7OBA: Human RNA Polymerase I

Cryo-EM structure of human RNA Polymerase I in complex with RRN3. Determined by electron microscopy at 3.1 Å resolution. Released 8 Dec 2021.

Method
Electron microscopy
Resolution
3.1 Å
Organism
Homo sapiens
Chains
14
Atoms
35,679
Mol. weight
677.43 kDa
Ligands
ZN
Released
8 Dec 2021

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

Secondary structure: helices and β-sheets

7OBA contains 186 α-helices and 243 β-strands across 14 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: 72 helices, 64 β-strands

ElementResiduesLengthSheet
β-strand14-1961
α-helix20-212
β-strand31-3222
β-strand3913
β-strand4513
α-helix461
β-strand79-8022
β-strand81-8884
α-helix93-986
β-strand10315
β-strand11015
α-helix114-12310
α-helix137-14812
α-helix159-17012
α-helix182-19817
β-strand215-21846
β-strand222-22546
β-strand25516
α-helix258-27215
α-helix285-2873
β-strand298-30254
α-helix303-3064
α-helix307-3093
α-helix325-34521
α-helix388-40215
α-helix417-4215
β-strand436-43727
β-strand440-44788
β-strand455-45848
β-strand467-47159
α-helix482-4854
β-strand49819
β-strand50419
α-helix513-5208
β-strand537-54159
α-helix5421
α-helix5461
β-strand547-55158
α-helix558-5603
β-strand561-56888
β-strand575-57738
α-helix581-5833
β-strand593-59758
α-helix606-6105
β-strand61318
β-strand619110
β-strand626110
α-helix634-6418
β-strand647-648211
α-helix650-66011
β-strand675-677312
β-strand681112
β-strand682-683211
α-helix684-69310
α-helix701-7044
β-strand705-706213
β-strand738-740313
β-strand743-746413
α-helix751-7544
α-helix761-7644
α-helix774-78613
β-strand804114
α-helix818-8203
α-helix825-8284
α-helix839-84911
α-helix862-8687
α-helix873-8808
β-strand885114
α-helix893-8997
α-helix908-9136
β-strand918115
β-strand921116
β-strand924116
α-helix926-9283
α-helix9391
α-helix945-9484
β-strand950115
α-helix961-97919
α-helix986-99510
β-strand1001117
β-strand1007-1008217
β-strand1014-1016317
α-helix1019-10213
β-strand1024118
α-helix1027-10293
α-helix1034-10363
α-helix1038-10414
α-helix1044-10474
α-helix1062-10643
α-helix1068-10758
α-helix1088-10969
α-helix1117-11259
α-helix1134-11374
α-helix1142-11454
α-helix1161-117717
α-helix1189-120214
β-strand1204118
α-helix1205-12062
α-helix1211-12144
α-helix1245-12528
β-strand1264-1267419
β-strand1268120
α-helix1273-128311
β-strand1289121
α-helix1290-12934
β-strand1294-1301822
β-strand1304-1305223
β-strand1311-1312223
β-strand1313-1314224
β-strand1317-1321522
α-helix1322-13232
α-helix1324-13263
α-helix1337-13415
α-helix1342-13465
α-helix1347-135711
β-strand1371125
α-helix1502-15065
β-strand1512126
β-strand1526-1527222
β-strand1529126
β-strand1530-1531224
α-helix1543-15475
β-strand1551121
β-strand1566119
β-strand1577-1580419
α-helix1585-15884
β-strand1595120
α-helix1597-15993
β-strand1601-1602219
α-helix1621-16299
α-helix1638-164811
α-helix1668-16747
α-helix1679-16868
β-strand169011
α-helix1698-17003
β-strand1713-1718627
Chain B: 44 helices, 71 β-strands
ElementResiduesLengthSheet
α-helix27-282
α-helix40-478
α-helix48-525
α-helix53-553
α-helix62-632
β-strand64-67428
β-strand72-75428
β-strand77-82629
α-helix83-853
β-strand86130
α-helix87-882
β-strand97130
α-helix100-1056
β-strand111-118829
β-strand121-122228
β-strand125-126228
β-strand130-138929
α-helix153-1575
α-helix161-1622
β-strand170-172331
β-strand175-179531
β-strand181-185532
α-helix1861
β-strand187125
β-strand191-194425
α-helix196-2005
β-strand205-2161225
β-strand220-2291025
β-strand234-239625
β-strand244-245225
β-strand248125
α-helix249-2568
α-helix261-2677
