7OZO: RNA Polymerase II dimer

RNA Polymerase II dimer (Class 2). Determined by electron microscopy at 3.8 Å resolution. Released 6 Oct 2021.

Method
Electron microscopy
Resolution
3.8 Å
Organism
Sus scrofa domesticus
Chains
24
Atoms
54,330
Mol. weight
1035.42 kDa
Ligands
ZN
Released
6 Oct 2021

Explore 7OZO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7OZO contains 302 α-helices and 388 β-strands across 24 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.

Chains A and M: 54 helices, 52 β-strands

ElementResiduesLengthSheet
α-helix361-3644
β-strand36511
β-strand367-36932
β-strand377-38152
α-helix382-3876
β-strand389-39353
α-helix396-3983
α-helix399-40810
β-strand416-42053
β-strand426-42833
α-helix435-4384
β-strand445-44953
α-helix4501
β-strand455-45842
β-strand470-47782
β-strand482-48432
β-strand50111
β-strand50412
α-helix509-51810
β-strand52012
α-helix521-5244
α-helix539-54810
β-strand554-55524
α-helix557-5659
α-helix5741
β-strand57515
α-helix576-5772
β-strand57916
β-strand58117
β-strand58516
β-strand586-58724
α-helix588-5958
β-strand602-60548
α-helix611-6155
β-strand627-63158
β-strand634-63748
α-helix652-6598
α-helix662-68322
β-strand68619
α-helix689-6924
α-helix696-72126
α-helix733-75927
α-helix765-7728
α-helix778-7814
α-helix782-7865
β-strand789-790210
β-strand793111
β-strand796111
α-helix8111
β-strand822-823210
α-helix833-86836
β-strand872-873212
β-strand879-880212
β-strand886-888312
α-helix891-8933
β-strand896113
β-strand902-905414
α-helix915-9206
α-helix927-9337
β-strand934115
α-helix936-9449
α-helix946-96924
β-strand976-979414
α-helix983-99311
α-helix10011
β-strand1002115
α-helix1006-101914
α-helix1028-103710
α-helix1039-104810
α-helix1051-10566
α-helix1062-107918
β-strand1080113
α-helix1081-10822
α-helix1087-109913
α-helix1121-11288
β-strand1139-1142416
α-helix1146-11483
α-helix1152-11543
α-helix1155-11617
β-strand1164117
α-helix1166-11694
β-strand1170-1176718
β-strand1177119
α-helix1190-11989
β-strand1210119
β-strand1214-1216318
α-helix1218-12247
α-helix1228-123912
β-strand1243-1247518
β-strand1255-1261718
α-helix1263-12664
α-helix1282-129211
β-strand1299117
β-strand1307-1310416
β-strand1320-1322320
β-strand1328-1330320
β-strand1335-1338416
α-helix1343-13475
β-strand1358-1359216
α-helix1362-13687
α-helix1371-138818
α-helix1395-140511
α-helix1413-14153
β-strand1471-1475521
α-helix1479-14813
β-strand1484122
Chains B and N: 47 helices, 64 β-strands
ElementResiduesLengthSheet
α-helix19-3618
α-helix41-499
α-helix50-545
α-helix55-606
α-helix62-643
β-strand65-67323
β-strand83-931123
β-strand97-98224
β-strand106-107224
α-helix110-1167
β-strand121-1331323
β-strand140-1531423
α-helix168-1736
β-strand185-187325
β-strand190-193425
β-strand196-200526
α-helix2011
β-strand206-209427
β-strand215-223927
β-strand233-240827
α-helix249-2524
β-strand256-259427
β-strand263128
β-strand266-268327
α-helix269-2768
α-helix281-2888
α-helix295-30915
α-helix314-32310
β-strand325128
α-helix332-34110
α-helix342-3465
α-helix358-37720
α-helix381-3844
α-helix388-3903
β-strand391-394426
α-helix396-42530
α-helix431-4344
α-helix437-45014
β-strand461129
β-strand468-469225
α-helix4701
α-helix475-4828
