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- PDB-6gym: Structure of a yeast closed complex with distorted DNA (CCdist) -

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Entry
Database: PDB / ID: 6gym
TitleStructure of a yeast closed complex with distorted DNA (CCdist)
Components
  • (DNA-directed RNA polymerase II subunit ...Polymerase) x 7
  • (DNA-directed RNA polymerases I, II, and III subunit ...RNA polymerase) x 5
  • (General transcription and DNA repair factor IIH helicase subunit ...) x 2
  • (General transcription and DNA repair factor IIH subunit ...) x 5
  • (Transcription initiation factor IIA ...) x 2
  • (Transcription initiation factor IIE subunit ...) x 2
  • (Transcription initiation factor IIF subunit ...) x 2
  • RNA polymerase II transcription factor B subunit 3
  • TATA-box-binding protein
  • Template DNA (HIS4)
  • Transcription initiation factor IIB
  • Unknown protein
  • non-template DNA (HIS4)
KeywordsTRANSCRIPTION / rna polymerase ii / transcription initiation / promoter opening
Function / homologyTFA2 Winged helix domain 2 / RPB6/omega subunit-like superfamily / Cyclin-like superfamily / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain superfamily / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / von Willebrand factor A-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily ...TFA2 Winged helix domain 2 / RPB6/omega subunit-like superfamily / Cyclin-like superfamily / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain superfamily / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / von Willebrand factor A-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / TFB5-like superfamily / RNA polymerase Rpb2, domain 2 superfamily / RPB5-like RNA polymerase subunit superfamily / Pol II subunit B9, C-terminal zinc ribbon / TATA-box binding protein, eukaryotic / Helicase XPB/Ssl2, N-terminal domain / ERCC3/RAD25/XPB helicase, C-terminal domain / TATA-box binding protein, conserved site / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / DNA-directed RNA polymerase, subunit RPB6 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase RBP11 / TFIIH subunit Tfb1/GTF2H1 / RNA polymerase Rpb1, domain 2 / RNA polymerases M/15 Kd subunit / TFIIE alpha subunit / RNA polymerases N / 8 kDa subunit / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase Rpb6 / RNA polymerase Rpb5, C-terminal domain / Transcription factor S-II (TFIIS) / RNA polymerase Rpb3/RpoA insert domain / S1 RNA binding domain / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase Rpb2, domain 6 / Transcription factor TFIIB repeat / Transcription factor TFIID (or TATA-binding protein, TBP) / Transcription factor E / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerase subunit Rpb5-like / RNA polymerase Rpb1, domain 7 superfamily / Rpb4/RPC9 superfamily / P-loop containing nucleoside triphosphate hydrolase / TFIIEalpha/SarR/Rpc3 HTH domain / Transcription initiation factor IIA, gamma subunit, helical domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / Zinc finger C2H2-type / Zinc finger, RING/FYVE/PHD-type / ATP-dependent helicase Rad3/Chl1-like / Nucleic acid-binding, OB-fold / TBP domain superfamily / RNA polymerase subunit, RPB6/omega / DNA-directed RNA polymerase subunit/transcription factor S / PH-like domain superfamily / DNA-directed RNA polymerase, insert domain / Transcription factor TFIIB, cyclin-like domain / Transcription Factor IIF, Rap30/Rap74, interaction / HRDC-like superfamily / Helical and beta-bridge domain / DEAD2 / TFIIH subunit TTDA/Tfb5 / Transcription factor IIA, beta-barrel / Transcription factor IIA, helical / DNA-directed RNA polymerase, RBP11-like dimerisation domain / Zinc finger, TFIIB-type / Cyclin-like / RNA polymerase subunit RPB10 / Zinc finger, RING-type, conserved site / Transcription factor TFIIB, conserved site / RNA-binding domain, S1 / RNA polymerases, subunit N, zinc binding site / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / Archaeal RpoH /eukaryotic RPB5 RNA polymerase subunit / RNA polymerase, subunit H/Rpb5, conserved site / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / Transcription factor TFE/TFIIEalpha HTH domain / Transcription initiation factor TFIIE, beta subunit / TFIIH p62 subunit, N-terminal / Cdk-activating kinase assembly factor MAT1, centre / Transcription initiation factor IIA, gamma subunit, N-terminal / Transcription initiation factor IIA, gamma subunit, C-terminal / DNA-directed RNA polymerase, subunit 2 / RNA polymerase Rpb2, OB-fold / DNA-directed RNA polymerase RPB5 subunit, eukaryote/virus / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / Helicase superfamily 1/2, ATP-binding domain / TFIIE beta subunit core domain / TFIIF, beta subunit HTH domain / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / Zinc finger TFIIB-type profile. / Formation of Incision Complex in GG-NER / rt:r-sce-2564818: / Formation of the Early Elongation Complex / TFIIE beta central core DNA-binding domain profile. / TFE/IIEalpha-type HTH domain profile. / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / Zinc finger TFIIS-type profile. / RNA Polymerase II Pre-transcription Events
Function and homology information
Specimen sourceSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 6.7 Å resolution
AuthorsDienemann, C. / Schwalb, B. / Schilbach, S. / Cramer, P.
CitationJournal: Mol. Cell / Year: 2018
Title: Promoter Distortion and Opening in the RNA Polymerase II Cleft.
Authors: Christian Dienemann / Björn Schwalb / Sandra Schilbach / Patrick Cramer
Abstract: Transcription initiation requires opening of promoter DNA in the RNA polymerase II (Pol II) pre-initiation complex (PIC), but it remains unclear how this is achieved. Here we report the cryo-electron ...Transcription initiation requires opening of promoter DNA in the RNA polymerase II (Pol II) pre-initiation complex (PIC), but it remains unclear how this is achieved. Here we report the cryo-electron microscopic (cryo-EM) structure of a yeast PIC that contains underwound, distorted promoter DNA in the closed Pol II cleft. The DNA duplex axis is offset at the upstream edge of the initially melted DNA region (IMR) where DNA opening begins. Unstable IMRs are found in a subset of yeast promoters that we show can still initiate transcription after depletion of the transcription factor (TF) IIH (TFIIH) translocase Ssl2 (XPB in human) from the nucleus in vivo. PIC-induced DNA distortions may thus prime the IMR for melting and may explain how unstable IMRs that are predicted in promoters of Pol I and Pol III can open spontaneously. These results suggest that DNA distortion in the polymerase cleft is a general mechanism that contributes to promoter opening.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 30, 2018 / Release: Dec 5, 2018

