6CNB: DNA-directed RNA polymerase III subunit RPC1

Yeast RNA polymerase III initial transcribing complex. Determined by electron microscopy at 4.1 Å resolution. Released 22 Aug 2018.

Method
Electron microscopy
Resolution
4.1 Å
Organisms
Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Saccharomyces cerevisiae S288c
Chains
21
Atoms
47,837
Mol. weight
886.1 kDa
Ligands
ZN
Released
22 Aug 2018

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

Secondary structure: helices and β-sheets

6CNB contains 239 α-helices and 253 β-strands across 19 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: 60 helices, 48 β-strands

ElementResiduesLengthSheet
β-strand411
β-strand11-1772
α-helix23-275
β-strand3313
α-helix39-413
α-helix73-764
β-strand82-8433
α-helix96-1027
β-strand10614
β-strand11314
α-helix117-12711
α-helix134-14916
β-strand15315
β-strand16015
β-strand16416
β-strand18016
α-helix192-20514
α-helix224-2318
α-helix239-2413
β-strand261-26333
α-helix270-2734
α-helix279-2813
α-helix285-30117
α-helix309-32719
α-helix364-3696
β-strand37317
β-strand377-37828
β-strand38019
β-strand381110
β-strand391-395511
α-helix396-3994
β-strand404-407412
α-helix413-42210
β-strand430-434512
β-strand442112
β-strand461-464412
β-strand471-475511
β-strand486-493811
β-strand498110
β-strand499111
α-helix502-5054
β-strand51619
β-strand518-520311
α-helix525-5306
α-helix531-5355
α-helix538-5403
α-helix556-56510
α-helix573-58210
β-strand597-599313
β-strand601-603313
α-helix606-6149
β-strand625-626214
β-strand629115
β-strand651115
β-strand653-655314
β-strand658-661414
α-helix667-6693
α-helix677-6859
α-helix687-70822
α-helix714-7174
α-helix723-74624
α-helix761-78323
α-helix7861
α-helix7901
α-helix791-7977
α-helix803-8064
α-helix807-8115
β-strand818116
β-strand821116
α-helix823-8253
α-helix858-89336
β-strand897-898217
β-strand904-905217
β-strand911117
α-helix928-9303
α-helix935-94612
α-helix958-97417
β-strand978118
β-strand982118
α-helix999-102527
α-helix10391
α-helix1052-10598
α-helix1065-108016
α-helix1089-109810
α-helix1123-11319
β-strand1140-1143419
α-helix1153-11608
α-helix1166-11694
β-strand1173-1178620
β-strand1181-1186620
α-helix1190-11956
α-helix1203-121210
α-helix1213-12153
β-strand1232120
α-helix1255-126612
β-strand1278-1283619
β-strand1293-1297519
α-helix1302-13054
β-strand1314-1316319
α-helix1319-13235
α-helix1329-134517
α-helix1351-136313
α-helix1392-140211
α-helix1414-14174
α-helix1424-14274
β-strand1430-1432321
α-helix1438-14403
α-helix1448-14536
Chain B: 48 helices, 77 β-strands
ElementResiduesLengthSheet
α-helix37-393
α-helix43-464
α-helix47-548
α-helix60-678
α-helix68-725
α-helix73-797
β-strand82-83222
β-strand93-94222
β-strand98-100323
α-helix115-1206
β-strand127-128224
β-strand129-131323
β-strand147123
β-strand151-152224
α-helix170-1734
β-strand185-187325
β-strand190-194525
α-helix1951
β-strand196-200526
β-strand205-207327
β-strand217-221527
β-strand228-236927
β-strand239-243527
β-strand247128
β-strand252127
α-helix253-2597
α-helix267-2682
α-helix269-2735
α-helix280-29112
α-helix300-3089
β-strand309128
α-helix317-3193
α-helix326-3305
α-helix343-36119
α-helix372-3743
β-strand375-378426
α-helix380-40829
α-helix421-4244
α-helix431-4399
β-strand442-444329
β-strand449-451329
β-strand455-457325
α-helix458-4592
α-helix463-4697
β-strand473-475326
α-helix491-4933
β-strand497130
