24QR: Yeast Pol II

Structure of yeast Pol II in complex with an oxaliplatin-ICL lesion at +2 position. Determined by electron microscopy at 2.67 Å resolution. Released 24 Jun 2026.

Method
Electron microscopy
Resolution
2.67 Å
Organisms
Saccharomyces cerevisiae S288C, synthetic construct
Chains
15
Atoms
32,853
Mol. weight
534.65 kDa
Ligands
MG, PT, DNH, ZN
Released
24 Jun 2026

Explore 24QR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

24QR contains 199 α-helices and 238 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: 82 helices, 76 β-strands

ElementResiduesLengthSheet
α-helix101
β-strand11122
β-strand16-18323
β-strand21124
α-helix24-307
β-strand34125
β-strand41126
β-strand48126
α-helix491
α-helix56-583
β-strand82-911025
α-helix93-953
α-helix96-10510
β-strand106127
β-strand113127
α-helix120-1267
α-helix131-14212
β-strand147128
β-strand151-153329
β-strand161-163329
α-helix1691
β-strand170128
α-helix1711
β-strand172-177630
β-strand180-185630
β-strand198-202530
α-helix204-2129
α-helix216-2216
β-strand225131
β-strand229131
α-helix231-2344
β-strand235-241725
α-helix242-2432
β-strand250-251232
β-strand257-258232
α-helix261-28222
α-helix286-30419
α-helix312-3143
β-strand315133
α-helix3201
β-strand321133
α-helix322-3232
α-helix325-3295
α-helix3351
α-helix336-3416
β-strand343-345334
β-strand348-355835
β-strand363-367535
α-helix368-3736
β-strand375-379536
α-helix385-39410
β-strand402-406536
β-strand412-414336
β-strand431-435536
α-helix4361
β-strand441-445535
α-helix452-4543
β-strand455-463935
β-strand468-470335
α-helix475-4784
β-strand486-490535
α-helix495-50410
β-strand506135
α-helix508-5103
β-strand512-513237
β-strand518-519237
α-helix525-53410
β-strand540-541238
α-helix543-5519
α-helix559-5635
β-strand565-567339
β-strand571139
β-strand572-573238
α-helix574-5818
α-helix5831
β-strand588-590340
β-strand605-608440
β-strand611-614440
α-helix619-6224
α-helix629-6368
α-helix639-66022
β-strand663141
α-helix666-6694
α-helix673-69826
α-helix702-7054
α-helix710-73627
α-helix742-7498
α-helix755-7628
β-strand766-767242
β-strand770143
β-strand773143
α-helix775-7762
β-strand779144
β-strand782144
α-helix7881
β-strand799-800242
α-helix810-84536
β-strand849-850245
β-strand856-857245
β-strand863-865345
α-helix868-8703
β-strand873146
α-helix875-8773
β-strand879-882447
α-helix890-8978
α-helix907-9093
α-helix910-9123
β-strand913148
α-helix923-94624
β-strand953-956447
α-helix960-97112
α-helix9781
β-strand979148
α-helix983-99614
α-helix1005-101410
α-helix1016-102510
α-helix1028-10303
α-helix1031-10355
α-helix1039-105517
β-strand1057146
α-helix1058-10592
α-helix1064-107815
α-helix1097-11059
β-strand1115-1119549
β-strand1120150
α-helix1122-11243
α-helix1128-113811
β-strand1141-1142251
α-helix1143-11464
β-strand1147-1154816
α-helix1167-11759
α-helix1185-11873
β-strand1188152
β-strand1191-1197716
α-helix1199-12046
α-helix1209-122012
β-strand1224-1228516
β-strand1236-1242716
β-strand1243152
α-helix1244-12452
α-helix1251-12544
α-helix1256-126813
β-strand1272-1274351
β-strand1281-12921249
β-strand1298-13091249
α-helix1313-13175
β-strand1322150
β-strand1328-1329249
α-helix1332-13387
α-helix1341-135818
α-helix1365-137612
α-helix1396-14005
α-helix1405-141511
β-strand1418-1419223
α-helix1424-14307
α-helix1437-14393
β-strand1441-1445510
α-helix1447-14537
Chain B: 58 helices, 83 β-strands
ElementResiduesLengthSheet
α-helix231
β-strand24153
α-helix251
α-helix29-4012
α-helix45-539
α-helix54-585
α-helix59-646
β-strand69-73554
α-helix80-823
β-strand84-971454
β-strand101-103355
β-strand109-111355
α-helix114-1207
β-strand125-1401654
β-strand150-151254
β-strand164-171854
β-strand173156
α-helix186-1916
β-strand203-205356
β-strand208-212556
α-helix2131
β-strand214-218557
α-helix2191
β-strand224-227458
α-helix228-2292
β-strand234-242958
β-strand252-259858
β-strand269-272458
β-strand276159
β-strand280-281258
α-helix282-2898
α-helix294-3018
α-helix308-32013
α-helix327-33610
β-strand338159
α-helix345-35410
α-helix355-3595
α-helix371-38919
α-helix394-3963
α-helix401-4033
β-strand404-407457
α-helix409-43729
α-helix444-4474
α-helix450-46213
β-strand480-482356
α-helix488-4947
β-strand497-499357
α-helix504-5085
α-helix514-5152
α-helix516-5183
β-strand522160
β-strand537-538257
β-strand539160
β-strand544-545261
α-helix552-5609
β-strand564-565262
α-helix5771
β-strand578-582562
β-strand585-590662
α-helix593-60513
β-strand614-618562
β-strand623-627562
β-strand633-639761
β-strand640-641263
β-strand650-651263
β-strand654153
α-helix655-66612
α-helix681-6866
β-strand690-694561
α-helix697-6993
β-strand703-704261
α-helix707-7104
α-helix728-7292
β-strand740-741261
α-helix745-7484
α-helix759-7613
β-strand762164
α-helix764-77411
β-strand777165
α-helix785-7873
β-strand793-796421
α-helix7991
β-strand800119
α-helix8011
β-strand804-805266
α-helix807-8104
β-strand821-827767
β-strand828141
β-strand839-842467
α-helix843-8486
β-strand853-8621021
β-strand865168
β-strand871168
β-strand873-874269
β-strand883169
β-strand904-905221
β-strand910-912370
β-strand914-917469
β-strand934-936369
β-strand939-940270
α-helix941-9422
β-strand947-9561021
β-strand962-9721121
β-strand979-981371
β-strand987-989371
β-strand990-994567
α-helix996-9983
β-strand1001-1002272
β-strand1010-1012367
α-helix1016-10205
β-strand1022164
α-helix1023-103816
β-strand1042-1043266
α-helix1052-106110
β-strand1069-1070267
β-strand1072-1073272
α-helix10791
β-strand1080172
α-helix10811
β-strand1085-1092867
β-strand1093-1094271
β-strand1095165
α-helix1099-11013
β-strand1104-1106335
β-strand1111173
β-strand1118173
α-helix1122-11243
α-helix1126-11272
β-strand1128-1130334
α-helix1132-114110
α-helix1144-11529
β-strand1158-1163622
β-strand1172-1174374
α-helix1175-11773
β-strand1179-1181374
β-strand1182175
β-strand1187175
β-strand1191-1196622
α-helix1198-120912
β-strand1212124
β-strand1215-1217323
Chain C: 11 helices, 12 β-strands
ElementResiduesLengthSheet
β-strand7-1371
β-strand17-2371
α-helix27-3913
β-strand43-54122
α-helix60-689
β-strand72-7433
β-strand97-10482
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-helix240-26728
Chain D: 10 helices, 5 β-strands
ElementResiduesLengthSheet
α-helix20-223
β-strand23176
α-helix24-263
β-strand28176
β-strand36-38377
β-strand44-46377
β-strand49-50210
α-helix52-7120
α-helix119-13315
α-helix139-15012
α-helix157-16913
α-helix174-1829
α-helix189-1924
α-helix196-1983
α-helix204-21714
Chain E: 14 helices, 14 β-strands
ElementResiduesLengthSheet
α-helix3-2523
β-strand2815
α-helix32-354
α-helix39-468
β-strand4716
α-helix521
β-strand5316
α-helix541
β-strand60-6237
β-strand6415
α-helix66-716
β-strand78-8257
β-strand87-8828
α-helix90-10314
β-strand107-11267
β-strand115-11628
α-helix118-1214
β-strand131-13667
α-helix144-1463
β-strand152-15549
α-helix156-1572
α-helix158-16811
α-helix1761
β-strand177-17829
α-helix183-1886
α-helix190-1912
β-strand195-20179
β-strand207-21489
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: 3 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-strand86-93812
β-strand98-103612
β-strand106-111612
β-strand120-122313
β-strand129-131313
β-strand136-137213
β-strand142-1521112
β-strand157-162612
Chain H: 3 helices, 8 β-strands
ElementResiduesLengthSheet
β-strand4-161339
β-strand23-30839
β-strand37-43739
β-strand54-60739
α-helix78-814
α-helix89-924
β-strand95-1061239
β-strand111-117739
β-strand122-128739
α-helix129-1324
β-strand139-145739

