7D59: Human RNA polymerase III in apo state

cryo-EM structure of human RNA polymerase III in apo state. Determined by electron microscopy at 3.1 Å resolution. Released 17 Feb 2021.

Method
Electron microscopy
Resolution
3.1 Å
Organism
Homo sapiens
Chains
17
Atoms
39,898
Mol. weight
709.13 kDa
Ligands
ZN, SF4
Released
17 Feb 2021

Explore 7D59 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7D59 contains 205 α-helices and 243 β-strands across 17 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: 68 helices, 56 β-strands

ElementResiduesLengthSheet
α-helix41
β-strand511
α-helix61
β-strand13-1972
α-helix25-317
β-strand3413
β-strand4214
β-strand5014
α-helix511
β-strand84-9293
α-helix98-10710
β-strand10815
β-strand11515
α-helix119-12911
α-helix136-15217
β-strand15516
β-strand16216
β-strand165-16957
β-strand173-17757
α-helix188-19811
α-helix199-2024
α-helix211-2133
β-strand216-21837
α-helix220-2289
α-helix236-2383
β-strand252-25763
α-helix258-2592
α-helix260-2623
β-strand266-26838
β-strand273-27538
α-helix278-29922
α-helix303-31816
α-helix341-3455
α-helix352-3565
β-strand36119
β-strand364-371810
β-strand379-383510
α-helix384-3896
β-strand391-395511
α-helix401-41010
β-strand418-422511
β-strand429-431311
α-helix438-4425
β-strand449-453511
β-strand459-463510
α-helix470-4723
β-strand473-481910
β-strand486-488310
α-helix490-4923
α-helix493-4964
β-strand504-508510
α-helix513-5219
β-strand524110
β-strand530112
β-strand537112
α-helix543-55210
β-strand558-559213
α-helix561-5677
α-helix569-5713
α-helix584-5863
β-strand588114
β-strand594114
β-strand595-596213
α-helix597-6015
β-strand616-620515
β-strand637-641515
β-strand645-647315
α-helix663-6708
α-helix683-69412
α-helix707-73327
α-helix744-7518
α-helix755-77016
α-helix776-7838
α-helix789-7957
β-strand800-801216
α-helix808-8114
α-helix828-8314
β-strand833-834216
α-helix844-86219
α-helix864-87613
β-strand883-884217
β-strand890-891217
β-strand897-899317
β-strand907118
α-helix921-93111
α-helix938-9392
α-helix942-95312
α-helix963-98725
α-helix1000-10023
α-helix1008-102417
β-strand1026118
α-helix1027-10282
α-helix1033-10386
α-helix1042-10465
α-helix1067-10759
β-strand1085-1089519
α-helix1095-110410
β-strand1108-1109220
α-helix1110-11134
β-strand1114-1121821
β-strand1127-1132621
α-helix1134-11407
α-helix1146-11549
β-strand1165-1167321
β-strand1172-1175421
α-helix1185-11939
β-strand1200-1202320
β-strand1209-1216819
β-strand1221-1228819
α-helix1232-12365
β-strand1241-1247719
α-helix1251-12577
α-helix1263-127513
α-helix1284-129310
α-helix1305-13117
α-helix1315-13217
α-helix1326-13349
α-helix13361
β-strand1337-133932
α-helix1343-13497
α-helix1351-13533
β-strand1361-1364422
α-helix1372-13743
α-helix1382-13854
Chain B: 48 helices, 72 β-strands
ElementResiduesLengthSheet
α-helix26-283
α-helix29-368
α-helix41-488
α-helix50-545
α-helix55-617
β-strand65-66223
β-strand74-82923
β-strand86-88324
β-strand94-96324
α-helix99-1057
β-strand110-1211223
β-strand124-1371423
α-helix152-1554
β-strand169-170225
β-strand175-178425
α-helix1791
β-strand180-183426
α-helix184-1852
β-strand188-193627
β-strand198-205827
β-strand211-219927
β-strand222-226527
β-strand234127
α-helix236-2438
α-helix248-2558
α-helix259-2635
α-helix266-2749
α-helix280-29011
α-helix305-31410
α-helix329-34517
β-strand361-363326
α-helix365-38723
α-helix409-42113
β-strand424-426328
