6CNC: Yeast RNA polymerase III open complex

Yeast RNA polymerase III open 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
47,836
Mol. weight
886.16 kDa
Ligands
ZN
Released
22 Aug 2018

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

Secondary structure: helices and β-sheets

6CNC contains 241 α-helices and 255 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: 62 helices, 53 β-strands

ElementResiduesLengthSheet
β-strand411
β-strand11-1222
β-strand1613
α-helix23-297
β-strand3314
α-helix73-764
β-strand82-8434
β-strand9015
α-helix93-10412
β-strand10616
β-strand11316
α-helix117-12711
α-helix134-14613
β-strand16417
β-strand178-17928
β-strand18017
α-helix192-20514
β-strand221-22228
α-helix224-2318
α-helix239-2424
β-strand25815
β-strand261-26334
α-helix264-2652
α-helix266-2683
α-helix270-2734
α-helix284-30118
α-helix313-32715
α-helix354-3574
α-helix364-3696
β-strand37219
β-strand376-379410
β-strand381111
β-strand391-395510
α-helix396-3994
β-strand404-407412
α-helix410-4123
α-helix413-42210
β-strand430-434512
β-strand442112
α-helix444-4463
β-strand461-464412
β-strand471-475510
β-strand486-493810
β-strand498111
β-strand499110
α-helix502-5043
α-helix505-5084
β-strand517-520410
α-helix525-5317
α-helix538-5403
β-strand542-543213
β-strand548-549213
α-helix556-56510
β-strand571114
α-helix573-58311
α-helix592-5954
β-strand597115
β-strand603115
β-strand604114
α-helix606-6149
β-strand629116
β-strand651116
β-strand653-655317
β-strand658-661417
β-strand671118
β-strand673118
α-helix677-6859
α-helix687-70822
α-helix714-7174
α-helix723-74624
α-helix760-78324
α-helix790-7912
α-helix792-7965
α-helix803-8097
β-strand818119
β-strand821119
α-helix858-87619
α-helix878-89316
β-strand897-898220
β-strand904-905220
β-strand911-913320
α-helix916-9183
β-strand928121
β-strand931121
α-helix935-94612
α-helix958-97417
α-helix999-102527
α-helix10391
α-helix1044-10474
α-helix1052-10598
α-helix1065-108016
α-helix1089-109810
α-helix1123-11319
β-strand1140-1142322
α-helix1150-11545
α-helix1155-11606
β-strand1173-1178623
β-strand1181-1186623
α-helix1190-11956
α-helix1203-121210
β-strand1232123
α-helix1255-126612
β-strand1281-1285522
β-strand1291-1296622
α-helix1302-13054
α-helix1319-13235
α-helix1329-134416
α-helix1352-136211
α-helix1385-13895
α-helix1393-14019
α-helix1411-14177
α-helix1424-14274
β-strand1430-1432324
α-helix1438-14403
α-helix1448-14536
Chain B: 49 helices, 72 β-strands
ElementResiduesLengthSheet
α-helix40-434
α-helix44-463
α-helix47-548
α-helix60-678
α-helix68-725
α-helix73-797
β-strand82-83225
β-strand93-100825
α-helix115-1206
β-strand127-135925
β-strand147-152625
α-helix154-1552
α-helix170-1734
β-strand187126
β-strand190126
β-strand197-200427
β-strand206-207228
β-strand217-221528
β-strand228-236928
β-strand239-243528
β-strand251-252228
α-helix253-2597
α-helix2681
α-helix269-2735
α-helix279-28911
α-helix300-3078
α-helix326-3305
α-helix334-3363
α-helix343-36119
α-helix372-3743
β-strand375-378427
α-helix380-40223
α-helix404-4074
α-helix421-4255
α-helix431-4399
β-strand441-442229
β-strand451-452229
α-helix463-4664
β-strand472-474327
α-helix491-4933
β-strand511-513327
β-strand515130
β-strand521131
α-helix527-5359
β-strand555-557332
β-strand561132
α-helix568-57912
β-strand589-593532
β-strand598-602532
β-strand607131
β-strand613-614233
