7OZN: RNA Polymerase II dimer

RNA Polymerase II dimer (Class 1). Determined by electron microscopy at 3.5 Å resolution. Released 6 Oct 2021.

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

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

Secondary structure: helices and β-sheets

7OZN contains 306 α-helices and 386 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: 55 helices, 51 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-strand579-58136
β-strand58516
β-strand586-58724
α-helix588-5958
β-strand602-60547
α-helix611-6155
β-strand627-63157
β-strand634-63747
α-helix652-6598
α-helix662-68322
β-strand68618
α-helix689-6924
α-helix693-6953
α-helix696-72126
α-helix733-75927
α-helix765-7728
α-helix778-7814
α-helix782-7865
β-strand789-79029
β-strand793110
β-strand796110
α-helix8111
β-strand822-82329
α-helix833-86836
β-strand872-873211
β-strand879-880211
β-strand886-888311
α-helix891-8933
β-strand896112
β-strand902-905413
α-helix915-9206
α-helix927-9337
β-strand934114
α-helix936-9449
α-helix946-96924
β-strand976-979413
α-helix983-99311
α-helix10011
β-strand1002114
α-helix1006-101914
α-helix1028-103710
α-helix1039-104810
α-helix1051-10566
α-helix1062-107918
β-strand1080112
α-helix1081-10822
α-helix1087-110014
α-helix1121-11288
β-strand1139-1142415
α-helix1146-11483
α-helix1152-11543
α-helix1155-11617
β-strand1164116
α-helix1166-11694
β-strand1170-1176717
β-strand1177118
α-helix1190-11989
β-strand1210118
β-strand1214-1216317
α-helix1218-12247
α-helix1228-123912
β-strand1243-1247517
β-strand1255-1261717
α-helix1263-12664
α-helix1282-129413
β-strand1299116
β-strand1307-1310415
β-strand1320-1322319
β-strand1328-1330319
β-strand1335-1338415
α-helix1343-13475
β-strand1359115
α-helix1362-13687
α-helix1371-138818
α-helix1395-140511
α-helix1413-14153
β-strand1471-1475520
α-helix1479-14813
β-strand1484121
Chains B and N: 48 helices, 64 β-strands
ElementResiduesLengthSheet
α-helix19-3618
α-helix41-499
α-helix50-545
α-helix55-606
α-helix62-643
β-strand65-67322
β-strand83-931122
β-strand97-98223
β-strand106-107223
α-helix110-1167
β-strand121-1331322
β-strand140-1531422
α-helix168-1736
β-strand185-187324
β-strand190-193424
β-strand196-200525
α-helix2011
β-strand206-209426
β-strand215-223926
β-strand233-240826
α-helix249-2524
β-strand256-259426
β-strand263127
β-strand266-268326
α-helix269-2768
α-helix281-2888
α-helix295-30915
α-helix314-32310
β-strand325127
α-helix332-34110
α-helix342-3465
α-helix358-37720
α-helix381-3844
α-helix388-3903
β-strand391-394425
α-helix396-42530
α-helix431-4344
α-helix437-45014
β-strand461128
β-strand468-469224
α-helix4701
α-helix475-4828
β-strand484-486325
α-helix491-4955
α-helix501-5022
α-helix503-5053
β-strand509129
β-strand523-525325
β-strand526129
β-strand531-532230
α-helix539-5479
α-helix558-5614
β-strand565131
β-strand566-569432
β-strand572-573232
β-strand577131
α-helix580-59213
β-strand602-606532
α-helix607-6093
β-strand611-615532
β-strand621-627730
β-strand628133
β-strand633133
α-helix637-6448
α-helix653-6597
β-strand662-666530
α-helix667-6704
α-helix679-6835
β-strand695-696230
α-helix700-7034
α-helix706-7094
α-helix719-73113
β-strand732134
β-strand748-751435
β-strand759-760236
α-helix763-7675
β-strand776-782737
β-strand78318
β-strand794-797437
α-helix798-8025
β-strand808-8181135
β-strand827-828238
β-strand837-839338
β-strand844139
β-strand853140
α-helix854-8552
β-strand859-860235
β-strand864139
β-strand865-867340
β-strand870-871238
β-strand889-891338
β-strand894-895240
β-strand902-9111035
β-strand917-9271135
β-strand934-937437
β-strand943-949737
β-strand956-957241
β-strand965-967337
α-helix969-9713
α-helix978-99316
α-helix9961
β-strand997-998236
α-helix1008-10169
β-strand1025-1026237
β-strand1028-1029241
α-helix10301
β-strand1036141
α-helix10371
α-helix10401
β-strand1041-10501037
β-strand1051134
α-helix1055-10606
Chains C and O: 9 helices, 13 β-strands
ElementResiduesLengthSheet
β-strand8-14742
β-strand18-24742
α-helix28-369
α-helix37-415
β-strand44-551243
α-helix61-7010
β-strand73144
α-helix78-814
β-strand99-106843
β-strand113-116445
α-helix117-1193
β-strand121-122243
β-strand129144
β-strand149-153545
β-strand158-1681143
α-helix174-1763
β-strand179-182442
β-strand185142
α-helix204-2063
α-helix218-2214
β-strand229-235742
α-helix241-27030
Chains D and P: 10 helices, 4 β-strands
ElementResiduesLengthSheet
β-strand16146
β-strand21146
α-helix25-284
β-strand30-31220
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-strand140147
Chains E and Q: 10 helices, 11 β-strands
ElementResiduesLengthSheet
α-helix3-2422
β-strand26-27248
α-helix30-334
α-helix37-448
β-strand60-64548
β-strand71-75548
β-strand81-82249
α-helix84-9714
β-strand101-106648
β-strand109-110249
α-helix112-1209
β-strand126-131648
α-helix132-1354
β-strand147-151550
α-helix1521
α-helix153-16311
α-helix1711
β-strand172-173250
α-helix178-1836
β-strand190-195650
β-strand203-209750
Chains F and R: 4 helices, 5 β-strands
ElementResiduesLengthSheet
β-strand56151
α-helix57-582
α-helix59-7416
β-strand79121
α-helix82-832
α-helix89-9911
β-strand105-109520
β-strand115-119520
β-strand124151
Chains G and S: 4 helices, 13 β-strands
ElementResiduesLengthSheet
β-strand2-131220
α-helix15-173
α-helix22-3312
β-strand38-39220
β-strand43-541220
β-strand57-59320
α-helix601
α-helix651
β-strand66-771220
β-strand83-921052
β-strand97-101552
β-strand104-108552
β-strand117-118253
β-strand128-130353
β-strand136-137253
β-strand142-1531252
β-strand156-162752
Chains H and T: 1 helix, 12 β-strands
ElementResiduesLengthSheet
β-strand4-15126
β-strand25-3176
β-strand38-4476
β-strand55-6176
β-strand65154
α-helix69-713
β-strand7415
β-strand83154
β-strand90-9896
β-strand101-10226
β-strand111-11886
β-strand121-12886
β-strand140-14786

