7B7U: Mammalian RNA polymerase II

Cryo-EM structure of mammalian RNA polymerase II in complex with human RPAP2. Determined by electron microscopy at 2.8 Å resolution. Released 19 May 2021.

Method
Electron microscopy
Resolution
2.8 Å
Organisms
Sus scrofa domesticus, Homo sapiens
Chains
12
Atoms
25,091
Mol. weight
553.88 kDa
Ligands
ZN
Released
19 May 2021

Explore 7B7U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7B7U contains 137 α-helices and 163 β-strands across 12 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: 45 helices, 46 β-strands

ElementResiduesLengthSheet
β-strand36511
β-strand367-36932
β-strand377-38152
α-helix382-3876
β-strand389-39353
α-helix399-40810
β-strand416-42053
β-strand426-42833
β-strand445-44953
β-strand455-45732
β-strand471-47772
β-strand482-48432
β-strand50111
β-strand50412
α-helix509-51810
α-helix542-5487
α-helix557-5659
α-helix573-5775
β-strand579-58134
β-strand58514
α-helix588-5958
β-strand602-60435
α-helix612-6154
β-strand628-63035
β-strand635-63735
α-helix642-6454
α-helix652-6609
α-helix662-68322
β-strand68616
α-helix689-6924
α-helix696-72227
α-helix726-7283
α-helix733-75927
α-helix765-7728
α-helix778-7858
β-strand789-79027
β-strand79318
β-strand79618
β-strand80219
β-strand80519
β-strand822-82327
α-helix833-86735
β-strand872-873210
β-strand879-880210
β-strand886-888310
α-helix891-8933
β-strand896111
β-strand902-905412
α-helix913-9197
α-helix929-9335
β-strand934113
α-helix936-9449
α-helix946-96924
α-helix971-9733
β-strand976-979412
α-helix983-99311
β-strand1002113
α-helix1006-101914
α-helix1028-104821
α-helix1051-10533
α-helix1054-10585
α-helix1062-107918
β-strand1080111
α-helix1087-109610
α-helix1097-11015
α-helix1121-11288
β-strand1140-1141214
α-helix1146-11494
α-helix1151-11599
β-strand1164115
β-strand1170-1177816
α-helix1187-11893
α-helix1190-11978
α-helix1204-12063
β-strand1207117
β-strand1210-1216716
α-helix1218-12236
α-helix1228-123912
β-strand1245-1247316
β-strand1256-1259416
β-strand1262117
α-helix1281-129212
β-strand1299115
β-strand1306-1310514
β-strand1319-1322418
β-strand1328-1331418
β-strand1335-1339514
α-helix1343-13486
α-helix1362-13687
α-helix1371-138717
α-helix1395-140410
Chain B: 47 helices, 59 β-strands
ElementResiduesLengthSheet
α-helix22-3615
α-helix41-499
α-helix50-545
α-helix56-583
α-helix63-642
β-strand65-67319
β-strand83-931119
β-strand97-99320
β-strand105-107320
α-helix110-1156
β-strand121-1331319
β-strand139-1531519
α-helix168-1714
β-strand185-187321
β-strand190-193421
α-helix194-1952
β-strand196-200522
α-helix2011
β-strand204-208523
β-strand215-222823
β-strand234-240723
β-strand256-259423
β-strand267-268223
α-helix269-2768
α-helix281-2888
α-helix295-30612
α-helix314-3229
α-helix332-34110
α-helix342-3465
α-helix358-37619
α-helix381-3844
α-helix388-3903
β-strand391-394422
α-helix396-42227
α-helix431-4344
α-helix437-44913