β-strand431-433328
β-strand437-439325
α-helix440-4412
α-helix445-4528
β-strand454-457426
α-helix471-4722
β-strand479129
β-strand493-495326
β-strand496129
β-strand501-502230
α-helix509-51810
α-helix5201
β-strand521131
α-helix5221
β-strand537-541531
β-strand545-549531
α-helix552-56514
β-strand573-577531
β-strand582-586531
β-strand592-593230
β-strand594-598532
β-strand599133
β-strand604133
α-helix608-6169
α-helix621-6266
β-strand630-633432
α-helix638-6403
β-strand643-644232
β-strand656-657232
α-helix661-6644
α-helix668-6714
α-helix680-69011
β-strand708-712534
β-strand716135
α-helix723-7286
α-helix730-7323
β-strand737-743736
β-strand755137
β-strand756136
β-strand757-758237
α-helix759-7646
β-strand769-7791134
β-strand789138
β-strand794-795239
β-strand802139
β-strand809140
β-strand815140
α-helix8161
β-strand820-821234
β-strand825-826241
β-strand831-833338
α-helix849-8502
β-strand851-853338
β-strand857-858241
β-strand864-8731034
β-strand879-8891134
β-strand896-898342
β-strand904-906342
β-strand907-911537
α-helix923-9253
β-strand927-929336
α-helix9301
α-helix934-9374
α-helix941-95515
α-helix958-9603
α-helix970-97910
β-strand986-987236
β-strand990143
β-strand997143
β-strand1002-1009836
β-strand1010-1011242
β-strand1020-1023410
β-strand1028144
β-strand1029145
β-strand1035144
α-helix10361
β-strand104519
α-helix1049-105810
α-helix1062-10654
α-helix1066-10705
β-strand1075-1079546
β-strand1086146
β-strand1102-1106546
α-helix1108-11169
α-helix1117-11204
β-strand1125-113062
Chain C: 10 helices, 20 β-strands
ElementResiduesLengthSheet
α-helix3-1210
β-strand13-16447
β-strand21147
β-strand30148
β-strand33148
α-helix42-487
β-strand50-56747
β-strand60-66747
α-helix70-7910
β-strand86-981349
α-helix103-1119
β-strand115-116250
β-strand138-145849
β-strand147-148251
α-helix159-1624
β-strand163-164251
β-strand167-168252
α-helix170-1723
β-strand174149
β-strand191-192250
β-strand200-201252
β-strand207-2171149
α-helix223-2253
β-strand228-2411447
α-helix244-2463
α-helix247-25610
β-strand262-267653
β-strand270-275653
β-strand297-3121647
α-helix318-34528
Chain D: 7 helices, 2 β-strands
ElementResiduesLengthSheet
β-strand2-321
β-strand1011
α-helix13-219
α-helix23-308
α-helix37-5519
α-helix63-7311
α-helix80-878
α-helix94-1007
α-helix110-12112
Chain E: 8 helices, 9 β-strands
ElementResiduesLengthSheet
α-helix2-2423
β-strand26-27254
α-helix30-334
α-helix37-437
β-strand59-64654
β-strand71-75554
α-helix85-9511
β-strand101-106654
α-helix112-1209
β-strand126-131654
β-strand147-150455
α-helix153-16311
α-helix1711
β-strand172-173255
α-helix178-1836
β-strand189-196855
β-strand202-209855
Chain F: 5 helices, 4 β-strands
ElementResiduesLengthSheet
β-strand56156
α-helix57-582
α-helix59-7315
α-helix77-793
α-helix89-9810
β-strand104-109622
α-helix1101
β-strand115-119522
β-strand124156
Chain G: 2 helices, 13 β-strands
ElementResiduesLengthSheet
β-strand3-13111
α-helix22-3312
β-strand3811
β-strand44-58151
β-strand66-77121
β-strand84-87457
β-strand88-92558
β-strand97-100458
β-strand107-109358
β-strand117-119359
β-strand127-131559
β-strand137-141559
β-strand148-1571057
α-helix159-1624
β-strand184-192957
Chain H: 0 helices, 9 β-strands
ElementResiduesLengthSheet
β-strand4-151260
β-strand25-32860
β-strand38-44760
β-strand55-61760
β-strand90-97860
β-strand101160
β-strand111-118860
β-strand121-128860
β-strand140-148960