α-helix277-29115
α-helix297-30711
α-helix327-3304
α-helix339-35719
α-helix369-3713
β-strand372-375432
α-helix379-40426
α-helix428-4369
β-strand454-456331
α-helix462-4665
β-strand471-473332
α-helix485-4873
α-helix491-4933
β-strand497133
β-strand511-513332
β-strand514133
β-strand519-520234
α-helix529-5368
β-strand539-541335
α-helix5491
β-strand553-558635
β-strand561-567735
α-helix572-5754
β-strand594-598535
α-helix607-6082
β-strand609-613535
β-strand619-625734
β-strand630-635634
α-helix638-6403
β-strand658-660334
α-helix669-6724
α-helix682-6887
β-strand695136
β-strand710-714537
β-strand718138
β-strand722-723239
α-helix726-7294
β-strand739-745740
β-strand756-760540
α-helix761-7666
β-strand771-7801037
β-strand792-794341
α-helix801-8033
β-strand807142
β-strand813142
α-helix8141
β-strand818-819237
β-strand824-826343
β-strand828-830341
β-strand836141
β-strand839-840243
β-strand847-854837
β-strand863144
β-strand866-873837
β-strand882-884340
β-strand891-897740
α-helix899-9013
β-strand905145
β-strand913-915340
α-helix927-93913
β-strand945-946239
α-helix962-9687
β-strand976-977240
β-strand979145
β-strand992-10011040
β-strand1002136
β-strand101318
α-helix1016-10172
β-strand1018146
β-strand1025146
β-strand1035-103627
α-helix1039-104810
α-helix1051-10555
α-helix1056-10616
β-strand1064-1070747
β-strand1079148
α-helix1081-10855
β-strand1098148
β-strand1103148
β-strand1107-1113747
α-helix1116-11238
β-strand1128-113361
Chain C: 15 helices, 18 β-strands
ElementResiduesLengthSheet
α-helix42-454
β-strand50149
β-strand53-57549
β-strand60-66749
α-helix70-8213
β-strand86-951050
α-helix105-1117
α-helix1141
β-strand115151
α-helix119-1213
α-helix123-1264
β-strand138150
β-strand140-144550
β-strand147-148252
α-helix159-1624
β-strand163-164252
β-strand169153
α-helix170-1723
β-strand173-175350
α-helix181-1844
β-strand192151
β-strand198153
β-strand208-2171050
α-helix223-2253
β-strand228-2401349
α-helix247-2493
α-helix250-2567
β-strand262-267654
β-strand270-275654
α-helix278-2803
α-helix286-2894
β-strand298-3121549
α-helix318-34326
Chain E: 9 helices, 10 β-strands
ElementResiduesLengthSheet
α-helix5-2117
α-helix22-243
α-helix30-323
α-helix39-424
β-strand60-63455
β-strand71-75555
β-strand82156
α-helix90-956
β-strand101-106655
β-strand110156
α-helix114-1196
β-strand126-131655
α-helix133-1353
α-helix139-1413
β-strand147-149357
α-helix153-16210
β-strand172-173257
β-strand190-195657
β-strand203-209757
Chain F: 3 helices, 4 β-strands
ElementResiduesLengthSheet
β-strand56158
α-helix59-7113
α-helix77-793
α-helix89-9810
β-strand105-109527
β-strand115-119527
β-strand124158
Chain G: 2 helices, 16 β-strands
ElementResiduesLengthSheet
α-helix35-406
β-strand43159
β-strand46159
β-strand49160
β-strand52-54361
β-strand57-59362
α-helix68-769
β-strand90160
β-strand97-98261
β-strand102-105427
β-strand112-114362
β-strand116-119461
β-strand122160
β-strand135-138463
β-strand143-147563
β-strand151-155563
β-strand183-185363
β-strand193-195363
Chain H: 0 helices, 15 β-strands
ElementResiduesLengthSheet
β-strand4-151212
β-strand25-32812
β-strand38-44712
β-strand55-61712
β-strand65164
β-strand84164
β-strand90-98912
β-strand101165
β-strand112165
β-strand115-117312
β-strand118-119266
β-strand121166
β-strand123-124212
β-strand127165
β-strand140-147812
Chain I: 3 helices, 10 β-strands
ElementResiduesLengthSheet
β-strand14167
β-strand19168
α-helix251
β-strand26168
α-helix271
β-strand35-37369
β-strand44-46369
α-helix48-525
β-strand55-60622
β-strand82-83270
β-strand95-99570
β-strand111-115570
β-strand121-124470