β-strand615-616234
β-strand619-620234
α-helix625-6317
α-helix639-6435
β-strand646133
α-helix651-6566
β-strand659-660233
β-strand672-673233
α-helix677-6804
β-strand682130
α-helix684-6874
α-helix691-6933
α-helix696-70510
α-helix706-7083
β-strand709135
α-helix717-7193
β-strand724-728536
α-helix739-7446
α-helix746-7483
β-strand753-755337
β-strand757-759338
β-strand774139
α-helix778-7803
β-strand785-7941036
β-strand798140
β-strand802140
β-strand805141
β-strand829142
β-strand835-836236
β-strand841-843342
β-strand846-848341
α-helix850-8523
β-strand866-868341
β-strand871-872242
β-strand879-8881036
β-strand894-902936
β-strand911143
β-strand912-913244
β-strand921143
β-strand926139
β-strand932-933245
β-strand942-944338
α-helix948-9525
α-helix956-97015
β-strand976-977246
β-strand980-981246
α-helix985-9917
α-helix992-9943
β-strand1001-1002238
β-strand1005-1006245
β-strand1012145
β-strand1017-1019338
β-strand1022-1024337
β-strand1025-1026244
β-strand1027135
α-helix1031-10344
β-strand1036-1038310
β-strand1043147
β-strand1050147
α-helix1051-10522
β-strand106119
α-helix1064-107310
α-helix1076-10805
α-helix1081-10866
β-strand1089-1095748
β-strand1101-1102248
β-strand1116-1122748
α-helix1123-113412
β-strand114113
β-strand1144-114522
Chain C: 15 helices, 23 β-strands
ElementResiduesLengthSheet
β-strand5-7349
β-strand12-13249
α-helix35-395
β-strand41-47749
β-strand51-57749
α-helix63-7210
β-strand77-881250
α-helix94-1018
β-strand107151
α-helix115-1173
α-helix122-1243
α-helix128-1303
β-strand132-138750
α-helix1411
β-strand142152
α-helix1431
β-strand157152
β-strand161-163353
α-helix164-1663
β-strand168-169250
α-helix175-1784
β-strand185151
β-strand192-195453
β-strand202-2111050
α-helix217-2193
β-strand222154
β-strand226-231649
β-strand234-235255
α-helix242-2509
β-strand257-258256
β-strand265-266256
α-helix279-2824
α-helix286-2883
β-strand289-290255
β-strand291-3031349
β-strand304154
α-helix310-33021
β-strand334157
Chain D: 6 helices, 1 β-strand
ElementResiduesLengthSheet
β-strand3-9724
α-helix16-2611
α-helix56-7116
α-helix102-1109
α-helix118-1225
α-helix131-1355
α-helix147-16014
Chain E: 11 helices, 12 β-strands
ElementResiduesLengthSheet
α-helix2-2524
β-strand28158
α-helix32-354
α-helix39-468
β-strand47159
β-strand53159
α-helix56-583
β-strand60-62360
β-strand64158
α-helix67-715
β-strand78-80360
α-helix90-10213
β-strand108-111460
α-helix118-1225
β-strand133-135360
α-helix137-1393
α-helix144-1463
β-strand152-155461
α-helix158-16710
β-strand177-178261
α-helix183-1886
β-strand195-202861
β-strand206-214961
Chain F: 2 helices, 4 β-strands
ElementResiduesLengthSheet
β-strand84162
α-helix89-10214
α-helix117-1259
β-strand133-134224
β-strand146-147224
β-strand152162
Chain G: 2 helices, 16 β-strands
ElementResiduesLengthSheet
β-strand4-131024
α-helix15-195
α-helix22-3312
β-strand3811
β-strand45163
β-strand52124
β-strand57-59324
β-strand66-751024
β-strand76163
β-strand83-85364
β-strand89165
β-strand98-99265
β-strand108-109265
β-strand120-121266
β-strand128-129266
β-strand148-150364
β-strand152-155465
β-strand194-197465
Chain H: 1 helix, 9 β-strands
ElementResiduesLengthSheet
β-strand4-151267
β-strand23-30867
β-strand37-43767
β-strand54-60767
β-strand95167
β-strand100-107867
β-strand111-117767
β-strand122-125467
α-helix131-1333
β-strand141-145567

