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5OQM

STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH AND CORE MEDIATOR

Entity
Entity IDChain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
1ADNA-directed RNA polymerase II subunit RPB1polymer1733191821.61UniProt (P04050)
Pfam (PF04997)
Pfam (PF00623)
Pfam (PF04983)
Pfam (PF05000)
Pfam (PF04998)
Pfam (PF04992)
Pfam (PF04990)
Pfam (PF05001)
In PDB
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RNA polymerase II subunit B1,DNA-directed RNA polymerase III largest subunit,RNA polymerase II subunit B220
2BDNA-directed RNA polymerase II subunit RPB2polymer1224138937.31UniProt (P08518)
Pfam (PF04563)
Pfam (PF04561)
Pfam (PF04565)
Pfam (PF04566)
Pfam (PF04567)
Pfam (PF00562)
Pfam (PF04560)
In PDB
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RNA polymerase II subunit 2,B150,DNA-directed RNA polymerase II 140 kDa polypeptide
3CDNA-directed RNA polymerase II subunit RPB3polymer31835330.51UniProt (P16370)
Pfam (PF01193)
Pfam (PF01000)
In PDB
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RNA polymerase II subunit B3,B44.5,DNA-directed RNA polymerase II 45 kDa polypeptide
4DDNA-directed RNA polymerase II subunit RPB4polymer22125451.21UniProt (P20433)
Pfam (PF03874)
In PDB
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RNA polymerase II subunit B4,B32,DNA-directed RNA polymerase II 32 kDa polypeptide
5EDNA-directed RNA polymerases I, II, and III subunit RPABC1polymer21525117.11UniProt (P20434)
Pfam (PF03871)
Pfam (PF01191)
In PDB
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RNA polymerases I,II,and III subunit ABC1,ABC27,DNA-directed RNA polymerases I,and III 27 kDa polypeptide
6FDNA-directed RNA polymerases I, II, and III subunit RPABC2polymer15517931.81UniProt (P20435)
Pfam (PF01192)
In PDB
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RNA polymerases I,II,and III subunit ABC2,ABC23,DNA-directed RNA polymerases I,and III 23 kDa polypeptide
7GDNA-directed RNA polymerase II subunit RPB7polymer17119081.11UniProt (P34087)
Pfam (PF03876)
Pfam (PF00575)
In PDB
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RNA polymerase II subunit B7,B16
8HDNA-directed RNA polymerases I, II, and III subunit RPABC3polymer14616525.41UniProt (P20436)
Pfam (PF03870)
In PDB
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RNA polymerases I,II,and III subunit ABC3,ABC14.4,ABC14.5,DNA-directed RNA polymerases I,and III 14.5 kDa polypeptide
9IDNA-directed RNA polymerase II subunit RPB9polymer12214308.21UniProt (P27999)
Pfam (PF02150)
Pfam (PF01096)
In PDB
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RNA polymerase II subunit B9,B12.6,DNA-directed RNA polymerase II 14.2 kDa polypeptide,DNA-directed RNA polymerase II subunit 9
10JDNA-directed RNA polymerases I, II, and III subunit RPABC5polymer708290.71UniProt (P22139)
Pfam (PF01194)
In PDB
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RNA polymerases I,II,and III subunit ABC5,ABC10-beta,ABC8,DNA-directed RNA polymerases I,and III 8.3 kDa polypeptide
11KDNA-directed RNA polymerase II subunit RPB11polymer12013633.51UniProt (P38902)
Pfam (PF13656)
Pfam (PF01193)
In PDB
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RNA polymerase II subunit B11,B13.6,DNA-directed RNA polymerase II 13.6 kDa polypeptide
12LDNA-directed RNA polymerases I, II, and III subunit RPABC4polymer707730.01UniProt (P40422)
Pfam (PF03604)
In PDB
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RNA polymerases I,II,and III subunit ABC4,ABC10-alpha
13MTranscription initiation factor IIBpolymer34538257.31UniProt (P29055)
Pfam (PF08271)
Pfam (PF00382)
In PDB
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)General transcription factor TFIIB,Transcription factor E
