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6GYM

Structure of a yeast closed complex with distorted DNA (CCdist)

Entity
Entity IDChain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
1A
(0)
General transcription and DNA repair factor IIH helicase subunit XPD,General transcription and DNA repair factor IIH helicase subunit XPD,DNA repair helicase RAD3,DNA repair helicase RAD3,General transcription and DNA repair factor IIH helicase subunit XPDpolymer77889111.51UniProt (P06839)
Pfam (PF06733)
Pfam (PF06777)
Pfam (PF13307)
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
2B
(1)
General transcription and DNA repair factor IIH subunit TFB1,General transcription and DNA repair factor IIH subunit TFB1,RNA polymerase II transcription factor B subunit 1,General transcription and DNA repair factor IIH subunit TFB1,RNA polymerase II transcription factor B subunit 1,General transcription and DNA repair factor IIH subunit TFB1,General transcription and DNA repair factor IIH subunit TFB1,General transcription and DNA repair factor IIH subunit TFB1,RNA polymerase II transcription factor B subunit 1,General transcription and DNA repair factor IIH subunit TFB1,RNA polymerase II transcription factor B subunit 1,General transcription and DNA repair factor IIH subunit TFB1,General transcription and DNA repair factor IIH subunit TFB1polymer64165440.91UniProt (P32776)
Pfam (PF08567)
Pfam (PF03909)
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,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
3C
(2)
General transcription and DNA repair factor IIH subunit TFB2,General transcription and DNA repair factor IIH subunit TFB2,General transcription and DNA repair factor IIH subunit TFB2,General transcription and DNA repair factor IIH subunit TFB2,General transcription and DNA repair factor IIH subunit TFB2,General transcription and DNA repair factor IIH subunit TFB2,General transcription and DNA repair factor IIH subunit TFB2polymer46248406.31UniProt (Q02939)
Pfam (PF03849)
Pfam (PF18307)
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
4D
(3)
RNA polymerase II transcription factor B subunit 3polymer32138188.41UniProt (Q03290)
Pfam (PF06391)
Pfam (PF17121)
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
5E
(4)
General transcription and DNA repair factor IIH subunit TFB4,General transcription and DNA repair factor IIH subunit TFB4,RNA polymerase II transcription factor B subunit 4,General transcription and DNA repair factor IIH subunit TFB4,General transcription and DNA repair factor IIH subunit TFB4polymer33836878.01UniProt (Q12004)
Pfam (PF03850)
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
6F
(5)
General transcription and DNA repair factor IIH subunit TFB5polymer728243.51UniProt (Q3E7C1)
Pfam (PF06331)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)TFIIH subunit TFB5,RNA polymerase II transcription factor B subunit 5
7G
(6)
General transcription and DNA repair factor IIH subunit SSL1,General transcription and DNA repair factor IIH subunit SSL1,General transcription and DNA repair factor IIH subunit SSL1,General transcription and DNA repair factor IIH subunit SSL1,General transcription and DNA repair factor IIH subunit SSL1,General transcription and DNA repair factor IIH subunit SSL1,General transcription and DNA repair factor IIH subunit SSL1polymer46151122.71UniProt (Q04673)
Pfam (PF04056)
Pfam (PF07975)
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
8H
(7)