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Structure visualization

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Assembly

Deposited unit
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 XPD
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 TFB1
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 TFB2
3: RNA polymerase II transcription factor B subunit 3
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 TFB4
5: General transcription and DNA repair factor IIH subunit TFB5
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 SSL1
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 XPB
A: DNA-directed RNA polymerase II subunit RPB1
B: DNA-directed RNA polymerase II subunit RPB2
C: DNA-directed RNA polymerase II subunit RPB3
D: DNA-directed RNA polymerase II subunit RPB4
E: DNA-directed RNA polymerases I, II, and III subunit RPABC1
F: DNA-directed RNA polymerases I, II, and III subunit RPABC2
G: DNA-directed RNA polymerase II subunit RPB7
H: DNA-directed RNA polymerases I, II, and III subunit RPABC3
I: DNA-directed RNA polymerase II subunit RPB9
J: DNA-directed RNA polymerases I, II, and III subunit RPABC5
K: DNA-directed RNA polymerase II subunit RPB11
L: DNA-directed RNA polymerases I, II, and III subunit RPABC4
M: Transcription initiation factor IIB
O: TATA-box-binding protein
Q: Transcription initiation factor IIF subunit alpha
R: Transcription initiation factor IIF subunit beta
U: Transcription initiation factor IIA large subunit,Transcription initiation factor IIA large subunit
V: Transcription initiation factor IIA subunit 2
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 alpha
X: Transcription initiation factor IIE subunit beta
Z: Unknown protein
N: non-template DNA (HIS4)
T: Template DNA (HIS4)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,297,09349
Polyers1,295,67031
Non-polymers1,42218
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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General transcription and DNA repair factor IIH helicase subunit ... , 2 types, 2 molecules 07

#1: Protein/peptide 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 XPD / TFIIH subunit XPD / DNA repair helicase RAD3 / RNA polymerase II transcription factor B subunit RAD3 / TFB subunit RAD3


Mass: 89111.453 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: RAD3, REM1, YER171W / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P06839, DNA helicase
#8: Protein/peptide 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 XPB / TFIIH subunit XPB / DNA repair helicase RAD25 / RNA polymerase II transcription factor B subunit SSL2 / TFB subunit SSL2 / Suppressor of stem-loop mutation 2


Mass: 94049.695 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: SSL2, LOM3, RAD25, UVS112, YIL143C / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q00578, DNA helicase