β-strand510-512326
β-strand514130
β-strand521131
α-helix527-5359
α-helix541-5433
β-strand555-557332
β-strand561132
α-helix568-57912
β-strand590-592332
β-strand599-601332
β-strand607131
β-strand609-614633
α-helix628-6314
α-helix640-6434
β-strand646-650533
α-helix651-6566
β-strand659-660233
β-strand672-673233
α-helix677-6793
α-helix685-6873
α-helix691-6933
α-helix696-7038
α-helix706-7083
β-strand709134
β-strand724-728535
α-helix742-7443
α-helix746-7483
β-strand753-757536
β-strand758-759237
β-strand771138
β-strand772137
β-strand774139
α-helix778-7803
β-strand785-7941035
β-strand797-798240
β-strand802-803240
β-strand805141
β-strand829142
β-strand835-837335
β-strand843142
β-strand846-848341
β-strand866-868341
α-helix8701
β-strand871142
α-helix872-8732
β-strand878-8881135
β-strand894-902935
β-strand911-913343
β-strand919-921343
β-strand922138
β-strand926139
β-strand943-944237
α-helix948-9525
α-helix956-97015
β-strand976-977244
β-strand980-981244
α-helix984-9929
β-strand1001-1002245
β-strand1005146
β-strand1012146
β-strand1017-1018245
β-strand1020-1024536
β-strand1026143
β-strand1027134
α-helix1031-10344
β-strand1036-103728
β-strand1043147
β-strand1044148
β-strand1050147
β-strand106017
α-helix1064-107310
α-helix1077-10793
α-helix1080-10856
β-strand1091-1095549
β-strand1101-1102249
β-strand1116-1120549
α-helix1123-113412
β-strand1140-114562
Chain C: 13 helices, 19 β-strands
ElementResiduesLengthSheet
β-strand4-7450
β-strand12-13250
β-strand41-47750
β-strand52-57650
α-helix61-7313
β-strand77-861051
α-helix96-1038
β-strand107152
α-helix115-1173
α-helix122-1243
α-helix128-1303
β-strand132-139851
β-strand142153
β-strand157153
β-strand161-163354
α-helix164-1663
β-strand168-169251
α-helix175-1795
β-strand185152
β-strand192-195454
β-strand201-2111151
α-helix213-2153
α-helix217-2193
β-strand225-2351150
α-helix242-2509
β-strand257-258255
β-strand265-266255
α-helix286-2883
β-strand289-3021450
α-helix310-32920
α-helix332-3332
β-strand334156
Chain D: 6 helices, 1 β-strand
ElementResiduesLengthSheet
β-strand3-9757
α-helix15-2612
α-helix56-7116
α-helix102-1109
α-helix118-1225
α-helix131-1355
α-helix147-15812
Chain E: 13 helices, 10 β-strands
ElementResiduesLengthSheet
α-helix2-2423
β-strand28158
α-helix32-354
α-helix39-468
α-helix55-584
β-strand60-62359
β-strand64158
α-helix67-715
β-strand78-80359
α-helix90-10213
β-strand107-111559
α-helix118-1225
β-strand131-135559
α-helix144-1463
β-strand152-155460
α-helix156-1572
α-helix158-16811
α-helix1761
β-strand177-178260
α-helix1791
α-helix183-1886
β-strand195-201760
β-strand207-214860
Chain F: 3 helices, 4 β-strands
ElementResiduesLengthSheet
α-helix73-753
β-strand84161
α-helix87-10216
α-helix117-1259
β-strand132-135421
β-strand145-147321
β-strand152161
Chain G: 4 helices, 15 β-strands
ElementResiduesLengthSheet
β-strand4-131057
α-helix15-195
α-helix22-3312
β-strand3811
β-strand45-48457
β-strand52157
β-strand57-58221
β-strand66-761157
β-strand85162
β-strand88-89263
β-strand99-100263
β-strand101164
β-strand105164
β-strand108165
β-strand148162
β-strand152-155465
α-helix163-1653
β-strand194-197465
α-helix208-2103
Chain H: 1 helix, 10 β-strands
ElementResiduesLengthSheet
β-strand4-161366
β-strand23-30866
β-strand38-43666
β-strand54-60766
β-strand99167
β-strand100-107866
β-strand111-117766
β-strand122-125466
α-helix131-1333
β-strand140167
β-strand141-145566

