9W8R: Yeast Pol II

Structure of yeast Pol II in complex with a short control scaffold lacking cisplatin-ICL lesion. Determined by electron microscopy at 2.68 Å resolution. Released 24 Jun 2026.

Method
Electron microscopy
Resolution
2.68 Å
Organisms
Saccharomyces cerevisiae (strain ATCC 204508 / S288c), synthetic construct
Chains
15
Atoms
32,477
Mol. weight
528.63 kDa
Ligands
MG, ZN
Released
24 Jun 2026

Explore 9W8R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9W8R contains 195 α-helices and 232 β-strands across 12 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: 80 helices, 71 β-strands

ElementResiduesLengthSheet
α-helix101
β-strand11122
β-strand16-18323
α-helix24-307
β-strand34124
β-strand41125
β-strand48125
α-helix491
α-helix56-583
β-strand82-911024
α-helix93-953
α-helix96-10510
β-strand106126
β-strand113126
α-helix120-1267
α-helix131-14212
β-strand151-153327
β-strand161-163327
α-helix169-1724
β-strand173-177528
β-strand180-185628
α-helix186-1872
β-strand198-201428
α-helix204-2129
α-helix216-2216
β-strand225129
β-strand229129
α-helix231-2344
β-strand235-241724
α-helix261-28222
α-helix286-30419
α-helix312-3132
β-strand315130
β-strand321130
α-helix325-3295
α-helix3351
α-helix336-3416
β-strand343-345331
β-strand348-355832
β-strand363-367532
α-helix368-3736
β-strand375-379533
α-helix3801
α-helix385-39410
β-strand402-406533
β-strand412-414333
β-strand431-435533
α-helix4361
β-strand441-445532
α-helix452-4543
β-strand455-463932
β-strand468-470332
α-helix475-4784
β-strand486-490532
α-helix495-50410
β-strand506132
α-helix508-5103
β-strand512-513234
β-strand518-519234
α-helix526-5349
β-strand540-541235
α-helix543-5519
α-helix560-5634
β-strand565-567336
β-strand571136
β-strand572-573235
α-helix574-5818
α-helix5831
β-strand588-590337
β-strand605-608437
β-strand611-614437
α-helix619-6224
α-helix629-6368
α-helix639-66022
β-strand663138
α-helix666-6694
α-helix673-69826
α-helix702-7054
α-helix710-73627
α-helix742-7498
α-helix755-7584
α-helix759-7635
β-strand766-767239
β-strand769-770240
β-strand773-774240
α-helix775-7762
β-strand779141
β-strand782141
β-strand799-800239
α-helix810-84536
β-strand849-850242
β-strand856-857242
β-strand863-865342
α-helix868-8703
β-strand873143
α-helix875-8773
β-strand879-882444
α-helix890-8978
β-strand913145
α-helix916-9194
α-helix924-94623
β-strand953-956444
α-helix960-97112
α-helix9781
β-strand979145
α-helix983-99412
α-helix1005-101410
α-helix1016-102510
α-helix1028-10292
α-helix1030-10356
α-helix1039-105517
β-strand1057143
α-helix1058-10592
α-helix1064-107815
α-helix1097-11059
β-strand1115-1119546
β-strand1120147
α-helix1122-11243
α-helix1128-113811
β-strand1141148
α-helix1143-11453
β-strand1147-1154816
α-helix1167-117610
α-helix1185-11873
β-strand1188149
β-strand1191-1197716
α-helix1201-12044
α-helix1209-122012
β-strand1224-1228516
β-strand1237-1242616
β-strand1243149
α-helix1244-12452
α-helix1256-126813
β-strand1274148
β-strand1281-12921246
α-helix12931
β-strand1298-13091246
α-helix1313-13175
β-strand1322147
β-strand1328-1329246
α-helix1332-13398
α-helix1341-135818
α-helix1365-137511
α-helix1389-13913
α-helix1396-14005
α-helix1405-141511
β-strand1418-1419223
α-helix1424-14307
α-helix1437-14393
β-strand1441-1445510
α-helix1447-14537
Chain B: 56 helices, 82 β-strands
ElementResiduesLengthSheet
α-helix231
β-strand24150
α-helix25-262
α-helix30-4011
α-helix45-539
α-helix54-585
α-helix59-646
β-strand68-73651
α-helix80-823
β-strand84-971451
β-strand101-102252
β-strand110-111252
α-helix114-1207
β-strand125-1401651
α-helix146-1472
β-strand150-151251
β-strand156151
β-strand164-171851
α-helix186-1916
β-strand203-205353
β-strand208-212553
α-helix2131
β-strand214-218554
α-helix2191
β-strand223-227555
β-strand234-242955
β-strand252-259855
β-strand269-272455
β-strand276156
β-strand280-281255
α-helix282-2898
α-helix294-3018
α-helix308-32114
α-helix327-33610
β-strand338156