β-strand468-469221
α-helix4701
α-helix475-4828
β-strand485-486222
α-helix501-5022
α-helix503-5053
β-strand509124
β-strand523-524222
β-strand526124
β-strand531-532225
α-helix539-5479
β-strand552126
α-helix553-5553
α-helix560-5634
β-strand565-569526
β-strand572-577626
α-helix580-59314
β-strand602-606526
β-strand611-615526
β-strand621-627725
β-strand628127
β-strand633127
α-helix637-6448
α-helix653-6586
β-strand662-666525
α-helix667-6704
β-strand675-676225
β-strand695-696225
α-helix700-7034
α-helix708-7103
α-helix714-7163
α-helix719-73012
β-strand732128
β-strand748-751429
β-strand755130
β-strand759-760231
α-helix763-7664
β-strand776-782732
β-strand78316
β-strand794-797432
α-helix798-8036
β-strand808-8171029
β-strand828-829233
β-strand853134
α-helix854-8552
β-strand859-860229
β-strand867134
β-strand869-871333
β-strand890-891233
β-strand894134
β-strand902-9111029
β-strand917-9271129
β-strand934-937432
β-strand943-949732
β-strand956-957235
β-strand965-967332
α-helix969-9713
α-helix978-99316
α-helix9961
β-strand997-998231
α-helix1008-10169
β-strand1025-1026232
β-strand1028-1029235
α-helix10351
β-strand1036135
α-helix10371
α-helix10401
β-strand1041-10501032
β-strand1051128
α-helix1055-10595
Chain C: 10 helices, 12 β-strands
ElementResiduesLengthSheet
β-strand8-14736
β-strand18-24736
α-helix28-4013
β-strand44-551237
α-helix61-699
β-strand73138
α-helix78-814
β-strand99-106837
α-helix1121
β-strand113-116439
α-helix117-1193
β-strand121-122237
β-strand129138
β-strand149-153539
β-strand158-1681137
α-helix174-1763
β-strand179-185736
α-helix200-2023
α-helix204-2063
α-helix218-2203
β-strand229-235736
α-helix241-27030
Chain E: 10 helices, 10 β-strands
ElementResiduesLengthSheet
α-helix4-2320
β-strand26140
α-helix30-334
α-helix37-437
α-helix49-513
β-strand60-61241
β-strand64140
β-strand73-75341
α-helix84-9613
β-strand101-105541
α-helix112-1209
β-strand126-130541
α-helix134-1363
α-helix139-1413
β-strand147-150442
α-helix153-16311
β-strand172-173242
α-helix178-1836
β-strand190-197842
β-strand201-209942
Chain F: 3 helices, 2 β-strands
ElementResiduesLengthSheet
α-helix59-7416
α-helix89-9810
β-strand105-107343
β-strand117-119343
α-helix120-1223
Chain H: 2 helices, 10 β-strands
ElementResiduesLengthSheet
β-strand4-14114
β-strand25-3284
β-strand38-4474
β-strand55-6174
α-helix84-874
β-strand90-100114
β-strand104144
β-strand107144
β-strand113-11864
β-strand121-12664
α-helix131-1333
β-strand139-14794
Chain I: 3 helices, 10 β-strands
ElementResiduesLengthSheet
β-strand16145
β-strand23145
β-strand25-29546
β-strand34-38546
β-strand45-47346
β-strand52-56516
α-helix64-674
α-helix70-745
β-strand80-81247
β-strand94-97447
α-helix109-1102
β-strand111-114447
β-strand122-124347
Chain J: 6 helices, 1 β-strand
ElementResiduesLengthSheet
α-helix3-42
α-helix18-269
α-helix31-377
α-helix43-519
β-strand52130
α-helix56-605
α-helix63-642