11 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 RPC1Aprotein1460Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P04051 (AlphaFold model)
DNA-directed RNA polymerase III subunit RPC2Bprotein1149Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P22276 (AlphaFold model)
DNA-directed RNA polymerases I and III subunit RPAC1Cprotein335Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P07703 (AlphaFold model)
DNA-directed RNA polymerase III subunit RPC9Dprotein161Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P47076 (AlphaFold model)
DNA-directed RNA polymerases I, II, and III subunit RPABC1Eprotein215Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P20434
DNA-directed RNA polymerases I, II, and III subunit RPABC2Fprotein155Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P20435
DNA-directed RNA polymerase III subunit RPC8Gprotein212Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P35718
DNA-directed RNA polymerases I, II, and III subunit RPABC3Hprotein146Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P20436
DNA-directed RNA polymerase III subunit RPC10Iprotein110Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Q04307
DNA-directed RNA polymerases I, II, and III subunit RPABC5Jprotein70Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P22139
DNA-directed RNA polymerases I and III subunit RPAC2Kprotein142Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P28000
DNA-directed RNA polymerases I, II, and III subunit RPABC4Lprotein70Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P40422

9 more molecules are not listed.

Sequence of entity 1 (A), FASTA
>6CNB_1 DNA-directed RNA polymerase III subunit RPC1 (chains A)
MKEVVVSETPKRIKGLEFSALSAADIVAQSEVEVSTRDLFDLEKDRAPKANGALDPKMGV
SSSSLECATCHGNLASCHGHFGHLKLALPVFHIGYFKATIQILQGICKNCSAILLSETDK
RQFLHELRRPGVDNLRRMGILKKILDQCKKQRRCLHCGALNGVVKKAAAGAGSAALKIIH
DTFRWVGKKSAPEKDIWVGEWKEVLAHNPELERYVKRCMDDLNPLKTLNLFKQIKSADCE
LLGIDATVPSGRPETYIWRYLPAPPVCIRPSVMMQDSPASNEDDLTVKLTEIVWTSSLIK
AGLDKGISINNMMEHWDYLQLTVAMYINSDSVNPAMLPGSSNGGGKVKPIRGFCQRLKGK
QGRFRGNLSGKRVDFSGRTVISPDPNLSIDEVAVPDRVAKVLTYPEKVTRYNRHKLQELI
VNGPNVHPGANYLLKRNEDARRNLRYGDRMKLAKNLQIGDVVERHLEDGDVVLFNRQPSL
HRLSILSHYAKIRPWRTFRLNECVCTPYNADFDGDEMNLHVPQTEEARAEAINLMGVKNN
LLTPKSGEPIIAATQDFITGSYLISHKDSFYDRATLTQLLSMMSDGIEHFDIPPPAIMKP
YYLWTGKQVFSLLIKPNHNSPVVINLDAKNKVFVPPKSKSLPNEMSQNDGFVIIRGSQIL
SGVMDKSVLGDGKKHSVFYTILRDYGPQEAANAMNRMAKLCARFLGNRGFSIGINDVTPA
DDLKQKKEELVEIAYHKCDELITLFNKGELETQPGCNEEQTLEAKIGGLLSKVREEVGDV
CINELDNWNAPLIMATCGSKGSTLNVSQMVAVVGQQIISGNRVPDGFQDRSLPHFPKNSK