α-helix348-35811
α-helix371-38919
α-helix394-3974
α-helix401-4033
β-strand404-407454
α-helix409-43729
α-helix444-4474
α-helix450-46213
β-strand480-482353
α-helix483-4842
α-helix488-4947
β-strand497-499354
α-helix516-5183
β-strand522157
β-strand533154
β-strand536-538354
β-strand539157
β-strand544-545258
α-helix552-5609
α-helix5631
β-strand564-565259
β-strand578-582559
β-strand585-590659
α-helix593-60513
β-strand614-618559
β-strand623-627559
β-strand633-639758
β-strand640-641260
β-strand650-651260
β-strand654150
α-helix655-66814
α-helix681-6866
β-strand690-694558
α-helix697-7004
β-strand703-704258
α-helix707-7104
α-helix728-7292
β-strand740-741258
α-helix745-7484
α-helix759-7613
α-helix764-77310
β-strand777161
α-helix785-7873
β-strand792-796521
β-strand800119
β-strand804-805262
α-helix807-8093
β-strand821-827763
β-strand828138
β-strand838-842563
α-helix843-8475
β-strand853-8621021
β-strand865164
β-strand871164
β-strand873-874265
β-strand883165
β-strand898166
α-helix899-9002
β-strand904-905221
β-strand910-912366
β-strand914-917465
β-strand924167
β-strand928167
β-strand934-936365
β-strand939-940266
α-helix941-9422
β-strand947-9561021
β-strand962-9721121
β-strand979-982463
β-strand987-994863
α-helix996-9983
β-strand1001-1002268
β-strand1010-1012363
α-helix1016-10205
α-helix1023-103816
β-strand1042-1043262
α-helix1052-106110
β-strand1069-1070263
β-strand1072-1073268
α-helix10791
β-strand1080168
α-helix10811
α-helix10841
β-strand1085-10941063
β-strand1095161
α-helix1099-11013
β-strand1104-1106332
β-strand1111169
β-strand1118169
α-helix11191
α-helix1122-11243
β-strand1128-1130331
α-helix1132-114110
α-helix1144-11485
α-helix1149-11535
β-strand1158-1163622
β-strand1172-1174370
β-strand1179-1181370
β-strand1182171
β-strand1187171
β-strand1191-1196622
α-helix1198-120912
β-strand1215-1217323
Chain C: 13 helices, 12 β-strands
ElementResiduesLengthSheet
β-strand7-1371
β-strand17-2371
α-helix27-3913
β-strand43-54122
α-helix60-689
β-strand72-7433
α-helix77-793
β-strand97-10482
α-helix1101
β-strand111-11334
α-helix115-1173
β-strand119-12022
β-strand129-13243
α-helix1331
β-strand145-14734
β-strand152-162112
α-helix168-1703
β-strand176-17941
α-helix197-2004
α-helix202-2043
α-helix205-2095
α-helix211-2133
α-helix218-2192
β-strand228-23361
α-helix240-26627
Chain D: 9 helices, 5 β-strands
ElementResiduesLengthSheet
α-helix20-223
β-strand23172
β-strand28172
β-strand36-38373
β-strand44-46373
β-strand49110
α-helix52-7221
α-helix119-13315
α-helix139-15012
α-helix157-17014
α-helix174-1829
α-helix188-1947
α-helix196-1983
α-helix204-21613
Chain E: 12 helices, 14 β-strands
ElementResiduesLengthSheet
α-helix3-2523
β-strand2815
α-helix32-354
α-helix39-468
β-strand4716
β-strand5316
β-strand60-6237
β-strand6415
α-helix66-716
β-strand78-8257
β-strand87-8828
α-helix90-10213
β-strand107-11267
β-strand115-11628
α-helix118-1214
β-strand131-13667
α-helix138-1403
α-helix144-1463
β-strand152-15549
α-helix156-1572
α-helix158-16710
α-helix1761
β-strand177-17829
α-helix183-1886
β-strand195-20069
β-strand208-21479
Chain F: 5 helices, 5 β-strands
ElementResiduesLengthSheet
β-strand73110
α-helix76-783
β-strand84111
α-helix85-862
α-helix87-10216
α-helix105-1073
α-helix117-12610
β-strand132-137610
β-strand143-147510
β-strand152111
Chain G: 4 helices, 14 β-strands
ElementResiduesLengthSheet
β-strand2-131210
α-helix15-173
α-helix22-309
β-strand37-39310
β-strand43-49710
β-strand55110
β-strand60-61210
α-helix621
β-strand68-791210
β-strand85-941012
β-strand98-103612
β-strand106-111612
α-helix112-1143
β-strand120-122313
β-strand129-131313
β-strand136113
β-strand142-1521112
β-strand157-162612
Chain H: 4 helices, 8 β-strands
ElementResiduesLengthSheet
β-strand4-161336
β-strand23-30836
β-strand37-43736
β-strand54-60736
α-helix67-682
α-helix78-792
α-helix89-924
β-strand95-1061236
β-strand111-118836
β-strand121-128836
α-helix129-1324
β-strand139-145736