β-strand484-486326
α-helix491-4955
α-helix501-5022
α-helix503-5053
β-strand509130
β-strand523-525326
β-strand526130
β-strand531-532231
α-helix539-5479
α-helix558-5614
β-strand565132
β-strand566-569433
β-strand572-573233
β-strand577132
α-helix580-59213
β-strand602-606533
α-helix607-6093
β-strand611-615533
β-strand621-627731
β-strand628134
β-strand633134
α-helix637-6448
α-helix653-6597
β-strand662-666531
α-helix667-6715
α-helix679-6835
β-strand695-696231
α-helix700-7034
α-helix706-7094
α-helix719-73113
β-strand732135
β-strand748-751436
β-strand759-760237
α-helix763-7675
β-strand776-782738
β-strand78319
β-strand794-797438
α-helix798-8025
β-strand808-8181136
β-strand827-828239
β-strand837-839339
β-strand844140
β-strand853141
α-helix854-8552
β-strand859-860236
β-strand864140
β-strand865-867341
β-strand870-871239
β-strand889-891339
β-strand894-895241
β-strand902-9111036
β-strand917-9271136
β-strand934-937438
β-strand943-949738
β-strand956-957242
β-strand965-967338
α-helix969-9713
α-helix978-99316
α-helix9961
β-strand997-998237
α-helix1008-10169
β-strand1025-1026238
β-strand1028-1029242
β-strand1036142
α-helix10371
α-helix10401
β-strand1041-10501038
β-strand1051135
α-helix1055-10606
Chains C and O: 9 helices, 13 β-strands
ElementResiduesLengthSheet
β-strand8-14743
β-strand18-24743
α-helix28-369
α-helix37-415
β-strand44-551244
α-helix61-7010
β-strand73145
α-helix78-814
β-strand99-106844
β-strand113-116446
α-helix117-1193
β-strand121-122244
β-strand129145
β-strand149-153546
β-strand158-1681144
α-helix174-1763
β-strand179-182443
β-strand185143
α-helix204-2063
α-helix218-2214
β-strand229-235743
α-helix241-27030
Chains D and P: 10 helices, 4 β-strands
ElementResiduesLengthSheet
β-strand16147
β-strand21147
α-helix25-284
β-strand30-31221
α-helix34-4613
α-helix47-515
α-helix55-584
α-helix59-7012
α-helix77-8812
α-helix94-10310
α-helix108-1147
α-helix116-1216
α-helix128-13710
β-strand140148
Chains E and Q: 10 helices, 11 β-strands
ElementResiduesLengthSheet
α-helix3-2422
β-strand26-27249
α-helix30-334
α-helix37-448
β-strand60-64549
β-strand71-75549
β-strand81-82250
α-helix84-9714
β-strand101-106649
β-strand109-110250
α-helix112-1209
β-strand126-131649
α-helix132-1354
β-strand147-151551
α-helix1521
α-helix153-16311
α-helix1711
β-strand172-173251
α-helix178-1836
β-strand190-195651
β-strand203-209751
Chains F and R: 4 helices, 5 β-strands
ElementResiduesLengthSheet
β-strand56152
α-helix57-582
α-helix59-7416
β-strand79122
α-helix82-832
α-helix89-9911
β-strand105-109521
β-strand115-119521
β-strand124152
Chains G and S: 4 helices, 13 β-strands
ElementResiduesLengthSheet
β-strand2-131221
α-helix15-173
α-helix22-3312
β-strand38-39221
β-strand43-541221
β-strand57-59321
α-helix601
α-helix651
β-strand66-771221
β-strand83-921053
β-strand97-101553
β-strand104-108553
β-strand117-118254
β-strand128-130354
β-strand136-137254
β-strand142-1531253
β-strand156-162753
Chains H and T: 1 helix, 12 β-strands
ElementResiduesLengthSheet
β-strand4-15127
β-strand25-3177
β-strand38-4477
β-strand55-6177
β-strand65155
α-helix69-713
β-strand7415
β-strand83155
β-strand90-9897
β-strand101-10227
β-strand111-11887
β-strand121-12887
β-strand140-14787