6 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 I subunit RPA1Aprotein1720Homo sapiensO95602 (AlphaFold model)
DNA-directed RNA polymerase I subunit RPA2Bprotein1135Homo sapiensQ9H9Y6 (AlphaFold model)
DNA-directed RNA polymerases I and III subunit RPAC1Cprotein346Homo sapiensO15160 (AlphaFold model)
DNA-directed RNA polymerases I, II, and III subunit RPABC1Eprotein210Homo sapiensP19388 (AlphaFold model)
DNA-directed RNA polymerases I, II, and III subunit RPABC2Fprotein127Homo sapiensP61218
DNA-directed RNA polymerase I subunit RPA43Gprotein338Homo sapiensQ3B726
DNA-directed RNA polymerases I, II, and III subunit RPABC3Hprotein150Homo sapiensP52434
DNA-directed RNA polymerase I subunit RPA12Iprotein126Homo sapiensQ9P1U0
DNA-directed RNA polymerases I, II, and III subunit RPABC5Jprotein67Homo sapiensP62875
DNA-directed RNA polymerases I and III subunit RPAC2Kprotein133Homo sapiensP0DPB6
DNA-directed RNA polymerases I, II, and III subunit RPABC4Lprotein58Homo sapiensP53803
DNA-directed RNA polymerase I subunit RPA49Mprotein419Homo sapiensQ9GZS1

2 more molecules are not listed.