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 subunitAprotein1970Sus scrofa domesticusI3LJR4
DNA-directed RNA polymerase subunit betaBprotein1174Sus scrofa domesticusI3LGP4 (AlphaFold model)
DNA-directed RNA polymerase II subunit RPB3Cprotein271Sus scrofa domesticusI3LCH3 (AlphaFold model)
DNA-directed RNA polymerase II subunit EEprotein210Sus scrofa domesticusI3LSI7 (AlphaFold model)
DNA-directed RNA polymerase II subunit FFprotein127Sus scrofa domesticusA0A4X1VEK9
DNA-directed RNA polymerases I, II, and III subunit RPABC3Hprotein150Sus scrofa domesticusI3LCB2
DNA-directed RNA polymerase II subunit RPB9Iprotein125Sus scrofa domesticusP60899
Uncharacterized ProteinJprotein67Sus scrofa domesticusA0A4X1VYD0
RNA_pol_L_2 domain-containing proteinKprotein117Sus scrofa domesticusF1RKE4
RNA polymerase II subunit KLprotein58Sus scrofa domesticusA0A4X1TRS6
Putative RNA polymerase II subunit B1 CTD phosphatase RPAP2Mprotein612Homo sapiensQ8IXW5
UnknownNprotein30Homo sapiens
Sequence of entity 1 (A), FASTA
>7B7U_1 DNA-directed RNA polymerase subunit (chains A)
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), FASTA
>7B7U_2 DNA-directed RNA polymerase subunit beta (chains B)
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), FASTA
>7B7U_3 DNA-directed RNA polymerase II subunit RPB3 (chains C)
MPYANQPTVRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLH
DEFIAHRLGLIPLTSDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDL
ISNSPRVIPVTSRNRDNDPSDYVEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA
GVAFEYDPDNALRHTVYPKPEEWPKSEYSELDEDESQAPYDPNGKPERFYYNVESCGSLR
PETIVLSALSGLKKKLSDLQTQLSHEIQSDV
Sequence of entity 4 (E), FASTA
>7B7U_4 DNA-directed RNA polymerase II subunit E (chains E)
MDDEEETYRLWKIRKTIMQLCHDRGYLVTQDELDQTLEEFKAQFGDKPSEGRPRRTDLTV
LVAHNDDPTDQMFVFFPEEPKVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVD
MAPKYILEQFLQQELLINITEHELVPEHVVMTKEEVTELLARYKLRENQLPRIQAGDPVA
RYFGIKRGQVVKIIRPSETAGRYITYRLVQ
Sequence of entity 5 (F), FASTA
>7B7U_5 DNA-directed RNA polymerase II subunit F (chains F)
MSDNEDNFDGDDFDDVEEDEGLDDLENAEEEGQENVEILPSGERPQANQKRITTPYMTKY
ERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDWGV
DELIISD
Sequence of entity 6 (H), FASTA
>7B7U_6 DNA-directed RNA polymerases I, II, and III subunit RPABC3 (chains H)
MAGILFEDIFDVKDIDPEGKKFDRVSRLHCESESFKMDLILDVNIQIYPVDLGDKFRLVI
ASTLYEDGTLDDGEYNPTDDRPSRADQFEYVMYGKVYRIEGDETSTEAATRLSAYVSYGG
LLMRLQGDANNLHGFEVDSRVYLLMKKLAF
Sequence of entity 7 (I), FASTA
>7B7U_7 DNA-directed RNA polymerase II subunit RPB9 (chains I)
MEPDGTYEPGFVGIRFCQECNNMLYPKEDKENRILLYACRNCDYQQEADNSCIYVNKITH
EVDELTQIIADVSQDPTLPRTEDHPCQKCGHKEAVFFQSHSARAEDAMRLYYVCTAPHCG
HRWTE
Sequence of entity 8 (J), FASTA
>7B7U_8 Uncharacterized Protein (chains J)
MIIPVRCFTCGKIVGNKWEAYLGLLQAEYTEGDALDALGLKRYCCRRMLLAHVDLIEKLL
NYAPLEK
Sequence of entity 9 (K), FASTA
>7B7U_9 RNA_pol_L_2 domain-containing protein (chains K)
MNAPPAFESFLLFEGEKKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAG
YKVPHPLEHKIIIRVQTTPDYSPQEAFTNAITDLISELSLLEERFRVAIKDKQEGIE
Sequence of entity 10 (L), FASTA
>7B7U_10 RNA polymerase II subunit K (chains L)
MDTQKDVQPPKQQPMIYICGECHTENEIKSRDPIRCRECGYRIMYKKRTKRLVVFDAR
Sequence of entity 11 (M), FASTA
>7B7U_11 Putative RNA polymerase II subunit B1 CTD phosphatase RPAP2 (chains M)
MADFAGPSSAGRKAGAPRCSRKAAGTKQTSTLKQEDASKRKAELEAAVRKKIEFERKALH
IVEQLLEENITEEFLMECGRFITPAHYSDVVDERSIVKLCGYPLCQKKLGIVPKQKYKIS
TKTNKVYDITERKSFCSNFCYQASKFFEAQIPKTPVWVREEERHPDFQLLKEEQSGHSGE
EVQLCSKAIKTSDIDNPSHFEKQYESSSSSTHSDSSSDNEQDFVSSILPGNRPNSTNIRP
QLHQKSIMKKKAGHKANSKHKDKEQTVVDVTEQLGDCKLDSQEKDATCELPLQKVNTQSS
SNSTLPERLKASENSESEYSRSEITLVGISKKSAEHFKRKFAKSNQVSRSVSSSVQVCPE
VGKRNLLKVLKETLIEWKTEETLRFLYGQNYASVCLKPEASLVKEELDEDDIISDPDSHF
PAWRESQNSLDESLPFRGSGTAIKPLPSYENLKKETEKLNLRIREFYRGRYVLGEETTKS
QDSEEHDSTFPLIDSSSQNQIRKRIVLEKLSKVLPGLLVPLQITLGDIYTQLKNLVRTFR
LTNRNIIHKPAEWTLIAMVLLSLLTPILGIQKHSQEGMVFTRFLDTLLEELHLKNEDLES
LTIIFRTSCLPE
Sequence of entity 12 (N), FASTA
>7B7U_12 Unknown (chains N)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Ligands and cofactors

IDNameFormulaCopies
ZNZinc ionZn6

Primary citation

Cryo-EM structure of mammalian RNA polymerase II in complex with human RPAP2. Fianu, I., Dienemann, C., Aibara, S. et al. Commun Biol (2021) 4:606-606. DOI 10.1038/s42003-021-02088-z · PubMed

Other PDB entries of the same protein (UniProt I3LJR4), best resolution first:

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