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- PDB-6gyk: Structure of a yeast closed complex (core CC1) -

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Entry
Database: PDB / ID: 6gyk
TitleStructure of a yeast closed complex (core CC1)
Components
  • (DNA-directed RNA polymerase II subunit ...Polymerase) x 7
  • (DNA-directed RNA polymerases I, II, and III subunit ...RNA polymerase) x 5
  • (Transcription initiation factor IIA ...) x 2
  • (Transcription initiation factor IIF subunit ...) x 2
  • GAT1 Promoter
  • GAT1 promoter DNA
  • TATA-box-binding protein
  • Transcription initiation factor IIB
KeywordsTRANSCRIPTION / Rna polymerase II / transcription initiation / promoter opening
Function / homology
Function and homology information


promoter clearance from RNA polymerase II promoter / TFIIA-class transcription factor complex binding / go:0001186: / dephosphorylation of RNA polymerase II C-terminal domain / transcriptional open complex formation at RNA polymerase II promoter / transcription factor TFIIF complex / transcriptional start site selection at RNA polymerase II promoter / RNA polymerase II complex recruiting activity / transcription factor TFIIIB complex / transcription factor TFIIA complex ...promoter clearance from RNA polymerase II promoter / TFIIA-class transcription factor complex binding / go:0001186: / dephosphorylation of RNA polymerase II C-terminal domain / transcriptional open complex formation at RNA polymerase II promoter / transcription factor TFIIF complex / transcriptional start site selection at RNA polymerase II promoter / RNA polymerase II complex recruiting activity / transcription factor TFIIIB complex / transcription factor TFIIA complex / RNA polymerase III general transcription initiation factor activity / RNA polymerase III preinitiation complex assembly / RNA polymerase I general transcription initiation factor binding / regulation of protein serine/threonine phosphatase activity / RNA polymerase III regulatory region DNA binding / nuclear-transcribed mRNA catabolic process, exonucleolytic / nucleolar large rRNA transcription by RNA polymerase I / transposon integration / RNA polymerase II general transcription initiation factor activity / recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex / mRNA export from nucleus in response to heat stress / maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter / DNA binding, bending / transcription factor TFIID complex / RNA polymerase II activity / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / positive regulation of transcription regulatory region DNA binding / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / RNA polymerase II complex binding / termination of RNA polymerase III transcription / positive regulation of translational initiation / protein phosphatase activator activity / RNA polymerase I activity / tRNA transcription by RNA polymerase III / RNA polymerase I complex / RNA polymerase III complex / mRNA cleavage / RNA polymerase II, core complex / RNA polymerase II preinitiation complex assembly / transcription by RNA polymerase I / transcription by RNA polymerase III / transcription, RNA-templated / transcriptional preinitiation complex / termination of RNA polymerase II transcription / translation initiation factor binding / transcription coregulator activity / RNA polymerase II core promoter sequence-specific DNA binding / transcription elongation from RNA polymerase II promoter / ribonucleoside binding / single-stranded RNA binding / TBP-class protein binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / DNA-templated transcription, initiation / RNA polymerase II activating transcription factor binding / positive regulation of transcription elongation from RNA polymerase II promoter / P-body / ribosome biogenesis / transcription-coupled nucleotide-excision repair / cytoplasmic stress granule / single-stranded DNA binding / translesion synthesis / disordered domain specific binding / transcription by RNA polymerase II / transcription factor complex / positive regulation of DNA-binding transcription factor activity / transcription initiation from RNA polymerase II promoter / nucleic acid binding / transcription coactivator activity / protein dimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / mRNA binding / transcription factor binding / cellular response to DNA damage stimulus / nucleolus / DNA-binding transcription factor activity / chromatin binding / regulation of transcription, DNA-templated / nucleotide binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
