6DRD: RNA Pol II(G)

RNA Pol II(G). Determined by electron microscopy at 3.9 Å resolution. Released 12 Jun 2019.

Method
Electron microscopy
Resolution
3.9 Å
Organism
Homo sapiens
Chains
13
Atoms
26,708
Mol. weight
523.57 kDa
Ligands
ZN
Released
12 Jun 2019

Explore 6DRD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6DRD contains 138 α-helices and 196 β-strands across 13 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: 53 helices, 48 β-strands

ElementResiduesLengthSheet
β-strand36511
β-strand367-36932
β-strand378-37922
β-strand390-39343
α-helix3941
α-helix398-4003
α-helix402-4087
β-strand416-42053
β-strand427-42823
α-helix435-4373
β-strand445-44843
β-strand45714
β-strand47114
β-strand474-47522
β-strand482-48432
β-strand50111
β-strand50414
α-helix513-5164
β-strand52014
α-helix539-54810
β-strand554-55525
α-helix560-5634
α-helix574-5763
α-helix5851
β-strand586-58725
α-helix588-5958
β-strand602-60436
α-helix611-6144
β-strand628-63146
β-strand634-63746
α-helix652-6554
α-helix663-67513
α-helix680-6834
α-helix689-6924
α-helix696-6994
α-helix701-7099
α-helix711-72010
α-helix726-7283
α-helix735-7417
α-helix748-75912
α-helix767-7693
α-helix782-7854
β-strand78917
β-strand79318
β-strand79618
β-strand82317
α-helix835-85218
α-helix857-86711
β-strand872-87329
β-strand879-88029
β-strand886-88839
α-helix891-8933
β-strand896110
β-strand902-905411
α-helix913-9197
α-helix929-9335
α-helix941-9444
α-helix946-9494
α-helix952-96918
β-strand976-979411
α-helix985-9906
α-helix1006-101712
α-helix1028-10358
α-helix1040-10478
α-helix1054-10585
α-helix1062-107918
β-strand1080110
α-helix1087-10926
α-helix1121-11244
β-strand1139-1141312
β-strand1143113
α-helix1146-11494
α-helix1155-11584
β-strand1164114
β-strand1172-1176515
α-helix1181-11833
α-helix1190-11989
β-strand1207116
β-strand1211-1215515
α-helix1219-12224
α-helix1228-123912
β-strand1244-1247415
β-strand1256-1260515
β-strand1262116
α-helix1281-129212
β-strand1299114
β-strand1310117
β-strand1319-1320218
β-strand1330-1331218
β-strand1335117
β-strand1336-1337212
α-helix1343-13486
β-strand1352113
β-strand1358-1359212
α-helix1362-13665
α-helix1379-13824
α-helix1387-13893
α-helix1395-13973
α-helix1402-14054
β-strand1472-1475419
α-helix1477-14815
Chain B: 36 helices, 63 β-strands
ElementResiduesLengthSheet
α-helix22-298
α-helix31-366
α-helix41-433
α-helix46-505
α-helix57-615
α-helix63-642
β-strand65120
β-strand83-921020
β-strand97-99321
β-strand105-107321
α-helix110-1156
β-strand121-1331320
β-strand139-1531520
α-helix154-1552
α-helix168-1714
β-strand185-187322
β-strand190-193422
β-strand196-197223
β-strand199-200224
α-helix201-2022
β-strand206-207225
β-strand219-220225
β-strand236-237225
β-strand238-239226
α-helix246-2483
β-strand256-257226
α-helix269-2746
α-helix295-30511
α-helix314-3229
α-helix332-34514
α-helix358-37619
α-helix381-3844
α-helix388-3903
β-strand391-392224
α-helix396-42025
α-helix440-4467
β-strand468-469222
α-helix476-4805
β-strand484127
β-strand485-486223
α-helix503-5053
β-strand509128
β-strand525127
β-strand526128
β-strand531129
α-helix539-5457
α-helix553-5553
β-strand566-567230
β-strand568-569231
β-strand572-573231
α-helix580-59112
β-strand602-606530
β-strand611-615530
β-strand622-627629
β-strand628-629232
β-strand632-633232
α-helix637-6437
β-strand662-666529
α-helix670-6723
β-strand695-696229
β-strand717133
α-helix720-7289
β-strand749-751334
β-strand755135
β-strand759-760236
β-strand775135
β-strand776-782737
β-strand794-795237
β-strand796-797238
α-helix798-8014
β-strand808-810334
β-strand817139
β-strand827-829340
β-strand837141
α-helix854-8552
β-strand858-859239
β-strand865-871740
β-strand889141
β-strand892-895440
α-helix897-8993
β-strand903-911939
β-strand917-924839
β-strand925-927334
β-strand935-936242
β-strand943142
β-strand948-949238
α-helix955-9562
β-strand965-967337
β-strand977133
α-helix980-98910
β-strand997-998236
α-helix1012-10154
β-strand1025-1026237
β-strand1029143
α-helix10351
β-strand1036143
α-helix10371
β-strand1041-1048837
β-strand1049-1050242
Chain C: 12 helices, 17 β-strands
ElementResiduesLengthSheet
β-strand8-15844
β-strand18-24744
α-helix28-3811
β-strand44-551245
α-helix61-7010
β-strand73146
β-strand101-103345
β-strand106-107247
α-helix1121
β-strand113-116448
α-helix117-1193
β-strand121-122245
α-helix1281
β-strand129146
α-helix146-1483
β-strand149-153548
β-strand157-158247
β-strand159-1681045
α-helix174-1763
β-strand179149
β-strand186144
α-helix203-2053
β-strand229144
β-strand232-234344
β-strand235149
α-helix243-2497
α-helix253-2564
α-helix260-2678
α-helix268-2703
Chain D: 7 helices, 1 β-strand
ElementResiduesLengthSheet
β-strand31119
α-helix38-4912
α-helix59-7012
α-helix77-8812
α-helix94-985
α-helix99-1035
α-helix108-1147
α-helix124-13411
Chain E: 7 helices, 10 β-strands
ElementResiduesLengthSheet
α-helix8-2316
β-strand26150
β-strand61-62251
β-strand64150
β-strand72-74351
α-helix84-9613
β-strand101-106651
α-helix114-1163
α-helix117-1204
β-strand127-131551
β-strand148-150352
α-helix151-1522
α-helix153-16210
β-strand172-173252
α-helix180-1834
β-strand190-195652
β-strand203-209752
Chain F: 2 helices, 4 β-strands
ElementResiduesLengthSheet
β-strand56153
α-helix61-7414
α-helix90-989
β-strand104-109619
β-strand115-119519
β-strand124153
Chain G: 2 helices, 19 β-strands
ElementResiduesLengthSheet
β-strand2-131219
α-helix24-3310
β-strand39154
β-strand43154
β-strand44-541119
β-strand57-59319
α-helix601
β-strand66-771219
β-strand85-88455
β-strand92156
β-strand97156
β-strand99-101357
β-strand104-108557
β-strand118-120358
β-strand127-129358
β-strand136158
β-strand142-145455
β-strand151-152259
β-strand157-158259
β-strand159-161357
β-strand170155
Chain H: 2 helices, 13 β-strands
ElementResiduesLengthSheet
β-strand4-10760
β-strand11-14461
β-strand25162
β-strand28-31461
β-strand39-41361
β-strand44162
β-strand56-61660
α-helix69-713
β-strand91-1001060
β-strand113-117560
β-strand118163
β-strand121163
β-strand123-124261
α-helix135-1362
β-strand139-147960