14NNONTEMPLATE DNApolymer10632717.01synthetic construct
15OTATA-box-binding proteinpolymer24027042.31UniProt (P13393)
Pfam (PF00352)
In PDB
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)TATA sequence-binding protein,TBP,TATA-binding factor,TATA-box factor,Transcription factor D,Transcription initiation factor TFIID TBP subunit
16QTranscription initiation factor IIF subunit alphapolymer74783341.81UniProt (P41895)
UniProt (A0A250WD40)
Pfam (PF05793)
In PDB
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)TFIIF-alpha,TFIIF large subunit,Transcription factor G 105 kDa subunit,P105
17RTranscription initiation factor IIF subunit betapolymer40046684.51UniProt (P41896)
Pfam (PF17683)
Pfam (PF02270)
In PDB
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)ATP-dependent helicase TFG2,TFIIF medium subunit,TFIIF-beta,Transcription factor G 54 kDa subunit
18TTEMPLATE DNApolymer10632680.91synthetic construct
19UTranscription initiation factor IIA large subunitpolymer28632230.81UniProt (P32773)
Pfam (PF03153)
In PDB
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)TFIIA large subunit,TFIIA 32 kDa subunit
20VTranscription initiation factor IIA subunit 2polymer12213473.11UniProt (P32774)
Pfam (PF02268)
Pfam (PF02751)
In PDB
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)General transcription factor IIA subunit 2,TFIIA 13.5 kDa subunit,Transcription initiation factor IIA small chain,Transcription initiation factor IIA small subunit
21WTranscription factor TFIIE subunitpolymer54159825.91UniProt (A0A250WIP3)
UniProt (P36100)
Pfam (PF02002)
In PDB
Saccharomyces cerevisiae (Baker's yeast)TFIIE-alpha,Factor A 66 kDa subunit,Transcription factor A large subunit,TFIIE-alpha,Factor A 66 kDa subunit,Transcription factor A large subunit
22XTranscription initiation factor IIE subunit betapolymer32837050.41UniProt (P36145)
Pfam (PF02186)
Pfam (PF18121)
In PDB
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)TFIIE-beta,Factor A 43 kDa subunit,Transcription factor A small subunit
230General transcription and DNA repair factor IIH helicase subunit XPDpolymer77889064.61UniProt (P06839)
Pfam (PF06733)
Pfam (PF06777)
Pfam (PF13307)
In PDB
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)TFIIH subunit XPD,DNA repair helicase RAD3,RNA polymerase II transcription factor B subunit RAD3,TFB subunit RAD3,TFIIH subunit XPD,DNA repair helicase RAD3,RNA polymerase II transcription factor B subunit RAD3,TFB subunit RAD3,TFIIH subunit XPD,DNA repair helicase RAD3,RNA polymerase II transcription factor B subunit RAD3,TFB subunit RAD3
241General transcription and DNA repair factor IIH subunit TFB1polymer51053385.31UniProt (P32776)
Pfam (PF08567)
Pfam (PF03909)
In PDB
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)TFIIH subunit TFB1,RNA polymerase II transcription factor B 73 kDa subunit,RNA polymerase II transcription factor B p73 subunit,RNA polymerase II transcription factor B subunit 1,TFIIH subunit TFB1,RNA polymerase II transcription factor B 73 kDa subunit,RNA polymerase II transcription factor B p73 subunit,RNA polymerase II transcription factor B subunit 1,TFIIH subunit TFB1,RNA polymerase II transcription factor B 73 kDa subunit,RNA polymerase II transcription factor B p73 subunit,RNA polymerase II transcription factor B subunit 1,TFIIH subunit TFB1,RNA polymerase II transcription factor B 73 kDa subunit,RNA polymerase II transcription factor B p73 subunit,RNA polymerase II transcription factor B subunit 1,TFIIH subunit TFB1,RNA polymerase II transcription factor B 73 kDa subunit,RNA polymerase II transcription factor B p73 subunit,RNA polymerase II transcription factor B subunit 1,TFIIH subunit TFB1,RNA polymerase II transcription factor B 73 kDa subunit,RNA polymerase II transcription factor B p73 subunit,RNA polymerase II transcription factor B subunit 1,TFIIH subunit TFB1,RNA polymerase II transcription factor B 73 kDa subunit,RNA polymerase II transcription factor B p73 subunit,RNA polymerase II transcription factor B subunit 1
