β-strand572-577646
α-helix580-59314
β-strand602-606546
β-strand611-615546
β-strand621-627745
β-strand628147
β-strand633147
α-helix637-6448
α-helix653-6597
β-strand662-666545
α-helix667-6704
β-strand695-696245
α-helix700-7034
α-helix706-7094
α-helix714-7163
α-helix719-72911
β-strand732148
β-strand749-751349
β-strand759-760250
α-helix764-7674
α-helix769-7713
β-strand776-782751
β-strand783117
β-strand793-797551
α-helix798-8025
β-strand808-8171049
β-strand826-829452
β-strand837-839352
β-strand853153
α-helix854-8552
β-strand859149
β-strand865154
β-strand867153
β-strand869-872452
β-strand889-890252
β-strand895154
α-helix896-8972
β-strand903-911949
β-strand917-9271149
β-strand934-937451
β-strand943-949751
β-strand956155
β-strand965-966251
α-helix971-9755
α-helix978-99316
β-strand997-998250
α-helix1008-10158
α-helix1016-10183
β-strand1025-1026251
β-strand1029155
α-helix10351
β-strand1036155
α-helix10371
β-strand1041-10501051
β-strand1051148
β-strand1060-1061211
β-strand1067156
β-strand1074156
β-strand1085-1086210
α-helix1088-109710
α-helix1100-11045
α-helix1105-11095
β-strand1115-111951
β-strand112511
β-strand1127157
β-strand1136157
β-strand1146-115051
α-helix1153-116412
β-strand117012
Chain c: 5 helices, 3 β-strands
ElementResiduesLengthSheet
α-helix17-215
α-helix27-359
β-strand42-43265
α-helix47-7226
β-strand77-78266
α-helix80-8910
α-helix91-966
β-strand101-102267
Chain C: 11 helices, 16 β-strands
ElementResiduesLengthSheet
β-strand8-14759
β-strand18160
β-strand19-24659
α-helix28-3912
β-strand44-551261
α-helix61-699
β-strand73162
α-helix85-873
α-helix95-973
β-strand99-106861
α-helix1121
β-strand113-116463
α-helix117-1193
β-strand121-122261
β-strand129162
β-strand149-153563
β-strand158-1681161
α-helix174-1763
β-strand179164
β-strand185-186259
α-helix200-2023
α-helix204-2063
α-helix218-2203
β-strand229-231359
β-strand234160
β-strand235164
α-helix241-26929
Chain d: 4 helices, 2 β-strands
ElementResiduesLengthSheet
α-helix38-4811
β-strand53-54266
α-helix56-8328
β-strand88-89265
α-helix91-10111
α-helix105-12218
Chain D: 10 helices, 2 β-strands
ElementResiduesLengthSheet
β-strand16168
α-helix17-193
α-helix24-274
β-strand31131
α-helix34-4916
α-helix55-584
α-helix59-6911
α-helix77-8812
α-helix95-1039
α-helix108-1147
α-helix116-1183
α-helix124-13714

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

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
DNA-directed RNA polymerase subunitAprotein1544Sus scrofaA0A8D1DPV6
DNA-directed RNA polymerase subunit betaBprotein1159Sus scrofaI3LGP4 (AlphaFold model)
DNA-directed RNA polymerase II subunit RPB3Cprotein269Sus scrofaI3LCH3 (AlphaFold model)
RNA polymerase Rpb4/RPC9 core domain-containing proteinDprotein126Sus scrofaA0A287ADR4 (AlphaFold model)
DNA-directed RNA polymerase II subunit EEprotein209Sus scrofaI3LSI7
DNA-directed RNA polymerases I, II, and III subunit RPABC2Fprotein78Sus scrofaA0A4X1VEK9
DNA-directed RNA polymerase subunitGprotein171Sus scrofaA0A4X1VKG7
DNA-directed RNA polymerases I, II, and III subunit RPABC3Hprotein149Sus scrofaI3LCB2
DNA-directed RNA polymerase II subunit RPB9Iprotein116Sus scrofaP60899
DNA-directed RNA polymerase I, II, and III subunit RPABC5Jprotein66Sus scrofaA0A8W4F9W9
DNA-directed RNA polymerase II subunit RPB11-aKprotein115Sus scrofaF1RKE4
RNA polymerase II subunit KLprotein47Sus scrofaA0A4X1TRS6

19 more molecules are not listed.