9 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 III subunit RPC1Aprotein1390Homo sapiensO14802 (AlphaFold model)
DNA-directed RNA polymerase III subunit RPC2Bprotein1133Homo sapiensQ9NW08 (AlphaFold model)
DNA-directed RNA polymerases I and III subunit RPAC1Cprotein346Homo sapiensO15160 (AlphaFold model)
DNA-directed RNA polymerase III subunit RPC9Dprotein148Homo sapiensO75575 (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 III subunit RPC8Gprotein204Homo sapiensQ9Y535
DNA-directed RNA polymerases I, II, and III subunit RPABC3Hprotein150Homo sapiensP52434
DNA-directed RNA polymerase III subunit RPC10Iprotein108Homo sapiensQ9Y2Y1
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

5 more molecules are not listed.

Sequence of entity 1 (A), FASTA
>7D59_1 DNA-directed RNA polymerase III subunit RPC1 (chains A)
MVKEQFRETDVAKKISHICFGMKSPEEMRQQAHIQVVSKNLYSQDNQHAPLLYGVLDHRM
GTSEKDRPCETCGKNLADCLGHYGYIDLELPCFHVGYFRAVIGILQMICKTCCHIMLSQE
EKKQFLDYLKRPGLTYLQKRGLKKKISDKCRKKNICHHCGAFNGTVKKCGLLKIIHEKYK
TNKKVVDPIVSNFLQSFETAIEHNKEVEPLLGRAQENLNPLVVLNLFKRIPAEDVPLLLM
NPEAGKPSDLILTRLLVPPLCIRPSVVSDLKSGTNEDDLTMKLTEIIFLNDVIKKHRISG
AKTQMIMEDWDFLQLQCALYINSELSGIPLNMAPKKWTRGFVQRLKGKQGRFRGNLSGKR
VDFSGRTVISPDPNLRIDEVAVPVHVAKILTFPEKVNKANINFLRKLVQNGPEVHPGANF
IQQRHTQMKRFLKYGNREKMAQELKYGDIVERHLIDGDVVLFNRQPSLHKLSIMAHLARV
KPHRTFRFNECVCTPYNADFDGDEMNLHLPQTEEAKAEALVLMGTKANLVTPRNGEPLIA
AIQDFLTGAYLLTLKDTFFDRAKACQIIASILVGKDEKIKVRLPPPTILKPVTLWTGKQI
FSVILRPSDDNPVRANLRTKGKQYCGKGEDLCANDSYVTIQNSELMSGSMDKGTLGSGSK
NNIFYILLRDWGQNEAADAMSRLARLAPVYLSNRGFSIGIGDVTPGQGLLKAKYELLNAG
YKKCDEYIEALNTGKLQQQPGCTAEETLEALILKELSVIRDHAGSACLRELDKSNSPLTM
ALCGSKGSFINISQMIACVGQQAISGSRVPDGFENRSLPHFEKHSKLPAAKGFVANSFYS
GLTPTEFFFHTMAGREGLVDTAVKTAETGYMQRRLVKSLEDLCSQYDLTVRSSTGDIIQF
IYGGDGLDPAAMEGKDEPLEFKRVLDNIKAVFPCPSEPALSKNELILTTESIMKKSEFLC
CQDSFLQEIKKFIKGVSEKIKKTRDKYGINDNGTTEPRVLYQLDRITPTQVEKFLETCRD
KYMRAQMEPGSAVGALCAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKAI
STPIITAQLDKDDDADYARLVKGRIEKTLLGEISEYIEEVFLPDDCFILVKLSLERIRLL
RLEVNAETVRYSICTSKLRVKPGDVAVHGEAVVCVTPRENSKSSMYYVLQFLKEDLPKVV
VQGIPEVSRAVIHIDEQSGKEKYKLLVEGDNLRAVMATHGVKGTRTTSNNTYEVEKTLGI
EAARTTIINEIQYTMVNHGMSIDRRHVMLLSDLMTYKGEVLGITRFGLAKMKESVLMLAS