Transcription initiation factor IIA, gamma subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / Transcription factor TFIIB, cyclin-like domain / Cyclin-like / DNA-directed RNA polymerase RPB5 subunit, eukaryote/virus / RNA polymerase Rpb2, OB-fold / DNA-directed RNA polymerase, subunit 2 / Transcription initiation factor IIA, gamma subunit, C-terminal / Transcription initiation factor IIA, gamma subunit, N-terminal / DNA-directed RNA polymerase M, 15kDa subunit, conserved site ...Transcription initiation factor IIA, gamma subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / Transcription factor TFIIB, cyclin-like domain / Cyclin-like / DNA-directed RNA polymerase RPB5 subunit, eukaryote/virus / RNA polymerase Rpb2, OB-fold / DNA-directed RNA polymerase, subunit 2 / Transcription initiation factor IIA, gamma subunit, C-terminal / Transcription initiation factor IIA, gamma subunit, N-terminal / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerase, subunit H/Rpb5, conserved site / Archaeal RpoH /eukaryotic RPB5 RNA polymerase subunit / RNA polymerases, subunit N, zinc binding site / Nucleic acid-binding, OB-fold / RNA-binding domain, S1 / Transcription factor TFIIB, conserved site / RNA polymerase subunit RPB10 / DNA-directed RNA polymerase, subunit RPB6 / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / TATA-box binding protein, conserved site / TATA-box binding protein, eukaryotic / Pol II subunit B9, C-terminal zinc ribbon / RPB5-like RNA polymerase subunit superfamily / RPB6/omega subunit-like superfamily / Zinc finger, TFIIB-type / TBP domain superfamily / Winged helix DNA-binding domain superfamily / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 2 / RNA polymerase, beta subunit, protrusion / RNA polymerase Rpb2, domain 4 / RNA polymerase subunit, RPB6/omega / RNA polymerase Rpb2, domain 5 / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / Transcription initiation factor IIF, alpha subunit / DNA-directed RNA polymerase, RBP11-like dimerisation domain / Transcription factor IIA, helical / Transcription factor IIA, beta-barrel / HRDC-like superfamily / Transcription Factor IIF, Rap30/Rap74, interaction / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / DNA-directed RNA polymerase subunit/transcription factor S / Winged helix-like DNA-binding domain superfamily / RNA polymerase, RBP11-like subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase Rpb8 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase Rpb4 / RNA polymerase Rpb5, C-terminal domain / RNA polymerase Rpb5, N-terminal domain / RNA polymerase Rpb6 / S1 RNA binding domain / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / Transcription factor S-II (TFIIS) / RNA polymerase beta subunit / RNA polymerases M/15 Kd subunit / RNA polymerases N / 8 kDa subunit / RNA polymerase Rpb3/Rpb11 dimerisation domain / DNA directed RNA polymerase, 7 kDa subunit / Transcription factor TFIIB repeat / TFIIB zinc-binding / Transcription factor TFIID (or TATA-binding protein, TBP) / Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) / TFIIF, beta subunit HTH domain / TFIIF, beta subunit N-terminus / Transcription initiation factor IIA, gamma subunit, helical domain / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, domain 2 / DNA-directed RNA polymerase, insert domain superfamily / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb7-like, N-terminal domain superfamily / Cyclin-like superfamily / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase RBP11 / RNA polymerase Rpb1, funnel domain superfamily / Rpb4/RPC9 superfamily / RNA polymerase Rpb1, domain 7 superfamily / DNA-directed RNA polymerase subunit Rpb5-like / TFIIF beta subunit, HTH domain / RNA polymerase Rpb2, domain 7 / TFIIF, beta subunit, N-terminal / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 6
DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerase II subunit RPB7 / Transcription initiation factor IIB / Transcription initiation factor IIA large subunit / Transcription initiation factor IIA subunit 2 ...DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerase II subunit RPB7 / Transcription initiation factor IIB / Transcription initiation factor IIA large subunit / Transcription initiation factor IIA subunit 2 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / Transcription initiation factor IIF subunit alpha / Transcription initiation factor IIF subunit beta / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB3 / TATA-box-binding protein
Biological speciesSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.1 Å
AuthorsDienemann, C. / Schwalb, B. / Schilbach, S. / Cramer, P.
Funding support Germany, 2items
OrganizationGrant numberCountry
European Research Council693023 Germany
German Research FoundationSFB860 Germany
CitationJournal: Mol. Cell / Year: 2019
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
History
DepositionJun 30, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: citation / pdbx_validate_close_contact ...citation / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]