Sequence of entity 1 (A), FASTA
>7OBA_1 DNA-directed RNA polymerase I subunit RPA1 (chains A)
MLISKNMPWRRLQGISFGMYSAEELKKLSVKSITNPRYLDSLGNPSANGLYDLALGPADS
KEVCSTCVQDFSNCSGHLGHIELPLTVYNPLLFDKLYLLLRGSCLNCHMLTCPRAVIHLL
LCQLRVLEVGALQAVYELERILNRFLEENPDPSASEIREELEQYTTEIVQNNLLGSQGAH
VKNVCESKSKLIALFWKAHMNAKRCPHCKTGRSVVRKEHNSKLTITFPAMVHRTAGQKDS
EPLGIEEAQIGKRGYLTPTSAREHLSALWKNEGFFLNYLFSGMDDDGMESRFNPSVFFLD
FLVVPPSRYRPVSRLGDQMFTNGQTVNLQAVMKDVVLIRKLLALMAQEQKLPEEVATPTT
DEEKDSLIAIDRSFLSTLPGQSLIDKLYNIWIRLQSHVNIVFDSEMDKLMMDKYPGIRQI
LEKKEGLFRKHMMGKRVDYAARSVICPDMYINTNEIGIPMVFATKLTYPQPVTPWNVQEL
RQAVINGPNVHPGASMVINEDGSRTALSAVDMTQREAVAKQLLTPATGAPKPQGTKIVCR
HVKNGDILLLNRQPTLHRPSIQAHRARILPEEKVLRLHYANCKAYNADFDGDEMNAHFPQ
SELGRAEAYVLACTDQQYLVPKDGQPLAGLIQDHMVSGASMTTRGCFFTREHYMELVYRG
LTDKVGRVKLLSPSILKPFPLWTGKQVVSTLLINIIPEDHIPLNLSGKAKITGKAWVKET
PRSVPGFNPDSMCESQVIIREGELLCGVLDKAHYGSSAYGLVHCCYEIYGGETSGKVLTC
LARLFTAYLQLYRGFTLGVEDILVKPKADVKRQRIIEESTHCGPQAVRAALNLPEAASYD
EVRGKWQDAHLGKDQRDFNMIDLKFKEEVNHYSNEINKACMPFGLHRQFPENSLQMMVQS
GAKGSTVNTMQISCLLGQIELEGRRPPLMASGKSLPCFEPYEFTPRAGGFVTGRFLTGIK
PPEFFFHCMAGREGLVDTAVKTSRSGYLQRCIIKHLEGLVVQYDLTVRDSDGSVVQFLYG
EDGLDIPKTQFLQPKQFPFLASNYEVIMKSQHLHEVLSRADPKKALHHFRAIKKWQSKHP
NTLLRRGAFLSYSQKIQEAVKALKLESENRNGRSPGTQEMLRMWYELDEESRRKYQKKAA
ACPDPSLSVWRPDIYFASVSETFETKVDDYSQEWAAQTEKSYEKSELSLDRLRTLLQLKW
QRSLCEPGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREILMVASANIK
TPMMSVPVLNTKKALKRVKSLKKQLTRVCLGEVLQKIDVQESFCMEEKQNKFQVYQLRFQ
FLPHAYYQQEKCLRPEDILRFMETRFFKLLMESIKKKNNKASAFRNVNTRRATQRDLDNA
GELGRSRGEQEGDEEEEGHIVDAEAEEGDADASDAKRKEKQEEEVDYESEEEEEREGEEN
DDEDMQEERNPHREGARKTQEQDEEVGLGTEEDPSLPALLTQPRKPTHSQEPQGPEAMER
RVQAVREIHPFIDDYQYDTEESLWCQVTVKLPLMKINFDMSSLVVSLAHGAVIYATKGIT
RCLLNETTNNKNEKELVLNTEGINLPELFKYAEVLDLRRLYSNDIHAIANTYGIEAALRV
IEKEIKDVFAVYGIAVDPRHLSLVADYMCFEGVYKPLNRFGIRSNSSPLQQMTFETSFQF
LKQATMLGSHDELRSPSACLVVGKVVRGGTGLFELKQPLR
Sequence of entity 2 (B), FASTA
>7OBA_2 DNA-directed RNA polymerase I subunit RPA2 (chains B)
MDPGSRWRNLPSGPSLKHLTDPSYGIPREQQKAALQELTRAHVESFNYAVHEGLGLAVQA
IPPFEFAFKDERISFTILDAVISPPTVPKGTICKEANVYPAECRGRRSTYRGKLTADINW
AVNGISKGIIKQFLGYVPIMVKSKLCNLRNLPPQALIEHHEEAEEMGGYFIINGIEKVIR
MLIMPRRNFPIAMIRPKWKTRGPGYTQYGVSMHCVREEHSAVNMNLHYLENGTVMLNFIY
RKELFFLPLGFALKALVSFSDYQIFQELIKGKEDDSFLRNSVSQMLRIVMEEGCSTQKQV