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 S288CP16370 (AlphaFold model)
DNA-directed RNA polymerases I, II, and III subunit RPABC1Eprotein215Saccharomyces cerevisiae S288CP20434 (AlphaFold model)
DNA-directed RNA polymerases I, II, and III subunit RPABC2Fprotein155Saccharomyces cerevisiae S288CP20435 (AlphaFold model)
DNA-directed RNA polymerase II subunit RPB7Gprotein171Saccharomyces cerevisiae S288CP34087 (AlphaFold model)
DNA-directed RNA polymerase II subunit RPB9Iprotein122Saccharomyces cerevisiae S288CP27999
DNA-directed RNA polymerases I, II, and III subunit RPABC5Jprotein70Saccharomyces cerevisiae S288CP22139
DNA-directed RNA polymerase II subunit RPB11Kprotein120Saccharomyces cerevisiae S288CP38902
DNA-directed RNA polymerases I, II, and III subunit RPABC4Lprotein70Saccharomyces cerevisiae S288CP40422
NTS(non-template strand)NDNA18synthetic construct
RNA (5'-r(*up*ap*cp*ap*ap*up*gp*up*up*gp*gp*ap*ap*ap*gp*gp*ap*gp*ap*g)-3')PRNA20synthetic construct
TS(template strand)TDNA25synthetic construct
DNA-directed RNA polymerase II subunit RPB1Aprotein1733Saccharomyces cerevisiae S288CP04050