FEKTADHLFDAAYFGQKDSVCGVSECIIMGIPMNIGTGLFKLLHKADRDPNPPKRPLIFD
TNEFHIPLVT
Sequence of entity 2 (B), FASTA
>7D59_2 DNA-directed RNA polymerase III subunit RPC2 (chains B)
MDVLAEEFGNLTPEQLAAPIPTVEEKWRLLPAFLKVKGLVKQHIDSFNYFINVEIKKIMK
ANEKVTSDADPMWYLKYLNIYVGLPDVEESFNVTRPVSPHECRLRDMTYSAPITVDIEYT
RGSQRIIRNALPIGRMPIMLRSSNCVLTGKTPAEFAKLNECPLDPGGYFIVKGVEKVILI
QEQLSKNRIIVEADRKGAVGASVTSSTHEKKSRTNMAVKQGRFYLRHNTLSEDIPIVIIF
KAMGVESDQEIVQMIGTEEHVMAAFGPSLEECQKAQIFTQMQALKYIGNKVRRQRMWGGG
PKKTKIEEARELLASTILTHVPVKEFNFRAKCIYTAVMVRRVILAQGDNKVDDRDYYGNK
RLELAGQLLSLLFEDLFKKFNSEMKKIADQVIPKQRAAQFDVVKHMRQDQITNGMVNAIS
TGNWSLKRFKMDRQGVTQVLSRLSYISALGMMTRISSQFEKTRKVSGPRSLQPSQWGMLC
PSDTPEGEACGLVKNLALMTHITTDMEDGPIVKLASNLGVEDVNLLCGEELSYPNVFLVF
LNGNILGVIRDHKKLVNTFRLMRRAGYINEFVSISTNLTDRCVYISSDGGRLCRPYIIVK
KQKPAVTNKHMEELAQGYRNFEDFLHESLVEYLDVNEENDCNIALYEHTINKDTTHLEIE
PFTLLGVCAGLIPYPHHNQSPRNTYQCAMGKQAMGTIGYNQRNRIDTLMYLLAYPQKPMV
KTKTIELIEFEKLPAGQNATVAVMSYSGYDIEDALVLNKASLDRGFGRCLVYKNAKCTLK
RYTNQTFDKVMGPMLDAATRKPIWRHEILDADGICSPGEKVENKQVLVNKSMPTVTQIPL
EGSNVPQQPQYKDVPITYKGATDSYIEKVMISSNAEDAFLIKMLLRQTRRPEIGDKFSSR
HGQKGVCGLIVPQEDMPFCDSGICPDIIMNPHGFPSRMTVGKLIELLAGKAGVLDGRFHY
GTAFGGSKVKDVCEDLVRHGYNYLGKDYVTSGITGEPLEAYIYFGPVYYQKLKHMVLDKM
HARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCLIGYGASMLLLERLMISSDAFEVDVC
GQCGLLGYSGWCHYCKSSCHVSSLRIPYACKLLFQELQSMNIIPRLKLSKYNE
Sequence of entity 3 (C), FASTA
>7D59_3 DNA-directed RNA polymerases I and III subunit RPAC1 (chains C)
MAASQAVEEMRSRVVLGEFGVRNVHTTDFPGNYSGYDDAWDQDRFEKNFRVDVVHMDENS
LEFDMVGIDAAIANAFRRILLAEVPTMAVEKVLVYNNTSIVQDEILAHRLGLIPIHADPR
LFEYRNQGDEEGTEIDTLQFRLQVRCTRNPHAAKDSSDPNELYVNHKVYTRHMTWIPLGN
QADLFPEGTIRPVHDDILIAQLRPGQEIDLLMHCVKGIGKDHAKFSPVATASYRLLPDIT
LLEPVEGEAAEELSRCFSPGVIEVQEVQGKKVARVANPRLDTFSREIFRNEKLKKVVRLA
RVRDHYIFSVESTGVLPPDVLVSEAIKVLMGKCRRFLDELDAVQMD
Sequence of entity 4 (D), FASTA
>7D59_4 DNA-directed RNA polymerase III subunit RPC9 (chains D)
MEVKDANSALLSNYEVFQLLTDLKEQRKESGKNKHSSGQQNLNTITYETLKYISKTPCRH
QSPEIVREFLTALKSHKLTKAEKLQLLNHRPVTAVEIQLMVEESEERLTEEQIEALLHTV
TSILPAEPEAEQKKNTNSNVAMDEEDPA
Sequence of entity 5 (E), FASTA
>7D59_5 DNA-directed RNA polymerases I, II, and III subunit RPABC1 (chains E)
MDDEEETYRLWKIRKTIMQLCHDRGYLVTQDELDQTLEEFKAQSGDKPSEGRPRRTDLTV