General transcription and DNA repair factor IIH helicase subunit XPB,General transcription and DNA repair factor IIH helicase subunit XPB,DNA repair helicase RAD25,General transcription and DNA repair factor IIH helicase subunit XPB,DNA repair helicase RAD25,General transcription and DNA repair factor IIH helicase subunit XPB,General transcription and DNA repair factor IIH helicase subunit XPB,DNA repair helicase RAD25,General transcription and DNA repair factor IIH helicase subunit XPB,DNA repair helicase RAD25,General transcription and DNA repair factor IIH helicase subunit XPB,General transcription and DNA repair factor IIH helicase subunit XPB,DNA repair helicase RAD25,General transcription and DNA repair factor IIH helicase subunit XPB,DNA repair helicase RAD25,General transcription and DNA repair factor IIH helicase subunit XPB,General transcription and DNA repair factor IIH helicase subunit XPBpolymer84394049.71UniProt (Q00578)
Pfam (PF13625)
Pfam (PF04851)
Pfam (PF16203)
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,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,TFIIH subunit XPB,DNA repair helicase RAD25,RNA polymerase II transcription factor B subunit SSL2,TFB subunit SSL2,Suppressor of stem-loop mutation 2
9I
(A)
DNA-directed RNA polymerase II subunit RPB1polymer1733191821.61UniProt (P04050)
Pfam (PF04997)
Pfam (PF00623)
Pfam (PF04983)
Pfam (PF05000)
Pfam (PF04998)
Pfam (PF04992)
Pfam (PF04990)
Pfam (PF05001)
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
10J
(B)
DNA-directed RNA polymerase II subunit RPB2polymer1224138937.31UniProt (P08518)
Pfam (PF04563)
Pfam (PF04561)
Pfam (PF04565)
Pfam (PF04566)
Pfam (PF04567)
Pfam (PF00562)
Pfam (PF04560)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RNA polymerase II subunit 2,B150,DNA-directed RNA polymerase II 140 kDa polypeptide
11K
(C)
DNA-directed RNA polymerase II subunit RPB3polymer31835330.51UniProt (P16370)
Pfam (PF01193)
Pfam (PF01000)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RNA polymerase II subunit B3,B44.5,DNA-directed RNA polymerase II 45 kDa polypeptide
12L
(D)
DNA-directed RNA polymerase II subunit RPB4polymer22125451.21UniProt (P20433)
Pfam (PF03874)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RNA polymerase II subunit B4,B32,DNA-directed RNA polymerase II 32 kDa polypeptide
13M
(E)
DNA-directed RNA polymerases I, II, and III subunit RPABC1polymer21525117.11UniProt (P20434)
Pfam (PF03871)
Pfam (PF01191)
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
14N
(F)
DNA-directed RNA polymerases I, II, and III subunit RPABC2polymer15517931.81UniProt (P20435)
Pfam (PF01192)
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
15O
(G)
DNA-directed RNA polymerase II subunit RPB7polymer17119081.11UniProt (P34087)
Pfam (PF03876)
Pfam (PF00575)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RNA polymerase II subunit B7,B16
16P
(H)
DNA-directed RNA polymerases I, II, and III subunit RPABC3polymer14616525.41UniProt (P20436)
Pfam (PF03870)
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
17Q
(I)
DNA-directed RNA polymerase II subunit RPB9polymer12214308.21UniProt (P27999)
Pfam (PF02150)
Pfam (PF01096)
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
18R
(J)
DNA-directed RNA polymerases I, II, and III subunit RPABC5polymer708290.71UniProt (P22139)
Pfam (PF01194)
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
19S
(K)
DNA-directed RNA polymerase II subunit RPB11polymer12013633.51UniProt (P38902)
Pfam (PF13656)
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
20T
(L)
DNA-directed RNA polymerases I, II, and III subunit RPABC4polymer707730.01UniProt (P40422)
Pfam (PF03604)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RNA polymerases I,II,and III subunit ABC4,ABC10-alpha
21U
(M)
Transcription initiation factor IIBpolymer34538257.31UniProt (P29055)
Pfam (PF08271)
Pfam (PF00382)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)General transcription factor TFIIB,Transcription factor E
22V
(O)
