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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

8CEO

Yeast RNA polymerase II transcription pre-initiation complex with core Mediator and the +1 nucleosome

This is a non-PDB format compatible entry.
Entity
Entity IDChain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
1A
(0)		General transcription and DNA repair factor IIH helicase subunit XPDpolymer77889899.01UniProt (P06839)
Pfam (PF06733)
Pfam (PF06777)
Pfam (PF13307)		Saccharomyces cerevisiae (baker's yeast)TFIIH subunit XPD,DNA repair helicase RAD3,RNA polymerase II transcription factor B subunit RAD3,TFB subunit RAD3
2B
(1)		TFB1 isoform 1polymer64272993.31UniProt (A0A6A5Q1T4)
Pfam (PF08567)
Pfam (PF03909)
UniProt (by SIFTS) (P32776)		Saccharomyces cerevisiae (baker's yeast)
3C
(2)		RNA polymerase II transcription factor B subunit 2polymer51358602.31UniProt (A0A6A5Q2X3)
Pfam (PF03849)
Pfam (PF18307)
UniProt (by SIFTS) (Q02939)		Saccharomyces cerevisiae (baker's yeast)
4D
(3)		RNA polymerase II transcription factor B subunit 3polymer32138188.41UniProt (A0A7I9BTI9)
Pfam (PF06391)
Pfam (PF17121)
UniProt (by SIFTS) (Q03290)		Saccharomyces cerevisiae (baker's yeast)
5E
(4)		General transcription and DNA repair factor IIH subunit TFB4polymer33837506.41UniProt (A0A8H4BW51)
Pfam (PF03850)
UniProt (by SIFTS) (Q12004)		Saccharomyces cerevisiae (baker's yeast)
6F
(5)		General transcription and DNA repair factor IIH subunit TFB5polymer728243.51UniProt (A0A8H8UMZ6)
Pfam (PF06331)
UniProt (by SIFTS) (Q3E7C1)		Saccharomyces cerevisiae (baker's yeast)
7G
(6)		General transcription and DNA repair factor IIHpolymer46152370.01UniProt (A0A6L0ZMK2)
Pfam (PF04056)
Pfam (PF07975)
UniProt (by SIFTS) (Q04673)		Saccharomyces cerevisiae (baker's yeast)
8H
(7)		General transcription and DNA repair factor IIH helicase subunit XPBpolymer84395461.71UniProt (Q00578)
Pfam (PF13625)
Pfam (PF04851)
Pfam (PF16203)		Saccharomyces cerevisiae (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
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 (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 (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 RPB3polymer34738635.91UniProt (P16370)
Pfam (PF01193)
Pfam (PF01000)		Saccharomyces cerevisiae (baker's yeast)RNA polymerase II subunit 3,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 (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 (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 (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 RPB7polymer17719909.91UniProt (P34087)
Pfam (PF03876)
Pfam (PF00575)		Saccharomyces cerevisiae (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 (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 (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 (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 (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 (baker's yeast)RNA polymerases I,II,and III subunit ABC4,ABC10-alpha
21U
(M)		Transcription initiation factor IIBpolymer35239215.41UniProt (P29055)
Pfam (PF08271)
Pfam (PF00382)		Saccharomyces cerevisiae (baker's yeast)General transcription factor TFIIB,Transcription factor E
22V
(N)		Nontemplate DNA (209-MER)polymer20964291.01synthetic construct
23W
(O)		TATA-binding proteinpolymer24027042.31UniProt (G4XSG8)
Pfam (PF00352)
UniProt (by SIFTS) (P13393)		Saccharomyces cerevisiae (baker's yeast)
24X
(Q)		Transcription initiation factor IIF subunit alphapolymer73582320.61UniProt (A0A8H4C1U9)
Pfam (PF05793)