4 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 subunitA, Mprotein1970Sus scrofa domesticus
DNA-directed RNA polymerase subunit betaB, Nprotein1174Sus scrofa domesticusA0A0B8RVL1 (AlphaFold model)
DNA-directed RNA polymerase II subunit RPB3C, Oprotein275Sus scrofa domesticusA0A481DF93 (AlphaFold model)
RNA polymerase II subunit DD, Pprotein142Sus scrofa domesticusA0A287ADR4 (AlphaFold model)
DNA-directed RNA polymerase II subunit EE, Qprotein210Sus scrofa domesticusI3LSI7 (AlphaFold model)
DNA-directed RNA polymerase II subunit FF, Rprotein127Sus scrofa domesticusA0A4X1VEK9
DNA-directed RNA polymerase II subunit RPB7G, Sprotein172Sus scrofa domesticusI3LJZ9
DNA-directed RNA polymerases I, II, and III subunit RPABC3H, Tprotein150Sus scrofa domesticusI3LCB2
DNA-directed RNA polymerase II subunit RPB9I, Uprotein125Sus scrofa domesticusP60899
DNA-directed RNA polymerases I, II, and III subunit RPABC5J, Vprotein67Sus scrofa domesticusA0A7K6NXI9
RNA_pol_L_2 domain-containing proteinK, Wprotein117Sus scrofa domesticusF1RKE4
RNA polymerase II subunit KL, Xprotein58Sus scrofa domesticusA0A4X1TRS6
Sequence of entity 1 (A, M), FASTA
>7OZO_1 DNA-directed RNA polymerase subunit (chains A, M)
MHGGGPPSGDSACPLRTIKRVQFGVLSPDELKRMSVTEGGIKYPETTEGGRPKLGGLMDP
RQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFHVGFLVKTMKVLRCVCFFCSKLLVD
SNNPKIKDILAKSKGQPKKRLTHVYDLCKGKNICEGGEEMDNKFGVEQPEGDEDLTKEKG
HGGCGRYQPRIRRSGLELYAEWKHVNEDSQEKKILLSPERVHEIFKRISDEECFVLGMEP
RYARPEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAA
HVIAEDVKLLQFHVATMVDNELPGLPRAMQKSGRPLKSLKQRLKGKEGRVRGNLMGKRVD
FSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRRGNSQYPGAKYII
RDNGDRIDLRFHPKPSDLHLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWS
TFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQD
TLTAVRKFTKRDVFLERGEVMNLLMFLSTWDGKVPQPAILKPRPLWTGKQIFSLIIPGHI
NCIRTHSTHPDDEDSGPYKHISPGDTKVVVENGELIMGILCKKSLGTSAGSLVHISYLEM
GHDITRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKA
HNNELEPTPGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKIN
ISQVIAVVGQQNVEGKRIPFGFKHRTLPHFIKDDYGPESRGFVENSYLAGLTPTEFFFHA
MGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSINQVVQLRYGEDGLAGES
VEFQNLATLKPSNKAFEKKFRFDYTNERALRRTLQEDLVKDVLSNAHIQNELEREFERMR
EDREVLRVIFPTGDSKVVLPCNLLRMIWNAQKIFHINPRLPSDLHPIKVVEGVKELSKKL
VIVNGDDPLSRQAQENATLLFNIHLRSTLCSRRMAEEFRLSGEAFDWLLGEIESKFNQAI
AHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKKPKTPSLT
VFLLGQSARDAERAKDILCRLEHTTLRKVTANTAIYYDPNPQSTVVAEDQEWVNVYYEMP
DFDVARISPWLLRVELDRKHMTDRKLTMEQIAEKINAGFGDDLNCIFNDDNAEKLVLRIR
IMNSDENKMQEEEEVVDKMDDDVFLRCIESNMLTDMTLQGIEQISKVYMHLPQTDNKKKI
IITEDGEFKALQEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIEAVRKALER
ELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLM
EAAAHGESDPMKGVSENIMLGQLAPAGTGCFDLLLDAEKCKYGMEIPTNIPGLGAAGPTG
MFFGSAPSPMGGISPAMTPWNQGATPAYGAWSPSVGSGMTPGAAGFSPSAASDASGFSPG
YSPAWSPTPGSPGSPGPSSPYIPSPGGAMSPSYSPTSPAYEPRSPGGYTPQSPSYSPTSP
SYSPTSPSYSPTSPNYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSP
TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS
YSPTSPNYSPTSPNYTPTSPSYSPTSPSYSPTSPNYTPTSPNYSPTSPSYSPTSPSYSPT
SPSYSPSSPRYTPQSPTYTPSSPSYSPSSPSYSPTSPKYTPTSPSYSPSSPEYTPTSPKY
SPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTS
PKYSPTSPTYSPTSPKGSTYSPTSPGYSPTSPTYSLTSPAISPDDSDEEN
Sequence of entity 2 (B, N), FASTA
>7OZO_2 DNA-directed RNA polymerase subunit beta (chains B, N)
MYDADEDMQYDEDDDEITPDLWQEACWIVISSYFDEKGLVRQQLDSFDEFIQMSVQRIVE
DAPPIDLQAEAQHASGEVEEPPRYLLKFEQIYLSKPTHWERDGAPSPMMPNEARLRNLTY
SAPLYVDITKTVIKEGEEQLQTQHQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLD
PGGYFIINGSEKVLIAQEKMATNTVYVFAKKDSKYAYTGECRSCLENSSRPTSTIWVSML
ARGGQGAKKSAIGQRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEM
VKPSLDEAFVIQEQNVALNFIGSRGAKPGVTKEKRIKYAKEVLQKEMLPHVGVSDFCETK
KAYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQ
KFIDRGKDFNLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLS
HLRRLNSPIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSP
ILEFLEEWSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSE
VSMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKEREYNNYSWQDLVASG
VVEYIDTLEEETVMLAMTPDDLQEKEVAYCSTYTHCEIHPSMILGVCASIIPFPDHNQSP
RNTYQSAMGKQAMGVYITNFHVRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIV
AIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESKKGFDQEEVFEKPTRETCQGM
RHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTLPENEDELEGTNRRYTKRDCSTFLRTSE
TGIVDQVMVTLNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEG
ITPDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFNDAVNVQKISNLLSDYGY
HLRGNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSR
DGGLRFGEMERDCQIAHGAAQFLRERLFEASDPYQVHVCNLCGIMAIANTRTHTYECRGC
RNKTQISLVRMPYACKLLFQELMSMSIAPRMMSV
Sequence of entity 3 (C, O), FASTA
>7OZO_3 DNA-directed RNA polymerase II subunit RPB3 (chains C, O)
MPYANQPTVRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLH
DEFIAHRLGLIPLTSDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDL
ISNSPRVIPVTSRNRDNDPSDYVEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA
GVAFEYDPDNALRHTVYPKPEEWPKSEYSELDEDESQAPYDPNGKPERFYYNVESCGSLR
PETIVLSALSGLKKKLSDLQTQLSHEIQSDVLTIN
Sequence of entity 4 (D, P), FASTA
>7OZO_4 RNA polymerase II subunit D (chains D, P)
MAAGGSDPRAGDVEEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNESAEDEQELSEV
FMKTLNYTARFSRFKNRETIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEG
RFEDEELQQILDDIQTKRSFQY
Sequence of entity 5 (E, Q), FASTA
>7OZO_5 DNA-directed RNA polymerase II subunit E (chains E, Q)
MDDEEETYRLWKIRKTIMQLCHDRGYLVTQDELDQTLEEFKAQFGDKPSEGRPRRTDLTV
LVAHNDDPTDQMFVFFPEEPKVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVD
MAPKYILEQFLQQELLINITEHELVPEHVVMTKEEVTELLARYKLRENQLPRIQAGDPVA
RYFGIKRGQVVKIIRPSETAGRYITYRLVQ
Sequence of entity 6 (F, R), FASTA
>7OZO_6 DNA-directed RNA polymerase II subunit F (chains F, R)
MSDNEDNFDGDDFDDVEEDEGLDDLENAEEEGQENVEILPSGERPQANQKRITTPYMTKY
ERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDWGV
DELIISD
Sequence of entity 7 (G, S), FASTA
>7OZO_7 DNA-directed RNA polymerase II subunit RPB7 (chains G, S)
MFYHISLEHEILLHPRYFGPNLLNTVKQKLFTEVEGTCTGKYGFVIAVTTIDNIGAGVIQ
PGRGFVLYPVKYKAIVFRPFKGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFD
PNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDKNDIFAIGSLMDDYLGLVS
Sequence of entity 8 (H, T), FASTA
>7OZO_8 DNA-directed RNA polymerases I, II, and III subunit RPABC3 (chains H, T)
MAGILFEDIFDVKDIDPEGKKFDRVSRLHCESESFKMDLILDVNIQIYPVDLGDKFRLVI
ASTLYEDGTLDDGEYNPTDDRPSRADQFEYVMYGKVYRIEGDETSTEAATRLSAYVSYGG
LLMRLQGDANNLHGFEVDSRVYLLMKKLAF
Sequence of entity 9 (I, U), FASTA
>7OZO_9 DNA-directed RNA polymerase II subunit RPB9 (chains I, U)
MEPDGTYEPGFVGIRFCQECNNMLYPKEDKENRILLYACRNCDYQQEADNSCIYVNKITH
EVDELTQIIADVSQDPTLPRTEDHPCQKCGHKEAVFFQSHSARAEDAMRLYYVCTAPHCG
HRWTE
Sequence of entity 10 (J, V), FASTA
>7OZO_10 DNA-directed RNA polymerases I, II, and III subunit RPABC5 (chains J, V)
MIIPVRCFTCGKIVGNKWEAYLGLLQAEYTEGDALDALGLKRYCCRRMLLAHVDLIEKLL
NYAPLEK
Sequence of entity 11 (K, W), FASTA
>7OZO_11 RNA_pol_L_2 domain-containing protein (chains K, W)
MNAPPAFESFLLFEGEKKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAG
YKVPHPLEHKIIIRVQTTPDYSPQEAFTNAITDLISELSLLEERFRVAIKDKQEGIE
Sequence of entity 12 (L, X), FASTA
>7OZO_12 RNA polymerase II subunit K (chains L, X)
MDTQKDVQPPKQQPMIYICGECHTENEIKSRDPIRCRECGYRIMYKKRTKRLVVFDAR

Ligands and cofactors

IDNameFormulaCopies
ZNZinc ionZn10

Primary citation

Structure of an inactive RNA polymerase II dimer. Aibara, S., Dienemann, C., Cramer, P. Nucleic Acids Res (2021) 49:10747-10755. DOI 10.1093/nar/gkab783 · PubMed

Other PDB entries of the same protein (UniProt A0A0B8RVL1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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