LNYLGECFRVKLNVPDWYPNEQAAEFLFNQCICIHLKSNTEKFYMLCLMTRKLFALAKGE
CMEDNPDSLVNQEVLTPGQLFLMFLKEKLEGWLVSIKIAFDKKAQKTSVSMNTDNLMRIF
TMGIDLTKPFEYLFATGNLRSKTGLGLLQDSGLCVVADKLNFIRYLSHFRCVHRGADFAK
MRTTTVRRLLPESWGFLCPVHTPDGEPCGLMNHLTAVCEVVTQFVYTASIPALLCNLGVT
PIDGAPHRSYSECYPVLLDGVMVGWVDKDLAPGIADSLRHFKVLREKRIPPWMEVVLIPM
TGKPSLYPGLFLFTTPCRLVRPVQNLALGKEELIGTMEQIFMNVAIFEDEVFAGVTTHQE
LFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRSDNKLYRLQTPQSP
LVRPSMYDYYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWERGFAHGSVYKSEFID
LSEKIKQGDSSLVFGIKPGDPRVLQKLDDDGLPFIGAKLQYGDPYYSYLNLNTGESFVMY
YKSKENCVVDNIKVCSNDTGSGKFKCVCITMRVPRNPTIGDKFASRHGQKGILSRLWPAE
DMPFTESGMVPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATPFIFSEENSALE
YFGEMLKAAGYNFYGTERLYSGISGLELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDR
VTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSDRSVAHVCVKCGSLLSPL
LEKPPPSWSAMRNRKYNCTLCSRSDTIDTVSVPYVFRYFVAELAAMNIKVKLDVV
Sequence of entity 3 (C), FASTA
>7OBA_3 DNA-directed RNA polymerases I and III subunit RPAC1 (chains C)
MAASQAVEEMRSRVVLGEFGVRNVHTTDFPGNYSGYDDAWDQDRFEKNFRVDVVHMDENS
LEFDMVGIDAAIANAFRRILLAEVPTMAVEKVLVYNNTSIVQDEILAHRLGLIPIHADPR
LFEYRNQGDEEGTEIDTLQFRLQVRCTRNPHAAKDSSDPNELYVNHKVYTRHMTWIPLGN
QADLFPEGTIRPVHDDILIAQLRPGQEIDLLMHCVKGIGKDHAKFSPVATASYRLLPDIT
LLEPVEGEAAEELSRCFSPGVIEVQEVQGKKVARVANPRLDTFSREIFRNEKLKKVVRLA
RVRDHYIFSVESTGVLPPDVLVSEAIKVLMGKCRRFLDELDAVQMD
Sequence of entity 4 (E), FASTA
>7OBA_4 DNA-directed RNA polymerases I, II, and III subunit RPABC1 (chains E)
MDDEEETYRLWKIRKTIMQLCHDRGYLVTQDELDQTLEEFKAQFGDKPSEGRPRRTDLTV
LVAHNDDPTDQMFVFFPEEPKVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVD
MAPKYILEQFLQQELLINITEHELVPEHVVMTKEEVTELLARYKLRENQLPRIQAGDPVA
RYFGIKRGQVVKIIRPSETAGRYITYRLVQ
Sequence of entity 5 (F), FASTA
>7OBA_5 DNA-directed RNA polymerases I, II, and III subunit RPABC2 (chains F)
MSDNEDNFDGDDFDDVEEDEGLDDLENAEEEGQENVEILPSGERPQANQKRITTPYMTKY
ERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDWGV
DELIITD
Sequence of entity 6 (G), FASTA
>7OBA_6 DNA-directed RNA polymerase I subunit RPA43 (chains G)
MAAGCSEAPRPAAASDGSLVGQAGVLPCLELPTYAAACALVNSRYSCLVAGPHQRHIALS
PRYLNRKRTGIREQLDAELLRYSESLLGVPIAYDNIKVVGELGDIYDDQGHIHLNIEADF