TPQSKGFVRNSFFSGLSPPEFLFHAISGREGLVDTAVKTAETGYMSRRLMKSLEDLSCQY
DNTVRTSANGIVQFTYGGDGLDPLEMEGNAQPVNFNRSWDHAYNITFNNQDKGLLPYAIM
ETANEILGPLEERLVRYDNSGCLVKREDLNKAEYVDQYDAERDFYHSLREYINGKATALA
NLRKSRGMLGLLEPPAKELQGIDPDETVPDNVKTSVSQLYRISEKSVRKFLEIALFKYRK
ARLEPGTAIGAIGAQSIGEPGTQMTLKTFHFAGVASMNVTLGVPRIKEIINASKVISTPI
INAVLVNDNDERAARVVKGRVEKTLLSDVAFYVQDVYKDNLSFIQVRIDLGTIDKLQLEL
TIEDIAVAITRASKLKIQASDVNIIGKDRIAINVFPEGYKAKSISTSAKEPSENDVFYRM
QQLRRALPDVVVKGLPDISRAVINIRDDGKRELLVEGYGLRDVMCTDGVIGSRTTTNHVL
EVFSVLGIEAARYSIIREINYTMSNHGMSVDPRHIQLLGDVMTYKGEVLGITRFGLSKMR
DSVLQLASFEKTTDHLFDAAFYMKKDAVEGVSECIILGQTMSIGTGSFKVVKGTNISEKD
LVPKRCLFESLSNEAALKAN
Sequence of entity 2 (B), FASTA
>6CNB_2 DNA-directed RNA polymerase III subunit RPC2 (chains B)
MVAATKRRKTHIHKHVKDEAFDDLLKPVYKGKKLTDEINTAQDKWHLLPAFLKVKGLVKQ
HLDSFNYFVDTDLKKIIKANQLILSDVDPEFYLKYVDIRVGKKSSSSTKDYLTPPHECRL
RDMTYSAPIYVDIEYTRGRNIIMHKDVEIGRMPIMLRSNKCILYDADESKMAKLNECPLD
PGGYFIVNGTEKVILVQEQLSKNRIIVEADEKKGIVQASVTSSTHERKSKTYVITKNGKI
YLKHNSIAEEIPIAIVLKACGILSDLEIMQLVCGNDSSYQDIFAVNLEESSKLDIYTQQQ
ALEYIGAKVKTMRRQKLTILQEGIEAIATTVIAHLTVEALDFREKALYIAMMTRRVVMAM
YNPKMIDDRDYVGNKRLELAGQLISLLFEDLFKKFNNDFKLSIDKVLKKPNRAMEYDALL
SINVHSNNITSGLNRAISTGNWSLKRFKMERAGVTHVLSRLSYISALGMMTRISSQFEKS
RKVSGPRALQPSQFGMLCTADTPEGEACGLVKNLALMTHITTDDEEEPIKKLCYVLGVED
ITLIDSASLHLNYGVYLNGTLIGSIRFPTKFVTQFRHLRRTGKVSEFISIYSNSHQMAVH
IATDGGRICRPLIIVSDGQSRVKDIHLRKLLDGELDFDDFLKLGLVEYLDVNEENDSYIA
LYEKDIVPSMTHLEIEPFTILGAVAGLIPYPHHNQSPRNTYQCAMGKQAIGAIAYNQFKR
IDTLLYLMTYPQQPMVKTKTIELIDYDKLPAGQNATVAVMSYSGYDIEDALVLNKSSIDR
GFGRCETRRKTTTVLKRYANHTQDIIGGMRVDENGDPIWQHQSLGPDGLGEVGMKVQSGQ
IYINKSVPTNSADAPNPNNVNVQTQYREAPVIYRGPEPSHIDQVMMSVSDNDQALIKVLL
RQNRRPELGDKFSSRHGQKGVCGIIVKQEDMPFNDQGIVPDIIMNPHGFPSRMTVGKMIE
LISGKAGVLNGTLEYGTCFGGSKLEDMSKILVDQGFNYSGKDMLYSGITGECLQAYIFFG
PIYYQKLKHMVLDKMHARARGPRAVLTRQPTEGRSRDGGLRLGEMERDCVIAYGASQLLL
ERLMISSDAFEVDVCDKCGLMGYSGWCTTCKSAENIIKMTIPYAAKLLFQELLSMNIAPR
LRLEDIFQQ
Sequence of entity 3 (C), FASTA
>6CNB_3 DNA-directed RNA polymerases I and III subunit RPAC1 (chains C)
MSNIVGIEYNRVTNTTSTDFPGFSKDAENEWNVEKFKKDFEVNISSLDAREANFDLINID
TSIANAFRRIMISEVPSVAAEYVYFFNNTSVIQDEVLAHRIGLVPLKVDPDMLTWVDSNL
PDDEKFTDENTIVLSLNVKCTRNPDAPKGSTDPKELYNNAHVYARDLKFEPQGRQSTTFA
DCPVVPADPDILLAKLRPGQEISLKAHCILGIGGDHAKFSPVSTASYRLLPQINILQPIK
GESARRFQKCFPPGVIGIDEGSDEAYVKDARKDTVSREVLRYEEFADKVKLGRVRNHFIF
NVESAGAMTPEEIFFKSVRILKNKAEYLKNCPITQ
Sequence of entity 4 (D), FASTA
>6CNB_4 DNA-directed RNA polymerase III subunit RPC9 (chains D)
MKVLEERNAFLSDYEVLKFLTDLEKKHLWDQKSLAALKKSRSKGKQNRPYNHPELQGITR
NVVNYLSINKNFINQEDEGEERESSGAKDAEKSGISKMSDESFAELMTKLNSFKLFKAEK