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
>6CNC_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
>6CNC_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
>6CNC_3 DNA-directed RNA polymerases I and III subunit RPAC1 (chains C)
MSNIVGIEYNRVTNTTSTDFPGFSKDAENEWNVEKFKKDFEVNISSLDAREANFDLINID
TSIANAFRRIMISEVPSVAAEYVYFFNNTSVIQDEVLAHRIGLVPLKVDPDMLTWVDSNL
PDDEKFTDENTIVLSLNVKCTRNPDAPKGSTDPKELYNNAHVYARDLKFEPQGRQSTTFA
DCPVVPADPDILLAKLRPGQEISLKAHCILGIGGDHAKFSPVSTASYRLLPQINILQPIK
GESARRFQKCFPPGVIGIDEGSDEAYVKDARKDTVSREVLRYEEFADKVKLGRVRNHFIF
NVESAGAMTPEEIFFKSVRILKNKAEYLKNCPITQ
Sequence of entity 4 (D), FASTA
>6CNC_4 DNA-directed RNA polymerase III subunit RPC9 (chains D)
MKVLEERNAFLSDYEVLKFLTDLEKKHLWDQKSLAALKKSRSKGKQNRPYNHPELQGITR
NVVNYLSINKNFINQEDEGEERESSGAKDAEKSGISKMSDESFAELMTKLNSFKLFKAEK
LQIVNQLPANMVHLYSIVEECDARFDEKTIEEMLEIISGYA
Sequence of entity 5 (E), FASTA
>6CNC_5 DNA-directed RNA polymerases I, II, and III subunit RPABC1 (chains E)
MDQENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSF
QANPTEESISKFPDMGSLWVEFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSA
MKLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDEKRELLKRYRLKESQLPRIQR
ADPVALYLGLKRGEVVKIIRKSETSGRYASYRICM
Sequence of entity 6 (F), FASTA
>6CNC_6 DNA-directed RNA polymerases I, II, and III subunit RPABC2 (chains F)
MSDYEEAFNDGNENFEDFDVEHFSDEETYEEKPQFKDGETTDANGKTIVTGGNGPEDFQQ
HEQIRRKTLKEKAIPKDQRATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRI
AMKELAEKKIPLVIRRYLPDGSFEDWSVEELIVDL
Sequence of entity 7 (G), FASTA
>6CNC_7 DNA-directed RNA polymerase III subunit RPC8 (chains G)
MFILSKIADLVRIPPDQFHRDTISAITHQLNNKFANKIIPNVGLCITIYDLLTVEEGQLK
PGDGSSYINVTFRAVVFKPFLGEIVTGWISKCTAEGIKVSLLGIFDDIFIPQNMLFEGCY
YTPEESAWIWPMDEETKLYFDVNEKIRFRIEREVFVDVKPKSPKERELEERAQLENEIEG
KNEETPQNEKPPAYALLGSCQTDGMGLVSWWE
Sequence of entity 8 (H), FASTA
>6CNC_8 DNA-directed RNA polymerases I, II, and III subunit RPABC3 (chains H)
MSNTLFDDIFQVSEVDPGRYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTVTIA
SSLNLEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYKFEEVSKDLIAVYYSFGG
LLMRLEGNYRNLNNLKQENAYLLIRR
Sequence of entity 9 (I), FASTA
>6CNC_9 DNA-directed RNA polymerase III subunit RPC10 (chains I)
MLSFCPSCNNMLLITSGDSGVYTLACRSCPYEFPIEGIEIYDRKKLPRKEVDDVLGGGWD
NVDQTKTQCPNYDTCGGESAYFFQLQIRSADEPMTTFYKCVNCGHRWKEN
Sequence of entity 10 (J), FASTA
>6CNC_10 DNA-directed RNA polymerases I, II, and III subunit RPABC5 (chains J)
MIVPVRCFSCGKVVGDKWESYLNLLQEDELDEGTALSRLGLKRYCCRRMILTHVDLIEKF
LRYNPLEKRD
Sequence of entity 11 (K), FASTA
>6CNC_11 DNA-directed RNA polymerases I and III subunit RPAC2 (chains K)
MTEDIEQKKTATEVTPQEPKHIQEEEEQDVDMTGDEEQEEEPDREKIKLLTQATSEDGTS
ASFQIVEEDHTLGNALRYVIMKNPDVEFCGYSIPHPSENLLNIRIQTYGETTAVDALQKG
LKDLMDLCDVVESKFTEKIKSM
Sequence of entity 12 (L), FASTA
>6CNC_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:

Browse structure collections

About this viewer

MolViewer shows 6CNC directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.