LVAHNDDPTDQMFVFFPEEPKVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVD
MAPKYILEQFLQQELLINITEHELVPEHVVMTKEEVTELLARYKLRENQLPRIQAGDPVA
RYFGIKRGQVVKIIRPSETAGRYITYRLVQ
Sequence of entity 6 (F), FASTA
>7D59_6 DNA-directed RNA polymerases I, II, and III subunit RPABC2 (chains F)
MSDNEDNFDGDDFDDVEEDEGLDDLENAEEEGQENVEILPSGERPQANQKRITTPYMTKY
ERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDWGV
DELIITD
Sequence of entity 7 (G), FASTA
>7D59_7 DNA-directed RNA polymerase III subunit RPC8 (chains G)
MFVLVEMVDTVRIPPWQFERKLNDSIAEELNKKLANKVVYNVGLCICLFDITKLEDAYVF
PGDGASHTKVHFRCVVFHPFLDEILIGKIKGCSPEGVHVSLGFFDDILIPPESLQQPAKF
DEAEQVWVWEYETEEGAHDLYMDTGEEIRFRVVDESFVDTSPTGPSSADATTSSEELPKK
EAPYTLVGSISEPGLGLLSWWTSN
Sequence of entity 8 (H), FASTA
>7D59_8 DNA-directed RNA polymerases I, II, and III subunit RPABC3 (chains H)
MAGILFEDIFDVKDIDPEGKKFDRVSRLHCESESFKMDLILDVNIQIYPVDLGDKFRLVI
ASTLYEDGTLDDGEYNPTDDRPSRADQFEYVMYGKVYRIEGDETSTEAATRLSAYVSYGG
LLMRLQGDANNLHGFEVDSRVYLLMKKLAF
Sequence of entity 9 (I), FASTA
>7D59_9 DNA-directed RNA polymerase III subunit RPC10 (chains I)
MLLFCPGCGNGLIVEEGQRCHRFSCNTCPYVHNITRKVTNRKYPKLKEVDDVLGGAAAWE
NVDSTAESCPKCEHPRAYFMQLQTRSADEPMTTFYKCCNAQCGHRWRD
Sequence of entity 10 (J), FASTA
>7D59_10 DNA-directed RNA polymerases I, II, and III subunit RPABC5 (chains J)
MIIPVRCFTCGKIVGNKWEAYLGLLQAEYTEGDALDALGLKRYCCRRMLLAHVDLIEKLL
NYAPLEK
Sequence of entity 11 (K), FASTA
>7D59_11 DNA-directed RNA polymerases I and III subunit RPAC2 (chains K)
MEEDQELERKISGLKTSMAEGERKTALEMVQAAGTDRHCVTFVLHEEDHTLGNSLRYMIM
KNPEVEFCGYTTTHPSESKINLRIQTRGTLPAVEPFQRGLNELMNVCQHVLDKFEASIKD
YKDQKASRNESTF
Sequence of entity 12 (L), FASTA
>7D59_12 DNA-directed RNA polymerases I, II, and III subunit RPABC4 (chains L)
MDTQKDVQPPKQQPMIYICGECHTENEIKSRDPIRCRECGYRIMYKKRTKRLVVFDAR

Ligands and cofactors

IDNameFormulaCopies
ZNZinc ionZn7
SF4Iron/sulfur clusterFe4 S41

Primary citation

Structural insights into transcriptional regulation of human RNA polymerase III. Wang, Q., Li, S., Wan, F. et al. Nat Struct Mol Biol (2021) 28:220-227. DOI 10.1038/s41594-021-00557-x · PubMed

Other PDB entries of the same protein (UniProt O14802 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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