LQIVNQLPANMVHLYSIVEECDARFDEKTIEEMLEIISGYA
Sequence of entity 5 (E), FASTA
>6CNB_5 DNA-directed RNA polymerases I, II, and III subunit RPABC1 (chains E)
MDQENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSF
QANPTEESISKFPDMGSLWVEFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSA
MKLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDEKRELLKRYRLKESQLPRIQR
ADPVALYLGLKRGEVVKIIRKSETSGRYASYRICM
Sequence of entity 6 (F), FASTA
>6CNB_6 DNA-directed RNA polymerases I, II, and III subunit RPABC2 (chains F)
MSDYEEAFNDGNENFEDFDVEHFSDEETYEEKPQFKDGETTDANGKTIVTGGNGPEDFQQ
HEQIRRKTLKEKAIPKDQRATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRI
AMKELAEKKIPLVIRRYLPDGSFEDWSVEELIVDL
Sequence of entity 7 (G), FASTA
>6CNB_7 DNA-directed RNA polymerase III subunit RPC8 (chains G)
MFILSKIADLVRIPPDQFHRDTISAITHQLNNKFANKIIPNVGLCITIYDLLTVEEGQLK
PGDGSSYINVTFRAVVFKPFLGEIVTGWISKCTAEGIKVSLLGIFDDIFIPQNMLFEGCY
YTPEESAWIWPMDEETKLYFDVNEKIRFRIEREVFVDVKPKSPKERELEERAQLENEIEG
KNEETPQNEKPPAYALLGSCQTDGMGLVSWWE
Sequence of entity 8 (H), FASTA
>6CNB_8 DNA-directed RNA polymerases I, II, and III subunit RPABC3 (chains H)
MSNTLFDDIFQVSEVDPGRYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTVTIA
SSLNLEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYKFEEVSKDLIAVYYSFGG
LLMRLEGNYRNLNNLKQENAYLLIRR
Sequence of entity 9 (I), FASTA
>6CNB_9 DNA-directed RNA polymerase III subunit RPC10 (chains I)
MLSFCPSCNNMLLITSGDSGVYTLACRSCPYEFPIEGIEIYDRKKLPRKEVDDVLGGGWD
NVDQTKTQCPNYDTCGGESAYFFQLQIRSADEPMTTFYKCVNCGHRWKEN
Sequence of entity 10 (J), FASTA
>6CNB_10 DNA-directed RNA polymerases I, II, and III subunit RPABC5 (chains J)
MIVPVRCFSCGKVVGDKWESYLNLLQEDELDEGTALSRLGLKRYCCRRMILTHVDLIEKF
LRYNPLEKRD
Sequence of entity 11 (K), FASTA
>6CNB_11 DNA-directed RNA polymerases I and III subunit RPAC2 (chains K)
MTEDIEQKKTATEVTPQEPKHIQEEEEQDVDMTGDEEQEEEPDREKIKLLTQATSEDGTS
ASFQIVEEDHTLGNALRYVIMKNPDVEFCGYSIPHPSENLLNIRIQTYGETTAVDALQKG
LKDLMDLCDVVESKFTEKIKSM
Sequence of entity 12 (L), FASTA
>6CNB_12 DNA-directed RNA polymerases I, II, and III subunit RPABC4 (chains L)
MSREGFQIPTNLDAAAAGTSQARTATLKYICAECSSKLSLSRTDAVRCKDCGHRILLKAR
TKRLVQFEAR

Ligands and cofactors

IDNameFormulaCopies
ZNZinc ionZn7

Primary citation

Structural visualization of RNA polymerase III transcription machineries. Han, Y., Yan, C., Fishbain, S. et al. Cell Discov (2018) 4:40-40. DOI 10.1038/s41421-018-0044-z · PubMed

Other PDB entries of the same protein (UniProt P04051 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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