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Assembly

Deposited unit
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
N: GAT1 Promoter
O: TATA-box-binding protein
Q: Transcription initiation factor IIF subunit alpha
R: Transcription initiation factor IIF subunit beta
T: GAT1 promoter DNA
U: Transcription initiation factor IIA large subunit,Transcription initiation factor IIA large subunit
V: Transcription initiation factor IIA subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)777,19430
Polymers776,58120
Non-polymers61310
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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

#1: Protein DNA-directed RNA polymerase II subunit RPB1 / Polymerase / RNA polymerase II subunit B1 / DNA-directed RNA polymerase III largest subunit / RNA polymerase II ...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 method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P04050, DNA-directed RNA polymerase
#2: Protein 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 method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P08518, DNA-directed RNA polymerase
#3: Protein 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 method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P16370
#4: Protein DNA-directed RNA polymerase II subunit RPB4 / Polymerase / RNA polymerase II subunit B4 / B32 / DNA-directed RNA polymerase II 32 kDa polypeptide


Mass: 25319.998 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P20433
#7: Protein DNA-directed RNA polymerase II subunit RPB7 / Polymerase / RNA polymerase II subunit B7 / B16


Mass: 19081.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P34087
#9: Protein 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- ...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 method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P27999
#11: Protein 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 method: isolated from a natural source
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

#5: Protein 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 ...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 method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P20434
#6: Protein 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 ...RNA polymerases I / II / and III subunit ABC2 / ABC23 / DNA-directed RNA polymerases I / and III 23 kDa polypeptide


Mass: 17800.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P20435
#8: Protein 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 ...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 method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P20436
#10: Protein 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 ...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 method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P22139
#12: Protein 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 method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P40422

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Protein , 2 types, 2 molecules MO

#13: Protein Transcription initiation factor IIB / General transcription factor TFIIB / Transcription factor E


Mass: 38257.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: SUA7, YPR086W, P9513.4 / Production host: Escherichia coli (E. coli) / References: UniProt: P29055
#15: Protein TATA-box-binding protein / TATA sequence-binding protein / TBP / TATA-binding factor / TATA-box factor / Transcription factor ...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 method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: SPT15, BTF1, TBP1, YER148W / Production host: Escherichia coli (E. coli) / References: UniProt: P13393

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DNA chain , 2 types, 2 molecules NT

#14: DNA chain GAT1 Promoter


Mass: 17153.965 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
#18: DNA chain GAT1 promoter DNA


Mass: 17363.100 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

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

#16: Protein 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 method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: TFG1, SSU71, YGR186W, G7526 / Production host: Escherichia coli (E. coli) / References: UniProt: P41895
#17: Protein 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 method: isolated from a genetically manipulated source
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

#19: Protein 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 method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: TOA1, YOR194C / Production host: Escherichia coli (E. coli) / References: UniProt: P32773
#20: Protein Transcription initiation factor IIA subunit 2 / General transcription factor IIA subunit 2 / TFIIA 13.5 kDa subunit / Transcription initiation ...General transcription factor IIA subunit 2 / TFIIA 13.5 kDa subunit / Transcription initiation factor IIA small chain / Transcription initiation factor IIA small subunit


Mass: 14431.131 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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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Non-polymers , 2 types, 10 molecules

#21: Chemical
ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#22: Chemical ChemComp-MG / MAGNESIUM ION / Magnesium


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component

Type: COMPLEX

IDNameEntity IDParent-IDSource
1Yeast pre-initiation complexPreinitiation complex1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 200MULTIPLE SOURCES
2RNA polymerase1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 121NATURAL
3TFs13,15,16,17,19,201RECOMBINANT
4Nucleic acidsNucleic acid14,181RECOMBINANT
Source (natural)

Ncbi tax-ID: 559292 / Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

IDEntity assembly-ID
12
23
34
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
13Escherichia coli (E. coli)562
24synthetic construct (others)32630
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
MicroscopyModel: 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: 37 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 5.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 39000 / Symmetry type: POINT

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