252General transcription and DNA repair factor IIH subunit TFB2polymer55360168.91UniProt (Q02939)
Pfam (PF03849)
Pfam (PF18307)
In PDB
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)TFIIH subunit TFB2,RNA polymerase II transcription factor B 52 kDa subunit,RNA polymerase II transcription factor B p52 subunit,RNA polymerase II transcription factor B subunit 2,TFIIH subunit TFB2,RNA polymerase II transcription factor B 52 kDa subunit,RNA polymerase II transcription factor B p52 subunit,RNA polymerase II transcription factor B subunit 2,TFIIH subunit TFB2,RNA polymerase II transcription factor B 52 kDa subunit,RNA polymerase II transcription factor B p52 subunit,RNA polymerase II transcription factor B subunit 2,TFIIH subunit TFB2,RNA polymerase II transcription factor B 52 kDa subunit,RNA polymerase II transcription factor B p52 subunit,RNA polymerase II transcription factor B subunit 2,TFIIH subunit TFB2,RNA polymerase II transcription factor B 52 kDa subunit,RNA polymerase II transcription factor B p52 subunit,RNA polymerase II transcription factor B subunit 2,TFIIH subunit TFB2,RNA polymerase II transcription factor B 52 kDa subunit,RNA polymerase II transcription factor B p52 subunit,RNA polymerase II transcription factor B subunit 2,TFIIH subunit TFB2,RNA polymerase II transcription factor B 52 kDa subunit,RNA polymerase II transcription factor B p52 subunit,RNA polymerase II transcription factor B subunit 2
263RNA polymerase II transcription factor B subunit 3polymer32138188.41UniProt (Q03290)
Pfam (PF06391)
Pfam (PF17121)
In PDB
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RNA polymerase II transcription factor B 38 kDa subunit,RNA polymerase II transcription factor B p38 subunit
274General transcription and DNA repair factor IIH subunit TFB4polymer33335978.11UniProt (Q12004)
Pfam (PF03850)
In PDB
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)TFIIH subunit TFB4,RNA polymerase II transcription factor B 34 kDa subunit,RNA polymerase II transcription factor B p34 subunit,RNA polymerase II transcription factor B subunit 4,TFIIH subunit TFB4,RNA polymerase II transcription factor B 34 kDa subunit,RNA polymerase II transcription factor B p34 subunit,RNA polymerase II transcription factor B subunit 4,TFIIH subunit TFB4,RNA polymerase II transcription factor B 34 kDa subunit,RNA polymerase II transcription factor B p34 subunit,RNA polymerase II transcription factor B subunit 4,TFIIH subunit TFB4,RNA polymerase II transcription factor B 34 kDa subunit,RNA polymerase II transcription factor B p34 subunit,RNA polymerase II transcription factor B subunit 4,TFIIH subunit TFB4,RNA polymerase II transcription factor B 34 kDa subunit,RNA polymerase II transcription factor B p34 subunit,RNA polymerase II transcription factor B subunit 4
285General transcription and DNA repair factor IIH subunit TFB5polymer728243.51UniProt (Q3E7C1)
Pfam (PF06331)
In PDB
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)TFIIH subunit TFB5,RNA polymerase II transcription factor B subunit 5
296General transcription and DNA repair factor IIH subunit SSL1polymer46151122.71UniProt (Q04673)
Pfam (PF04056)
Pfam (PF07975)
In PDB