VIFCPEPGQKLMGIVNKVSSSHIGCLVHGCFNASIPKPEQLSAEQWQTMEINMGDELEFE
VFRLDSDAAGVFCIRGKLNITSLQFKRSEVSEEVTENGTEEAAKKPKKKKKKKDPETYEV
DSGTTKLADDADDTPMEESALQNTNNANGIWEEEPKKKKKKKKHQEVQDQDPVFQGSDSS
GYQSDHKKKKKKRKHSEEAEFTPPLKCSPKRKGKSNFL
Sequence of entity 7 (H), FASTA
>7OBA_7 DNA-directed RNA polymerases I, II, and III subunit RPABC3 (chains H)
MAGILFEDIFDVKDIDPEGKKFDRVSRLHCESESFKMDLILDVNIQIYPVDLGDKFRLVI
ASTLYEDGTLDDGEYNPTDDRPSRADQFEYVMYGKVYRIEGDETSTEAATRLSAYVSYGG
LLMRLQGDANNLHGFEVDSRVYLLMKKLAF
Sequence of entity 8 (I), FASTA
>7OBA_8 DNA-directed RNA polymerase I subunit RPA12 (chains I)
MSVMDLANTCSSFQSDLDFCSDCGSVLPLPGAQDTVTCIRCGFNINVRDFEGKVVKTSVV
FHQLGTAMPMSVEEGPECQGPVVDRRCPRCGHEGMAYHTRQMRSADEGQTVFYTCTNCKF
QEKEDS
Sequence of entity 9 (J), FASTA
>7OBA_9 DNA-directed RNA polymerases I, II, and III subunit RPABC5 (chains J)
MIIPVRCFTCGKIVGNKWEAYLGLLQAEYTEGDALDALGLKRYCCRRMLLAHVDLIEKLL
NYAPLEK
Sequence of entity 10 (K), FASTA
>7OBA_10 DNA-directed RNA polymerases I and III subunit RPAC2 (chains K)
MEEDQELERKISGLKTSMAEGERKTALEMVQAAGTDRHCVTFVLHEEDHTLGNSLRYMIM
KNPEVEFCGYTTTHPSESKINLRIQTRGTLPAVEPFQRGLNELMNVCQHVLDKFEASIKD
YKDQKASRNESTF
Sequence of entity 11 (L), FASTA
>7OBA_11 DNA-directed RNA polymerases I, II, and III subunit RPABC4 (chains L)
MDTQKDVQPPKQQPMIYICGECHTENEIKSRDPIRCRECGYRIMYKKRTKRLVVFDAR
Sequence of entity 12 (M), FASTA
>7OBA_12 DNA-directed RNA polymerase I subunit RPA49 (chains M)
MAAEVLPSARWQYCGAPDGSQRAVLVQFSNGKLQSPGNMRFTLYENKDSTNPRKRNQRIL
AAETDRLSYVGNNFGTGALKCNTLCRHFVGILNKTSGQMEVYDAELFNMQPLFSDVSVES
ELALESQTKTYREKMDSCIEAFGTTKQKRALNTRRMNRVGNESLNRAVAKAAETIIDTKG
VTALVSDAIHNDLQDDSLYLPPCYDDAAKPEDVYKFEDLLSPAEYEALQSPSEAFRNVTS
EEILKMIEENSHCTFVIEALKSLPSDVESRDRQARCIWFLDTLIKFRAHRVVKRKSALGP
GVPHIINTKLLKHFTCLTYNNGRLRNLISDSMKAKITAYVIILALHIHDFQIDLTVLQRD
LKLSEKRMMEIAKAMRLKISKRRVSVAAGSEEDHKLGTLSLPLPPAQTSDRLAKRRKIT

Ligands and cofactors

IDNameFormulaCopies
ZNZinc ionZn7

Primary citation

Cryo-EM structures of human RNA polymerase I. Misiaszek, A.D., Girbig, M., Grotsch, H. et al. Nat Struct Mol Biol (2021) 28:997-1008. DOI 10.1038/s41594-021-00693-4 · PubMed

Other PDB entries of the same protein (UniProt O95602 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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