4 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 RPB3Cprotein318Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P16370 (AlphaFold model)
DNA-directed RNA polymerases I, II, and III subunit RPABC1Eprotein215Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P20434 (AlphaFold model)
DNA-directed RNA polymerases I, II, and III subunit RPABC2Fprotein155Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P20435 (AlphaFold model)
DNA-directed RNA polymerase II subunit RPB7Gprotein171Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P34087 (AlphaFold model)
DNA-directed RNA polymerase II subunit RPB9Iprotein122Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P27999
DNA-directed RNA polymerases I, II, and III subunit RPABC5Jprotein70Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P22139
DNA-directed RNA polymerase II subunit RPB11Kprotein120Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P38902
DNA-directed RNA polymerases I, II, and III subunit RPABC4Lprotein70Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P40422
DNA (NTS, non-template strand)NDNA10synthetic construct
RNA (5'-r(*up*ap*up*up*ap*up*gp*ap*gp*gp*gp*gp*ap*ap*a)-3')PRNA15synthetic construct
DNA (TS, template strand)TDNA20synthetic construct
DNA-directed RNA polymerase II subunit RPB1Aprotein1733Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P04050

3 more molecules are not listed.

Sequence of entity 1 (C), FASTA
>9W8R_1 DNA-directed RNA polymerase II subunit RPB3 (chains C)
MSEEGPQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLAD
EFIAHRLGLIPLQSMDIEQLEYSRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVI
VSNLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAKKGIAKEHAKWGPAAAIEFEY
DPWNKLKHTDYWYEQDSAKEWPQSKNCEYEDPPNEGDPFDYKAQADTFYMNVESVGSIPV
DQVVVRGIDTLQKKVASILLALTQMDQDKVNFASGDNNTASNMLGSNEDVMMTGAEQDPY
SNASQMGNTGSGGYDNAW
Sequence of entity 2 (E), FASTA
>9W8R_2 DNA-directed RNA polymerases I, II, and III subunit RPABC1 (chains E)
MDQENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSF
QANPTEESISKFPDMGSLWVEFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSA
MKLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDEKRELLKRYRLKESQLPRIQR
ADPVALYLGLKRGEVVKIIRKSETSGRYASYRICM
Sequence of entity 3 (F), FASTA
>9W8R_3 DNA-directed RNA polymerases I, II, and III subunit RPABC2 (chains F)
MSDYEEAFNDGNENFEDFDVEHFSDEETYEEKPQFKDGETTDANGKTIVTGGNGPEDFQQ
HEQIRRKTLKEKAIPKDQRATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRI
AMKELAEKKIPLVIRRYLPDGSFEDWSVEELIVDL
Sequence of entity 4 (G), FASTA
>9W8R_4 DNA-directed RNA polymerase II subunit RPB7 (chains G)
MFFIKDLSLNITLHPSFFGPRMKQYLKTKLLEEVEGSCTGKFGYILCVLDYDNIDIQRGR
ILPTDGSAEFNVKYRAVVFKPFKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLT
FNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSSIHAIGSIKEDYLGAI
Sequence of entity 5 (I), FASTA
>9W8R_5 DNA-directed RNA polymerase II subunit RPB9 (chains I)
MTTFRFCRDCNNMLYPREDKENNRLLFECRTCSYVEEAGSPLVYRHELITNIGETAGVVQ
DIGSDPTLPRSDRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIFTSDQKNKRTQ
FS
Sequence of entity 6 (J), FASTA
>9W8R_6 DNA-directed RNA polymerases I, II, and III subunit RPABC5 (chains J)