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
RPB1A, 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
RPB10J, Vprotein67Sus scrofa domesticus
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
>7OZN_1 RPB1 (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
>7OZN_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
>7OZN_3 DNA-directed RNA polymerase II subunit RPB3 (chains C, O)
MPYANQPTVRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLH
DEFIAHRLGLIPLTSDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDL
ISNSPRVIPVTSRNRDNDPSDYVEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA
GVAFEYDPDNALRHTVYPKPEEWPKSEYSELDEDESQAPYDPNGKPERFYYNVESCGSLR
PETIVLSALSGLKKKLSDLQTQLSHEIQSDVLTIN
Sequence of entity 4 (D, P), FASTA
>7OZN_4 RNA polymerase II subunit D (chains D, P)
MAAGGSDPRAGDVEEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNESAEDEQELSEV
FMKTLNYTARFSRFKNRETIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEG
RFEDEELQQILDDIQTKRSFQY
Sequence of entity 5 (E, Q), FASTA
>7OZN_5 DNA-directed RNA polymerase II subunit E (chains E, Q)
MDDEEETYRLWKIRKTIMQLCHDRGYLVTQDELDQTLEEFKAQFGDKPSEGRPRRTDLTV
LVAHNDDPTDQMFVFFPEEPKVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVD
MAPKYILEQFLQQELLINITEHELVPEHVVMTKEEVTELLARYKLRENQLPRIQAGDPVA
RYFGIKRGQVVKIIRPSETAGRYITYRLVQ
Sequence of entity 6 (F, R), FASTA
>7OZN_6 DNA-directed RNA polymerase II subunit F (chains F, R)
MSDNEDNFDGDDFDDVEEDEGLDDLENAEEEGQENVEILPSGERPQANQKRITTPYMTKY
ERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDWGV
DELIISD
Sequence of entity 7 (G, S), FASTA
>7OZN_7 DNA-directed RNA polymerase II subunit RPB7 (chains G, S)
MFYHISLEHEILLHPRYFGPNLLNTVKQKLFTEVEGTCTGKYGFVIAVTTIDNIGAGVIQ
PGRGFVLYPVKYKAIVFRPFKGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFD
PNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDKNDIFAIGSLMDDYLGLVS
Sequence of entity 8 (H, T), FASTA
>7OZN_8 DNA-directed RNA polymerases I, II, and III subunit RPABC3 (chains H, T)
MAGILFEDIFDVKDIDPEGKKFDRVSRLHCESESFKMDLILDVNIQIYPVDLGDKFRLVI
ASTLYEDGTLDDGEYNPTDDRPSRADQFEYVMYGKVYRIEGDETSTEAATRLSAYVSYGG
LLMRLQGDANNLHGFEVDSRVYLLMKKLAF
Sequence of entity 9 (I, U), FASTA
>7OZN_9 DNA-directed RNA polymerase II subunit RPB9 (chains I, U)
MEPDGTYEPGFVGIRFCQECNNMLYPKEDKENRILLYACRNCDYQQEADNSCIYVNKITH
EVDELTQIIADVSQDPTLPRTEDHPCQKCGHKEAVFFQSHSARAEDAMRLYYVCTAPHCG
HRWTE
Sequence of entity 10 (J, V), FASTA
>7OZN_10 RPB10 (chains J, V)
MIIPVRCFTCGKIVGNKWEAYLGLLQAEYTEGDALDALGLKRYCCRRMLLAHVDLIEKLL
NYAPLEK
Sequence of entity 11 (K, W), FASTA
>7OZN_11 RNA_pol_L_2 domain-containing protein (chains K, W)
MNAPPAFESFLLFEGEKKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAG
YKVPHPLEHKIIIRVQTTPDYSPQEAFTNAITDLISELSLLEERFRVAIKDKQEGIE
Sequence of entity 12 (L, X), FASTA
>7OZN_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:

Browse structure collections

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