3 more molecules are not listed.

Sequence of entity 1 (C), FASTA
>24QR_1 DNA-directed RNA polymerase II subunit RPB3 (chains C)
MSEEGPQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLAD
EFIAHRLGLIPLQSMDIEQLEYSRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVI
VSNLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAKKGIAKEHAKWGPAAAIEFEY
DPWNKLKHTDYWYEQDSAKEWPQSKNCEYEDPPNEGDPFDYKAQADTFYMNVESVGSIPV
DQVVVRGIDTLQKKVASILLALTQMDQDKVNFASGDNNTASNMLGSNEDVMMTGAEQDPY
SNASQMGNTGSGGYDNAW
Sequence of entity 2 (E), FASTA
>24QR_2 DNA-directed RNA polymerases I, II, and III subunit RPABC1 (chains E)
MDQENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSF
QANPTEESISKFPDMGSLWVEFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSA
MKLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDEKRELLKRYRLKESQLPRIQR
ADPVALYLGLKRGEVVKIIRKSETSGRYASYRICM
Sequence of entity 3 (F), FASTA
>24QR_3 DNA-directed RNA polymerases I, II, and III subunit RPABC2 (chains F)
MSDYEEAFNDGNENFEDFDVEHFSDEETYEEKPQFKDGETTDANGKTIVTGGNGPEDFQQ
HEQIRRKTLKEKAIPKDQRATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRI
AMKELAEKKIPLVIRRYLPDGSFEDWSVEELIVDL
Sequence of entity 4 (G), FASTA
>24QR_4 DNA-directed RNA polymerase II subunit RPB7 (chains G)
MFFIKDLSLNITLHPSFFGPRMKQYLKTKLLEEVEGSCTGKFGYILCVLDYDNIDIQRGR
ILPTDGSAEFNVKYRAVVFKPFKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLT
FNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSSIHAIGSIKEDYLGAI
Sequence of entity 5 (I), FASTA
>24QR_5 DNA-directed RNA polymerase II subunit RPB9 (chains I)
MTTFRFCRDCNNMLYPREDKENNRLLFECRTCSYVEEAGSPLVYRHELITNIGETAGVVQ
DIGSDPTLPRSDRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIFTSDQKNKRTQ
FS
Sequence of entity 6 (J), FASTA
>24QR_6 DNA-directed RNA polymerases I, II, and III subunit RPABC5 (chains J)
MIVPVRCFSCGKVVGDKWESYLNLLQEDELDEGTALSRLGLKRYCCRRMILTHVDLIEKF
LRYNPLEKRD
Sequence of entity 7 (K), FASTA
>24QR_7 DNA-directed RNA polymerase II subunit RPB11 (chains K)
MNAPDRFELFLLGEGESKLKIDPDTKAPNAVVITFEKEDHTLGNLIRAELLNDRKVLFAA
YKVEHPFFARFKLRIQTTEGYDPKDALKNACNSIINKLGALKTNFETEWNLQTLAADDAF
Sequence of entity 8 (L), FASTA
>24QR_8 DNA-directed RNA polymerases I, II, and III subunit RPABC4 (chains L)
MSREGFQIPTNLDAAAAGTSQARTATLKYICAECSSKLSLSRTDAVRCKDCGHRILLKAR
TKRLVQFEAR
Sequence of entity 9 (N), FASTA
>24QR_9 NTS(non-template strand) (chains N)
GAGAGCGAGGAGAGAAGA
Sequence of entity 10 (P), FASTA
>24QR_10 RNA (5'-R(*UP*AP*CP*AP*AP*UP*GP*UP*UP*GP*GP*AP*AP*AP*GP*GP*AP*GP*AP*G)-3') (chains P)
UACAAUGUUGGAAAGGAGAG
Sequence of entity 11 (T), FASTA
>24QR_11 TS(template strand) (chains T)
TCTTCTCTCCTCGCTCTCCTTTCCC
Sequence of entity 12 (A), FASTA
>24QR_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
PTPlatinum (II) ionPt1
DNH1R,2R-diaminocyclohexaneC6 H14 N21
ZNZinc ionZn8

Primary citation

Structure of yeast Pol II in complex with an oxaliplatin-ICL lesion at +2 position. Xu, J. 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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