TATA-box-binding proteinpolymer24027042.31UniProt (P13393)
Pfam (PF00352)
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
23W
(Q)
Transcription initiation factor IIF subunit alphapolymer73582320.61UniProt (P41895)
Pfam (PF05793)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)TFIIF-alpha,TFIIF large subunit,Transcription factor G 105 kDa subunit,P105
24X
(R)
Transcription initiation factor IIF subunit betapolymer40046684.51UniProt (P41896)
Pfam (PF17683)
Pfam (PF02270)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)ATP-dependent helicase TFG2,TFIIF medium subunit,TFIIF-beta,Transcription factor G 54 kDa subunit
25Y
(U)
Transcription initiation factor IIA large subunit,Transcription initiation factor IIA large subunitpolymer17119432.01UniProt (P32773)
Pfam (PF03153)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)TFIIA large subunit,TFIIA 32 kDa subunit,TFIIA large subunit,TFIIA 32 kDa subunit
26Z
(V)
Transcription initiation factor IIA subunit 2polymer12213473.11UniProt (P32774)
Pfam (PF02268)
Pfam (PF02751)
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
27AA
(W)
Transcription initiation factor IIE subunit alpha,Transcription initiation factor IIE subunit alpha,Transcription initiation factor IIE subunit alpha,Transcription initiation factor IIE subunit alpha,Transcription initiation factor IIE subunit alphapolymer33235921.51UniProt (P36100)
Pfam (PF02002)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (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,TFIIE-alpha,Factor A 66 kDa subunit,Transcription factor A large subunit,TFIIE-alpha,Factor A 66 kDa subunit,Transcription factor A large subunit
28BA
(X)
Transcription initiation factor IIE subunit betapolymer32837050.41UniProt (P36145)
Pfam (PF02186)
Pfam (PF18121)
Pfam (PF22254)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)TFIIE-beta,Factor A 43 kDa subunit,Transcription factor A small subunit
29CA
(Z)
Unknown proteinpolymer433677.51Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
30DA
(N)
non-template DNA (HIS4)polymer7523150.91Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
31EA
(T)
Template DNA (HIS4)polymer7523060.81Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
32FA
(0)
IRON/SULFUR CLUSTERnon-polymer351.61Chemie (SF4)
33GA, HA, IA, JA, KA...
(3, 4, 6, A, B...)
ZINC IONnon-polymer65.416Chemie (ZN)
34OA
(A)
MAGNESIUM IONnon-polymer24.31Chemie (MG)
Sequence modifications
0: 1 - 293 (UniProt: P06839)
0: 294 - 326 (PDB: 6GYM)
0: 327 - 778 (UniProt: P06839)
1: 1 - 218 (UniProt: P32776)
1: 219 - 249 (PDB: 6GYM)
1: 250 - 295 (UniProt: P32776)
1: 296 - 519 (PDB: 6GYM)
1: 537 - 642 (UniProt: P32776)
2: 1 - 112 (UniProt: Q02939)
2: 113 - 159 (PDB: 6GYM)
2: 160 - 194 (UniProt: Q02939)
2: 195 - 214 (PDB: 6GYM)
2: 215 - 281 (UniProt: Q02939)
2: 320 - 419 (PDB: 6GYM)
2: 433 - 513 (UniProt: Q02939)
4: 1 - 88 (UniProt: Q12004)
4: 89 - 114 (PDB: 6GYM)
4: 115 - 338 (UniProt: Q12004)
6: 1 - 307 (UniProt: Q04673)
6: 308 - 324 (PDB: 6GYM)
6: 325 - 372 (UniProt: Q04673)
6: 373 - 386 (PDB: 6GYM)
6: 387 - 411 (UniProt: Q04673)
6: 412 - 424 (PDB: 6GYM)
6: 425 - 461 (UniProt: Q04673)
7: 1 - 425 (UniProt: Q00578)
7: 426 - 451 (PDB: 6GYM)
7: 452 - 462 (PDB: 6GYM)
7: 463 - 481 (PDB: 6GYM)
7: 482 - 843 (UniProt: Q00578)
U: 1 - 209 (UniProt: P32773)
U: 210 - 286 (UniProt: P32773)
W: 1 - 194 (UniProt: P36100)
W: 253 - 409 (PDB: 6GYM)
W: 410 - 482 (UniProt: P36100)
Sequence viewer
Contents of the asymmetric unit
PolymersNumber of chains31
Total formula weight1295670.2
Non-Polymers*Number of molecules18
Total formula weight1422.5
All*Total formula weight1297092.7
*Water molecules are not included.

246704

PDB entries from 2025-12-24

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