Sequence of entity 1 (A), FASTA
>9EH1_1 DNA-directed RNA polymerase subunit (chains A)
DSACPLRTIKRVQFGVLSPDELKRMSVTEGGIKYPETTEGGRPKLGGLMDPRQGVIERTG
RCQTCAGNMTECPGHFGHIELAKPVFHVGFLVKTMKVLRCVCFFCSKLLVDSNNPKIKDI
LAKSKGQPKKRLTHVYDLCKGKNICEGGEEMDNKFGVEQPEGDEDLTKEKGHGGCGRYQP
RIRRSGLELYAEWKHVNEDSQEKKILLSPERVHEIFKRISDEECFVLGMEPRYARPEWMI
VTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKL
LQFHVATMVDNELPGLPRAMQKSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITP
DPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRRGNSQYPGAKYIIRDNGDRIDL
RFHPKPSDLHLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVT
TPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFT
KRDVFLERGEVMNLLMFLSTWDGKVPQPAILKPRPLWTGKQIFSLIIPGHINCIRTHSTH
PDDEDSGPYKHISPGDTKVVVENGELIMGILCKKSLGTSAGSLVHISYLEMGHDITRLFY
SNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKAHNNELEPTP
GNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVG
QQNVEGKRIPFGFKHRTLPHFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREGLID
TAVKTAETGYIQRRLIKSMESVMVKYDATVRNSINQVVQLRYGEDGLAGESVEFQNLATL
KPSNKAFEKKFRFDYTNERALRRTLQEDLVKDVLSNAHIQNELEREFERMREDREVLRVI
FPTGDSKVVLPCNLLRMIWNAQKIFHINPRLPSDLHPIKVVEGVKELSKKLVIVNGDDPL
SRQAQENATLLFNIHLRSTLCSRRMAEEFRLSGEAFDWLLGEIESKFNQAIAHPGEMVGA
LAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKKPKTPSLTVFLLGQSAR
DAERAKDILCRLEHTTLRKVTANTAIYYDPNPQSTVVAEDQEWVNVYYEMPDFDVARISP
WLLRVELDRKHMTDRKLTMEQIAEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDENKM
QEEEEVVDKMDDDVFLRCIESNMLTDMTLQGIEQISKVYMHLPQTDNKKKIIITEDGEFK
ALQEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIEAVRKALERELYHVISFD
GSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLMEAAAHGESD
PMKGVSENIMLGQLAPAGTGCFDLLLDAEKCKYGMEIPTNIPGLGAAGPTGMFFGSAPSP
MGGISPAMTPWNQGATPAYGAWSPSVGSGMTPGAAGFSPSAASD
Sequence of entity 2 (B), FASTA
>9EH1_2 DNA-directed RNA polymerase subunit beta (chains B)
EITPDLWQEACWIVISSYFDEKGLVRQQLDSFDEFIQMSVQRIVEDAPPIDLQAEAQHAS
GEVEEPPRYLLKFEQIYLSKPTHWERDGAPSPMMPNEARLRNLTYSAPLYVDITKTVIKE
GEEQLQTQHQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLI
AQEKMATNTVYVFAKKDSKYAYTGECRSCLENSSRPTSTIWVSMLARGGQGAKKSAIGQR
IVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQEQN
VALNFIGSRGAKPGVTKEKRIKYAKEVLQKEMLPHVGVSDFCETKKAYFLGYMVHRLLLA
ALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRGKDFNLELAI
KTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLNSPIGRDGKL
AKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEE
ISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEVSMIRDIREREIRIY
TDAGRICRPLLIVEKQKLLLKKRHIDQLKEREYNNYSWQDLVASGVVEYIDTLEEETVML
AMTPDDLQEKEVAYCSTYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGV
YITNFHVRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVI
MNRSAVDRGFFRSVFYRSYKEQESKKGFDQEEVFEKPTRETCQGMRHAIYDKLDDDGLIA
PGVRVSGDDVIIGKTVTLPENEDELEGTNRRYTKRDCSTFLRTSETGIVDQVMVTLNQEG
YKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSR
MTIGHLIECLQGKVSANKGEIGDATPFNDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGR
KITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQI
AHGAAQFLRERLFEASDPYQVHVCNLCGIMAIANTRTHTYECRGCRNKTQISLVRMPYAC
KLLFQELMSMSIAPRMMSV
Sequence of entity 3 (C), FASTA
>9EH1_3 DNA-directed RNA polymerase II subunit RPB3 (chains C)
PYANQPTVRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLHD
EFIAHRLGLIPLTSDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDLI
SNSPRVIPVTSRNRDNDPSDYVEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAG
VAFEYDPDNALRHTVYPKPEEWPKSEYSELDEDESQAPYDPNGKPERFYYNVESCGSLRP
ETIVLSALSGLKKKLSDLQTQLSHEIQSD
Sequence of entity 4 (D), FASTA
>9EH1_4 RNA polymerase Rpb4/RPC9 core domain-containing protein (chains D)
EEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNESAEDEQELSEVFMKTLNYTARFSR
FKNRETIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEGRFEDEELQQILDD
IQTKRS
Sequence of entity 5 (E), FASTA
>9EH1_5 DNA-directed RNA polymerase II subunit E (chains E)
DDEEETYRLWKIRKTIMQLCHDRGYLVTQDELDQTLEEFKAQFGDKPSEGRPRRTDLTVL
VAHNDDPTDQMFVFFPEEPKVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVDM
APKYILEQFLQQELLINITEHELVPEHVVMTKEEVTELLARYKLRENQLPRIQAGDPVAR
YFGIKRGQVVKIIRPSETAGRYITYRLVQ
Sequence of entity 6 (F), FASTA
>9EH1_6 DNA-directed RNA polymerases I, II, and III subunit RPABC2 (chains F)
KRITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRY
LPDGSYEDWGVDELIISD
Sequence of entity 7 (G), FASTA
>9EH1_7 DNA-directed RNA polymerase subunit (chains G)
MFYHISLEHEILLHPRYFGPNLLNTVKQKLFTEVEGTCTGKYGFVIAVTTIDNIGAGVIQ
PGRGFVLYPVKYKAIVFRPFKGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFD
PNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDKNDIFAIGSLMDDYLGLV
Sequence of entity 8 (H), FASTA
>9EH1_8 DNA-directed RNA polymerases I, II, and III subunit RPABC3 (chains H)
AGILFEDIFDVKDIDPEGKKFDRVSRLHCESESFKMDLILDVNIQIYPVDLGDKFRLVIA
STLYEDGTLDDGEYNPTDDRPSRADQFEYVMYGKVYRIEGDETSTEAATRLSAYVSYGGL
LMRLQGDANNLHGFEVDSRVYLLMKKLAF
Sequence of entity 9 (I), FASTA
>9EH1_9 DNA-directed RNA polymerase II subunit RPB9 (chains I)
GFVGIRFCQECNNMLYPKEDKENRILLYACRNCDYQQEADNSCIYVNKITHEVDELTQII
ADVSQDPTLPRTEDHPCQKCGHKEAVFFQSHSARAEDAMRLYYVCTAPHCGHRWTE
Sequence of entity 10 (J), FASTA
>9EH1_10 DNA-directed RNA polymerase I, II, and III subunit RPABC5 (chains J)
MIIPVRCFTCGKIVGNKWEAYLGLLQAEYTEGDALDALGLKRYCCRRMLLAHVDLIEKLL
NYAPLE
Sequence of entity 11 (K), FASTA
>9EH1_11 DNA-directed RNA polymerase II subunit RPB11-a (chains K)
MNAPPAFESFLLFEGEKKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAG
YKVPHPLEHKIIIRVQTTPDYSPQEAFTNAITDLISELSLLEERFRVAIKDKQEG
Sequence of entity 12 (L), FASTA
>9EH1_12 RNA polymerase II subunit K (chains L)
QQPMIYICGECHTENEIKSRDPIRCRECGYRIMYKKRTKRLVVFDAR

Ligands and cofactors

IDNameFormulaCopies
MGMagnesium ionMg1
ZNZinc ionZn9

Primary citation

Structural basis of H3K36 trimethylation by SETD2 during chromatin transcription. Markert, J.W., Soffers, J.H., Farnung, L. Science (2025) 387:528-533. DOI 10.1126/science.adn6319 · PubMed

Other PDB entries of the same protein (UniProt A0A8D1DPV6), best resolution first:

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