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)TFIIH subunit SSL1,RNA polymerase II transcription factor B subunit SSL1,TFB subunit SSL1,Suppressor of stem-loop protein 1,TFIIH subunit SSL1,RNA polymerase II transcription factor B subunit SSL1,TFB subunit SSL1,Suppressor of stem-loop protein 1,TFIIH subunit SSL1,RNA polymerase II transcription factor B subunit SSL1,TFB subunit SSL1,Suppressor of stem-loop protein 1,TFIIH subunit SSL1,RNA polymerase II transcription factor B subunit SSL1,TFB subunit SSL1,Suppressor of stem-loop protein 1,TFIIH subunit SSL1,RNA polymerase II transcription factor B subunit SSL1,TFB subunit SSL1,Suppressor of stem-loop protein 1,TFIIH subunit SSL1,RNA polymerase II transcription factor B subunit SSL1,TFB subunit SSL1,Suppressor of stem-loop protein 1,TFIIH subunit SSL1,RNA polymerase II transcription factor B subunit SSL1,TFB subunit SSL1,Suppressor of stem-loop protein 1,TFIIH subunit SSL1,RNA polymerase II transcription factor B subunit SSL1,TFB subunit SSL1,Suppressor of stem-loop protein 1,TFIIH subunit SSL1,RNA polymerase II transcription factor B subunit SSL1,TFB subunit SSL1,Suppressor of stem-loop protein 1,TFIIH subunit SSL1,RNA polymerase II transcription factor B subunit SSL1,TFB subunit SSL1,Suppressor of stem-loop protein 1
307General transcription and DNA repair factor IIH helicase subunit XPBpolymer84394049.71UniProt (Q00578)
Pfam (PF13625)
Pfam (PF04851)
Pfam (PF16203)
In PDB
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)TFIIH subunit XPB,DNA repair helicase RAD25,RNA polymerase II transcription factor B subunit SSL2,TFB subunit SSL2,Suppressor of stem-loop mutation 2,TFIIH subunit XPB,DNA repair helicase RAD25,RNA polymerase II transcription factor B subunit SSL2,TFB subunit SSL2,Suppressor of stem-loop mutation 2,TFIIH subunit XPB,DNA repair helicase RAD25,RNA polymerase II transcription factor B subunit SSL2,TFB subunit SSL2,Suppressor of stem-loop mutation 2,TFIIH subunit XPB,DNA repair helicase RAD25,RNA polymerase II transcription factor B subunit SSL2,TFB subunit SSL2,Suppressor of stem-loop mutation 2,TFIIH subunit XPB,DNA repair helicase RAD25,RNA polymerase II transcription factor B subunit SSL2,TFB subunit SSL2,Suppressor of stem-loop mutation 2
31ZUnknown proteinpolymer433677.51Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
32aMediator of RNA polymerase II transcription subunit 6polymer29532844.71UniProt (P38782)
Pfam (PF04934)
In PDB
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Mediator complex subunit 6
33bMediator of RNA polymerase II transcription subunit 8polymer22325297.21UniProt (P38304)
Pfam (PF10232)
In PDB
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Mediator complex subunit 8
34cMediator of RNA polymerase II transcription subunit 11polymer11513324.21UniProt (Q99278)
Pfam (PF10280)
In PDB
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Mediator complex subunit 11
35dMediator of RNA polymerase II transcription subunit 17polymer68778582.81UniProt (P32569)
Pfam (PF10156)
In PDB
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Mediator complex subunit 17,Suppressor of RNA polymerase B 4
36eMediator of RNA polymerase II transcription subunit 18polymer30734316.51UniProt (P32585)
Pfam (PF09637)
In PDB
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Mediator complex subunit 18,Suppressor of RNA polymerase B 5
37fMediator of RNA polymerase II transcription subunit 20polymer21022918.11UniProt (P34162)
Pfam (PF08612)
In PDB
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Hyper-recombination suppressor protein 2,Mediator complex subunit 20,Suppressor of RNA polymerase B 2
38gMediator of RNA polymerase II transcription subunit 22polymer12113875.71UniProt (P32570)
Pfam (PF06179)
In PDB
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Mediator complex subunit 22,Suppressor of RNA polymerase B 6
39hMediator of RNA polymerase II transcription subunit 4polymer30033606.51UniProt (Q12343)
Pfam (PF10018)
In PDB