MIVPVRCFSCGKVVGDKWESYLNLLQEDELDEGTALSRLGLKRYCCRRMILTHVDLIEKF
LRYNPLEKRD
Sequence of entity 7 (K), FASTA
>9W8R_7 DNA-directed RNA polymerase II subunit RPB11 (chains K)
MNAPDRFELFLLGEGESKLKIDPDTKAPNAVVITFEKEDHTLGNLIRAELLNDRKVLFAA
YKVEHPFFARFKLRIQTTEGYDPKDALKNACNSIINKLGALKTNFETEWNLQTLAADDAF
Sequence of entity 8 (L), FASTA
>9W8R_8 DNA-directed RNA polymerases I, II, and III subunit RPABC4 (chains L)
MSREGFQIPTNLDAAAAGTSQARTATLKYICAECSSKLSLSRTDAVRCKDCGHRILLKAR
TKRLVQFEAR
Sequence of entity 9 (N), FASTA
>9W8R_9 DNA (NTS, non-template strand) (chains N)
GAGAGCGAGG
Sequence of entity 10 (P), FASTA
>9W8R_10 RNA (5'-R(*UP*AP*UP*UP*AP*UP*GP*AP*GP*GP*GP*GP*AP*AP*A)-3') (chains P)
UAUUAUGAGGGGAAA
Sequence of entity 11 (T), FASTA
>9W8R_11 DNA (TS, template strand) (chains T)
CCTCGCTCTCCTTTCCCCTC
Sequence of entity 12 (A), FASTA
>9W8R_12 DNA-directed RNA polymerase II subunit RPB1 (chains A)
MVGQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGLNDPRLGS
IDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNE
LMRQALAIKDSKKRFAAIWTLCKTKMVCETDVPSEDDPTQLVSRGGCGNTQPTIRKDGLK
LVGSWKKDRATGDADEPELRVLSTEEILNIFKHISVKDFTSLGFNEVFSRPEWMILTCLP
VPPPPVRPSISFNESQRGEDDLTFKLADILKANISLETLEHNGAPHHAIEEAESLLQFHV
ATYMDNDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLE
LDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKR
AGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNA
DFDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTF
IELDQVLNMLYWVPDWDGVIPTPAIIKPKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSP
KDNGMLIIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQKVVNFWLLHN
GFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVR
FLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGKRIAFGFV
DRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRR
LVKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQSLDTIGGSDAAFEKRYRVD
LLNTDHTLDPSLLESGSEILGDLKLQVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVNI
RRIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLRGKNEIIQNAQRDAVTLFCC
LLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMT
LNTFHFAGVASKKVTSGVPRLKEILNVAKNMKTPSLTVYLEPGHAADQEQAKLIRSAIEH
TTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSLLDEEAEQSFDQQSPWLLRLELDRA
AMNDKDLTMGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVRPKSLDAETEAEEDHML
KKIENTMLENITLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVP
GIDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGG
LTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMAPIGTGA
FDVMIDEESLVKYMPEQKITEIEDGQDGGVTPYSNESGLVNADLDVKDELMFSPLVDSGS
NDAMAGGFTAYGGADYGEATSPFGAYGEAPTSPGFGVSSPGFSPTSPTYSPTSPAYSPTS
PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS
PTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSYSPTSP
SYSPTSPSYSPTSPNYSPTSPSYSPTSPGYSPGSPAYSPKQDEQKHNENENSR

Ligands and cofactors

IDNameFormulaCopies
MGMagnesium ionMg1
ZNZinc ionZn8

Primary citation

Structure of yeast Pol II in complex with a short control scaffold lacking cisplatin-ICL lesion. Xu, J., Zhu, L. To be published.

Other PDB entries of the same protein (UniProt P16370 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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