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General transcription and DNA repair factor IIH subunit ... , 5 types, 5 molecules 12456

#2: Protein/peptide 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 TFB1 / 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


Mass: 65440.922 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: TFB1, YDR311W, D9740.3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P32776
#3: Protein/peptide 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 TFB2 / 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


Mass: 48406.277 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: TFB2, YPL122C / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q02939
#5: Protein/peptide 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 TFB4 / 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


Mass: 36878.043 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: TFB4, YPR056W / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q12004
#6: Protein/peptide General transcription and DNA repair factor IIH subunit TFB5 / TFIIH subunit TFB5 / RNA polymerase II transcription factor B subunit 5


Mass: 8243.490 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: TFB5, YDR079C-A / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q3E7C1
#7: Protein/peptide 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 SSL1 / TFIIH subunit SSL1 / RNA polymerase II transcription factor B subunit SSL1 / TFB subunit SSL1 / Suppressor of stem-loop protein 1


Mass: 51122.695 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: SSL1, YLR005WPresqualene diphosphate synthase / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q04673

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Protein/peptide , 4 types, 4 molecules 3MOZ

#4: Protein/peptide RNA polymerase II transcription factor B subunit 3 / RNA polymerase II transcription factor B 38 kDa subunit / RNA polymerase II transcription factor B p38 subunit


Mass: 38188.438 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: TFB3, RIG2, YDR460W / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q03290
#21: Protein/peptide Transcription initiation factor IIB / General transcription factor TFIIB / Transcription factor E


Mass: 38257.340 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: SUA7, YPR086W, P9513.4 / Production host: Escherichia coli (E. coli) / References: UniProt: P29055
#22: Protein/peptide TATA-box-binding protein / TATA sequence-binding protein / TBP / TATA-binding factor / TATA-box factor / Transcription factor D / Transcription initiation factor TFIID TBP subunit


Mass: 27042.275 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: SPT15, BTF1, TBP1, YER148W / Production host: Escherichia coli (E. coli) / References: UniProt: P13393
#29: Protein/peptide Unknown protein


Mass: 3677.524 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Production host: Escherichia coli (E. coli)

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DNA-directed RNA polymerase II subunit ... , 7 types, 7 molecules ABCDGIK

#9: Protein/peptide DNA-directed RNA polymerase II subunit RPB1 / Polymerase / RNA polymerase II subunit B1 / DNA-directed RNA polymerase III largest subunit / RNA polymerase II subunit B220


Mass: 191821.578 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P04050, DNA-directed RNA polymerase
#10: Protein/peptide DNA-directed RNA polymerase II subunit RPB2 / Polymerase / RNA polymerase II subunit 2 / B150 / DNA-directed RNA polymerase II 140 kDa polypeptide


Mass: 138937.297 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P08518, DNA-directed RNA polymerase
#11: Protein/peptide DNA-directed RNA polymerase II subunit RPB3 / Polymerase / RNA polymerase II subunit B3 / B44.5 / DNA-directed RNA polymerase II 45 kDa polypeptide


Mass: 35330.457 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P16370
#12: Protein/peptide DNA-directed RNA polymerase II subunit RPB4 / Polymerase / RNA polymerase II subunit B4 / B32 / DNA-directed RNA polymerase II 32 kDa polypeptide


Mass: 25451.191 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P20433
#15: Protein/peptide DNA-directed RNA polymerase II subunit RPB7 / Polymerase / RNA polymerase II subunit B7 / B16


Mass: 19081.053 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P34087
#17: Protein/peptide DNA-directed RNA polymerase II subunit RPB9 / Polymerase / RNA polymerase II subunit B9 / B12.6 / DNA-directed RNA polymerase II 14.2 kDa polypeptide / DNA-directed RNA polymerase II subunit 9


Mass: 14308.161 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P27999
#19: Protein/peptide DNA-directed RNA polymerase II subunit RPB11 / Polymerase / RNA polymerase II subunit B11 / B13.6 / DNA-directed RNA polymerase II 13.6 kDa polypeptide


Mass: 13633.493 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P38902

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DNA-directed RNA polymerases I, II, and III subunit ... , 5 types, 5 molecules EFHJL

#13: Protein/peptide DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerase / RNA polymerases I / II / and III subunit ABC1 / ABC27 / DNA-directed RNA polymerases I / and III 27 kDa polypeptide