UniProt (by SIFTS) (P41895)		Saccharomyces cerevisiae (baker's yeast)
25Y
(R)		Transcription initiation factor IIF subunit betapolymer40046684.51UniProt (P41896)
Pfam (PF17683)
Pfam (PF02270)		Saccharomyces cerevisiae (baker's yeast)TFIIF medium subunit,TFIIF-beta,Transcription factor G 54 kDa subunit
26Z
(T)		Template DNA (209-MER)polymer20964754.31synthetic construct
27AA
(U)		TOA1 isoform 1polymer28632230.81UniProt (A0A6A5Q2T8)
Pfam (PF03153)
UniProt (by SIFTS) (P32773)		Saccharomyces cerevisiae (baker's yeast)
28BA
(V)		Transcription initiation factor IIA subunit 2polymer12213473.11UniProt (A0A6A5PRZ0)
Pfam (PF02268)
Pfam (PF02751)
UniProt (by SIFTS) (P32774)		Saccharomyces cerevisiae (baker's yeast)
29CA
(W)		Transcription initiation factor IIE subunit alphapolymer49255951.01UniProt (P36100)
Pfam (PF02002)		Saccharomyces cerevisiae (baker's yeast)TFIIE-alpha,Factor A 66 kDa subunit,Transcription factor A large subunit
30DA
(X)		Transcription initiation factor IIE subunit betapolymer32837050.41UniProt (P36145)
Pfam (PF02186)
Pfam (PF18121)
Pfam (PF22254)		Saccharomyces cerevisiae (baker's yeast)TFIIE-beta,Factor A 43 kDa subunit,Transcription factor A small subunit
31EA
(a)		Mediator of RNA polymerase II transcription subunit 6polymer29532844.71UniProt (A0A8H4C0R2)
Pfam (PF04934)
UniProt (by SIFTS) (P38782)		Saccharomyces cerevisiae (baker's yeast)
32FA
(b)		Mediator of RNA polymerase II transcription subunit 8polymer22325297.21UniProt (A0A6A5Q217)
Pfam (PF10232)
UniProt (by SIFTS) (P38304)		Saccharomyces cerevisiae (baker's yeast)Mediator complex subunit 8
33GA
(c)		Mediator of RNA polymerase II transcription subunit 11polymer11513324.21UniProt (A0A6A5PPQ0)
Pfam (PF10280)
UniProt (by SIFTS) (Q99278)		Saccharomyces cerevisiae (baker's yeast)
34HA
(d)		Mediator of RNA polymerase II transcription subunit 17polymer68778582.81UniProt (A0A8H8ULN4)
Pfam (PF10156)
UniProt (by SIFTS) (P32569)		Saccharomyces cerevisiae (baker's yeast)
35IA
(e)		Mediator of RNA polymerase II transcription subunit 18polymer30734316.51UniProt (A0A8H4C0I9)
Pfam (PF09637)
UniProt (by SIFTS) (P32585)		Saccharomyces cerevisiae (baker's yeast)Mediator complex subunit 18
36JA
(f)		Mediator of RNA polymerase II transcription subunit 20polymer21022918.11UniProt (P34162)
Pfam (PF08612)		Saccharomyces cerevisiae (baker's yeast)Hyper-recombination suppressor protein 2,Mediator complex subunit 20,Suppressor of RNA polymerase B 2
37KA
(g)		Mediator of RNA polymerase II transcription subunit 22polymer12113875.71UniProt (P32570)
Pfam (PF06179)		Saccharomyces cerevisiae (baker's yeast)Mediator complex subunit 22,Suppressor of RNA polymerase B 6
38LA
(h)		Mediator of RNA polymerase II transcription subunit 4polymer28432244.91UniProt (A0A6A5Q2S0)
Pfam (PF10018)
UniProt (by SIFTS) (Q12343)		Saccharomyces cerevisiae (baker's yeast)
39MA
(i)		Mediator of RNA polymerase II transcription subunit 7polymer22225616.11UniProt (A0A6V8RKA4)
Pfam (PF05983)
UniProt (by SIFTS) (Q08278)		Saccharomyces cerevisiae (baker's yeast)
40NA
(j)		Mediator of RNA polymerase II transcription subunit 9polymer14917400.41UniProt (A0A6A5Q7U4)
Pfam (PF07544)
UniProt (by SIFTS) (P33308)		Saccharomyces cerevisiae (baker's yeast)
41OA
(k)		Mediator of RNA polymerase II transcription subunit 10polymer15717927.91UniProt (A0A6A5Q608)
Pfam (PF09748)
UniProt (by SIFTS) (Q06213)		Saccharomyces cerevisiae (baker's yeast)
42PA
(l)		Mediator of RNA polymerase II transcription subunit 14polymer1082123500.71UniProt (A0A8H4F9X3)