5 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 II subunit RPB1Aprotein1970Homo sapiensP24928 (AlphaFold model)
DNA-directed RNA polymerase II subunit RPB2Bprotein1174Homo sapiensP30876 (AlphaFold model)
DNA-directed RNA polymerase II subunit RPB3Cprotein275Homo sapiensP19387 (AlphaFold model)
DNA-directed RNA polymerase II subunit RPB4Dprotein142Homo sapiensO15514 (AlphaFold model)
DNA-directed RNA polymerases I, II, and III subunit RPABC1Eprotein210Homo sapiensP19388
DNA-directed RNA polymerases I, II, and III subunit RPABC2Fprotein127Homo sapiensP61218
DNA-directed RNA polymerase II subunit RPB7Gprotein172Homo sapiensP62487
DNA-directed RNA polymerases I, II, and III subunit RPABC3Hprotein150Homo sapiensP52434
DNA-directed RNA polymerase II subunit RPB9Iprotein125Homo sapiensP36954
DNA-directed RNA polymerases I, II, and III subunit RPABC5Jprotein67Homo sapiensP62875
DNA-directed RNA polymerase II subunit RPB11-aKprotein117Homo sapiensP52435
DNA-directed RNA polymerases I, II, and III subunit RPABC4Lprotein58Homo sapiensP53803

1 more molecules are not listed.