Mass: 25117.094 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P20434
#14: Protein/peptide DNA-directed RNA polymerases I, II, and III subunit RPABC2 / RNA polymerase / RNA polymerases I / II / and III subunit ABC2 / ABC23 / DNA-directed RNA polymerases I / and III 23 kDa polypeptide


Mass: 17931.834 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: RPO26, RPB6, YPR187W, P9677.8 / Production host: Escherichia coli (E. coli) / References: UniProt: P20435
#16: Protein/peptide DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerase / RNA polymerases I / II / and III subunit ABC3 / ABC14.4 / ABC14.5 / DNA-directed RNA polymerases I / and III 14.5 kDa polypeptide


Mass: 16525.363 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P20436
#18: Protein/peptide DNA-directed RNA polymerases I, II, and III subunit RPABC5 / RNA polymerase / RNA polymerases I / II / and III subunit ABC5 / ABC10-beta / ABC8 / DNA-directed RNA polymerases I / and III 8.3 kDa polypeptide


Mass: 8290.732 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P22139
#20: Protein/peptide DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase / RNA polymerases I / II / and III subunit ABC4 / ABC10-alpha


Mass: 7729.969 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P40422

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Transcription initiation factor IIF subunit ... , 2 types, 2 molecules QR

#23: Protein/peptide Transcription initiation factor IIF subunit alpha / TFIIF-alpha / TFIIF large subunit / Transcription factor G 105 kDa subunit / P105


Mass: 82320.570 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: TFG1, SSU71, YGR186W, G7526 / Production host: Escherichia coli (E. coli) / References: UniProt: P41895
#24: Protein/peptide Transcription initiation factor IIF subunit beta / ATP-dependent helicase TFG2 / TFIIF medium subunit / TFIIF-beta / Transcription factor G 54 kDa subunit


Mass: 46684.492 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: TFG2, YGR005C / Production host: Escherichia coli (E. coli) / References: UniProt: P41896, DNA helicase

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Transcription initiation factor IIA ... , 2 types, 2 molecules UV

#25: Protein/peptide Transcription initiation factor IIA large subunit,Transcription initiation factor IIA large subunit / TFIIA large subunit / TFIIA 32 kDa subunit


Mass: 19432.029 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: TOA1, YOR194C / Production host: Escherichia coli (E. coli) / References: UniProt: P32773
#26: Protein/peptide Transcription initiation factor IIA subunit 2 / General transcription factor IIA subunit 2 / TFIIA 13.5 kDa subunit / Transcription initiation factor IIA small chain / Transcription initiation factor IIA small subunit


Mass: 13473.070 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: TOA2, YKL058W / Production host: Escherichia coli (E. coli) / References: UniProt: P32774

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Transcription initiation factor IIE subunit ... , 2 types, 2 molecules WX

#27: Protein/peptide 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 alpha / TFIIE-alpha / Factor A 66 kDa subunit / Transcription factor A large subunit


Mass: 35921.543 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: TFA1, YKL028W / Production host: Escherichia coli (E. coli) / References: UniProt: P36100
#28: Protein/peptide Transcription initiation factor IIE subunit beta / TFIIE-beta / Factor A 43 kDa subunit / Transcription factor A small subunit


Mass: 37050.434 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: TFA2, YKR062W / Production host: Escherichia coli (E. coli) / References: UniProt: P36145

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DNA chain , 2 types, 2 molecules NT

#30: DNA chain non-template DNA (HIS4)


Mass: 23150.875 Da / Num. of mol.: 1
Source: (synth.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
#31: DNA chain Template DNA (HIS4)


Mass: 23060.822 Da / Num. of mol.: 1
Source: (synth.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

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Non-polymers , 3 types, 18 molecules

#32: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Formula: Fe4S4 / Iron–sulfur cluster
#33: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Formula: Zn / Zinc
#34: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg / Magnesium

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent IDSource
1complexCOMPLEX1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 310MULTIPLE SOURCES
2transcription factorsCOMPLEX1, 2, 3, 4, 5, 6, 7, 81RECOMBINANT
3PolymeraseCOMPLEX9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 201NATURAL
4Nucleic acidCOMPLEX30, 311RECOMBINANT
5transcription factorsCOMPLEX14, 21, 22, 23, 24, 25, 26, 27, 28, 291RECOMBINANT
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
12559292Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
23559292Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
34559292Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
45559292Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (recombinant)
IDEntity assembly IDNcbi tax IDOrganism
127111Trichoplusia ni (cabbage looper)
2432630synthetic construct (others)
35562Escherichia coli (E. coli)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 42 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 6.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 60000 / Symmetry type: POINT

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