Pfam (PF08638)
UniProt (by SIFTS) (P19263)		Saccharomyces cerevisiae (baker's yeast)Mediator complex subunit 14
43QA
(m)		Mediator of RNA polymerase II transcription subunit 19polymer22024885.31UniProt (A0A6A5Q3S8)
Pfam (PF08633)
UniProt (by SIFTS) (P25046)		Saccharomyces cerevisiae (baker's yeast)
44RA
(n)		Mediator of RNA polymerase II transcription subunit 21polymer14016093.41UniProt (A0A6A5Q418)
Pfam (PF11221)
UniProt (by SIFTS) (P47822)		Saccharomyces cerevisiae (baker's yeast)
45SA
(o)		Mediator of RNA polymerase II transcription subunit 31polymer12714747.71UniProt (A0A8H4C1B0)
Pfam (PF05669)
UniProt (by SIFTS) (P38633)		Saccharomyces cerevisiae (baker's yeast)
46TA
(p)		Mediator of RNA polymerase II transcription subunit 1polymer56664315.01UniProt (A0A8H4BU46)
Pfam (PF10744)
UniProt (by SIFTS) (Q12321)		Saccharomyces cerevisiae (baker's yeast)
47UA, YA
(r, v)		Histone H3.2polymer13515271.92UniProt (P84233)
Pfam (PF00125)		Xenopus laevis (African clawed frog)
48VA, ZA
(s, w)		Histone H4polymer10211263.22UniProt (P62799)
Pfam (PF15511)		Xenopus laevis (African clawed frog)
49AB, WA
(t, x)		Histone H2Apolymer12913978.22UniProt (Q6AZJ8)
Pfam (PF00125)
Pfam (PF16211)
UniProt (by SIFTS) (P06897)		Xenopus laevis (African clawed frog)
50BB, XA
(u, y)		Histone H2Bpolymer12513848.12Pfam (PF00125)
UniProt (by SIFTS) (P02281)		Saccharomyces cerevisiae
51CB
(0)		IRON/SULFUR CLUSTERnon-polymer351.61Chemie (SF4)
52DB, EB, FB, GB, HB...
(3, 4, 6, A, B...)		ZINC IONnon-polymer65.417Chemie (ZN)
53MB
(A)		MAGNESIUM IONnon-polymer24.31Chemie (MG)
Sequence modifications
C: 4 - 318 (UniProt: P16370)
PDBExternal DatabaseDetails
Met -28-initiating methionine
Gly -27-expression tag
Ser -26-expression tag
His -25-expression tag
His -24-expression tag
His -23-expression tag
His -22-expression tag
His -21-expression tag
His -20-expression tag
Ser -19-expression tag
Asn -18-expression tag
Ser -17-expression tag
Gly -16-expression tag
Leu -15-expression tag
Asn -14-expression tag
Asp -13-expression tag
Ile -12-expression tag
Phe -11-expression tag
Glu -10-expression tag
Ala -9-expression tag
Gln -8-expression tag
Lys -7-expression tag
Ile -6-expression tag
Glu -5-expression tag
Trp -4-expression tag
His -3-expression tag
Glu -2-expression tag
Asp -1-expression tag
Thr 0-expression tag
Gly 1-expression tag
Ser 2-expression tag
Ser 3-expression tag
G: 1 - 171 (UniProt: P34087)
PDBExternal DatabaseDetails
His 172-expression tag
His 173-expression tag
His 174-expression tag
His 175-expression tag
His 176-expression tag
His 177-expression tag
M: 1 - 345 (UniProt: P29055)
PDBExternal DatabaseDetails
Lys 346-expression tag
His 347-expression tag
His 348-expression tag
His 349-expression tag
His 350-expression tag
His 351-expression tag
His 352-expression tag
W: 1 - 482 (UniProt: P36100)
PDBExternal DatabaseDetails
Ala 483-expression tag
Ala 484-expression tag
Ala 485-expression tag
Leu 486-expression tag
Glu 487-expression tag
His 488-expression tag
His 489-expression tag
His 490-expression tag
His 491-expression tag
His 492-expression tag
r, v: 1 - 135 (UniProt: P84233)
PDBExternal DatabaseDetails
Ala 102Gly 103conflict
Ala 110Cys 111engineered mutation
Sequence viewer
Contents of the asymmetric unit
PolymersNumber of chains54
Total formula weight2101184.2
Non-Polymers*Number of molecules19
Total formula weight1487.9
All*Total formula weight2102672.1
*Water molecules are not included.

227111

PDB entries from 2024-11-06

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