Sequence of entity 1 (A), FASTA
>6DRD_1 DNA-directed RNA polymerase II subunit RPB1 (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
>6DRD_2 DNA-directed RNA polymerase II subunit RPB2 (chains B)
MYDADEDMQYDEDDDEITPDLWQEACWIVISSYFDEKGLVRQQLDSFDEFIQMSVQRIVE
DAPPIDLQAEAQHASGEVEEPPRYLLKFEQIYLSKPTHWERDGAPSPMMPNEARLRNLTY
SAPLYVDITKTVIKEGEEQLQTQHQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLD
PGGYFIINGSEKVLIAQEKMATNTVYVFAKKDSKYAYTGECRSCLENSSRPTSTIWVSML
ARGGQGAKKSAIGQRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEM
VKPSLDEAFVIQEQNVALNFIGSRGAKPGVTKEKRIKYAKEVLQKEMLPHVGVSDFCETK
KAYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQ
KFIDRGKDFNLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLS
HLRRLNSPIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSP
ILEFLEEWSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSE
VSMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKEREYNNYSWQDLVASG
VVEYIDTLEEETVMLAMTPDDLQEKEVAYCSTYTHCEIHPSMILGVCASIIPFPDHNQSP
RNTYQSAMGKQAMGVYITNFHVRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIV
AIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESKKGFDQEEVFEKPTRETCQGM
RHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTLPENEDELESTNRRYTKRDCSTFLRTSE
TGIVDQVMVTLNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEG
ITPDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFNDAVNVQKISNLLSDYGY
HLRGNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSR
DGGLRFGEMERDCQIAHGAAQFLRERLFEASDPYQVHVCNLCGIMAIANTRTHTYECRGC
RNKTQISLVRMPYACKLLFQELMSMSIAPRMMSV
Sequence of entity 3 (C), FASTA
>6DRD_3 DNA-directed RNA polymerase II subunit RPB3 (chains C)
MPYANQPTVRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLH
DEFIAHRLGLIPLISDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDL
ISNSPRVIPVTSRNRDNDPNDYVEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA
GVAFEYDPDNALRHTVYPKPEEWPKSEYSELDEDESQAPYDPNGKPERFYYNVESCGSLR
PETIVLSALSGLKKKLSDLQTQLSHEIQSDVLTIN
Sequence of entity 4 (D), FASTA
>6DRD_4 DNA-directed RNA polymerase II subunit RPB4 (chains D)
MAAGGSDPRAGDVEEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNESAEDEQELSEV
FMKTLNYTARFSRFKNRETIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEG
RFEDEELQQILDDIQTKRSFQY
Sequence of entity 5 (E), FASTA
>6DRD_5 DNA-directed RNA polymerases I, II, and III subunit RPABC1 (chains E)
MDDEEETYRLWKIRKTIMQLCHDRGYLVTQDELDQTLEEFKAQFGDKPSEGRPRRTDLTV
LVAHNDDPTDQMFVFFPEEPKVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVD
MAPKYILEQFLEQELLINITEHELVPEHVVMTKEEVSELLARYKLRENQLPRIQAGDPVA
RYFGIRRGQVVKIIRPSETAGRYITYRLVQ
Sequence of entity 6 (F), FASTA
>6DRD_6 DNA-directed RNA polymerases I, II, and III subunit RPABC2 (chains F)
MSDNEDNFDGDDFDDVEEDEGLDDLENAEEEGQENVEILPSGERPQANQKRITTPYMTKY
ERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDWGV
DELIITD
Sequence of entity 7 (G), FASTA
>6DRD_7 DNA-directed RNA polymerase II subunit RPB7 (chains G)
MFYHISLEHEILLHPRYFGPNLLNTVKQKLFTEVEGTCTGKYGFVIAVTTIDNIGAGVIQ
PGRGFVLYPVKYKAIVFRPFKGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFD
PNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDKNDIFAIGSLMDDYLGLVS
Sequence of entity 8 (H), FASTA
>6DRD_8 DNA-directed RNA polymerases I, II, and III subunit RPABC3 (chains H)
MAGILFEDIFDVKDIDPEGKKFDRVSRLHCESESFKMDLILDVNIQIYPVDLGDKFRLVI
ASTLYEDGTLDDGEYNPTDDRPSRADQFEYVMYGKVYRIEGDETSTEAATRLSAYVSYGG
LLMRLQGDANNLHGFEVDSRVYLLMKKLAF
Sequence of entity 9 (I), FASTA
>6DRD_9 DNA-directed RNA polymerase II subunit RPB9 (chains I)
MEPDGTYEPGFVGIRFCQECNNMLYPKEDKENRILLYACRNCDYQQEADNSCIYVNKITH
EVDELTQIIADVSQDPTLPRTEDHPCQKCGHKEAVFFQSHSARAEDAMRLYYVCTAPHCG
HRWTE
Sequence of entity 10 (J), FASTA
>6DRD_10 DNA-directed RNA polymerases I, II, and III subunit RPABC5 (chains J)
MIIPVRCFTCGKIVGNKWEAYLGLLQAEYTEGDALDALGLKRYCCRRMLLAHVDLIEKLL
NYAPLEK
Sequence of entity 11 (K), FASTA
>6DRD_11 DNA-directed RNA polymerase II subunit RPB11-a (chains K)
MNAPPAFESFLLFEGEKKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAG
YKVPHPLEHKIIIRVQTTPDYSPQEAFTNAITDLISELSLLEERFRVAIKDKQEGIE
Sequence of entity 12 (L), FASTA
>6DRD_12 DNA-directed RNA polymerases I, II, and III subunit RPABC4 (chains L)
MDTQKDVQPPKQQPMIYICGECHTENEIKSRDPIRCRECGYRIMYKKRTKRLVVFDAR

Ligands and cofactors

IDNameFormulaCopies
ZNZinc ionZn5

Primary citation

Architecture of Pol II(G) and molecular mechanism of transcription regulation by Gdown1. Jishage, M., Yu, X., Shi, Y. et al. Nat Struct Mol Biol (2018) 25:859-867. DOI 10.1038/s41594-018-0118-5 · PubMed

Other PDB entries of the same protein (UniProt P24928 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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