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Mediator complex subunit 4,Mediator complex subunit 4,Mediator complex subunit 4
40iMediator of RNA polymerase II transcription subunit 7polymer22325687.11UniProt (Q08278)
Pfam (PF05983)
In PDB
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Mediator complex subunit 7
41jMediator of RNA polymerase II transcription subunit 9polymer14917400.41UniProt (P33308)
Pfam (PF07544)
In PDB
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Chromosome segregation protein 2,Mediator complex subunit 9
42kMediator of RNA polymerase II transcription subunit 10polymer15717927.91UniProt (Q06213)
Pfam (PF09748)
In PDB
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Mediator complex subunit 10,Negative regulator of URS2 protein 2
43lMediator of RNA polymerase II transcription subunit 14polymer74584746.51UniProt (P19263)
Pfam (PF08638)
In PDB
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Glucose repression regulatory protein 1,Mediator complex subunit 14
44mMediator of RNA polymerase II transcription subunit 19polymer22024885.31UniProt (P25046)
Pfam (PF08633)
In PDB
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Hypoxic gene repressor protein 3,Mediator complex subunit 19,Negative regulator of URS2 protein 3,SNF1 suppressor protein 7
45nMediator of RNA polymerase II transcription subunit 21polymer14016093.41UniProt (P47822)
Pfam (PF11221)
In PDB
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Mediator complex subunit 21,RNAPII complex component SRB7,Suppressor of RNA polymerase B 7
46oMediator of RNA polymerase II transcription subunit 31,Mediator of RNA polymerase II transcription subunit 31polymer15116790.21UniProt (P38633)
Pfam (PF05669)
In PDB
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Hpr1 suppressor protein 1,Mediator complex subunit 31,Hpr1 suppressor protein 1,Mediator complex subunit 31
47I, J, L, M, W...ZINC IONnon-polymer65.416Chemie (ZN)
48AMAGNESIUM IONnon-polymer24.31Chemie (MG)
490IRON/SULFUR CLUSTERnon-polymer351.61Chemie (SF4)
Sequence modifications
Q: 1 - 403 (UniProt: P41895)
Q: 404 - 415 (PDB: 5OQM)
Q: 416 - 747 (UniProt: A0A250WD40)
W: 1 - 194 (UniProt: A0A250WIP3)
W: 259 - 373 (PDB: 5OQM)
W: 373 - 482 (UniProt: P36100)
0: 1 - 293 (UniProt: P06839)
0: 294 - 327 (PDB: 5OQM)
0: 328 - 778 (UniProt: P06839)
1: 1 - 121 (UniProt: P32776)
1: 168 - 175 (PDB: 5OQM)
1: 176 - 218 (UniProt: P32776)
1: 219 - 249 (PDB: 5OQM)
1: 250 - 295 (UniProt: P32776)
1: 296 - 521 (PDB: 5OQM)
1: 522 - 642 (UniProt: P32776)
2: 1 - 112 (UniProt: Q02939)
2: 113 - 159 (PDB: 5OQM)
2: 160 - 194 (UniProt: Q02939)
2: 195 - 214 (PDB: 5OQM)
2: 215 - 281 (UniProt: Q02939)
2: 380 - 419 (PDB: 5OQM)
2: 419 - 513 (UniProt: Q02939)
4: 1 - 88 (UniProt: Q12004)
4: 89 - 119 (PDB: 5OQM)
4: 120 - 256 (UniProt: Q12004)
4: 257 - 273 (PDB: 5OQM)
4: 274 - 338 (UniProt: Q12004)
6: 1 - 307 (UniProt: Q04673)
6: 308 - 324 (PDB: 5OQM)
6: 325 - 372 (UniProt: Q04673)
6: 373 - 386 (PDB: 5OQM)
6: 387 - 411 (UniProt: Q04673)
6: 412 - 424 (PDB: 5OQM)
6: 425 - 461 (UniProt: Q04673)
7: 1 - 425 (UniProt: Q00578)
7: 426 - 451 (PDB: 5OQM)
7: 452 - 462 (PDB: 5OQM)
7: 463 - 481 (PDB: 5OQM)
7: 482 - 843 (UniProt: Q00578)
h: 1 - 125 (UniProt: Q12343)
h: 130 - 145 (PDB: 5OQM)
h: 145 - 284 (UniProt: Q12343)
i: 1 - 222 (UniProt: Q08278)
PDBExternal DatabaseDetails
Ser 14-insertion
Thr 16Pro 15conflict
Ser 17Pro 16conflict
Ser 19Pro 18conflict
o: 4 - 95 (UniProt: P38633)
o: 99 - 122 (PDB: 5OQM)
Sequence viewer
Contents of the asymmetric unit
PolymersNumber of chains46
Total formula weight1809637.7
Non-Polymers*Number of molecules18
Total formula weight1422.5
All*Total formula weight1811060.2
*Water molecules are not included.

219869

PDB entries from 2024-05-15

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