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- PDB-5fz5: Transcription initiation complex structures elucidate DNA opening (CC) -

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Basic information

Entry
Database: PDB / ID: 5fz5
TitleTranscription initiation complex structures elucidate DNA opening (CC)
Components
  • (DNA-DIRECTED RNA POLYMERASE II SUBUNIT ...Polymerase) x 7
  • (DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC ...RNA polymerase) x 5
  • (SYNTHETIC CLOSED PROMOTER DNA ...) x 2
  • (TRANSCRIPTION INITIATION FACTOR IIA ...) x 2
  • (TRANSCRIPTION INITIATION FACTOR IIE SUBUNIT ...) x 2
  • (TRANSCRIPTION INITIATION FACTOR IIF SUBUNIT ...) x 2
  • TATA-BOX-BINDING PROTEIN
  • TRANSCRIPTION INITIATION FACTOR IIB
KeywordsTRANSCRIPTION / GENE EXPRESSION / TRANSCRIPTION INITIATION
Function / homology
Function and homology information


promoter clearance from RNA polymerase II promoter / transcription factor TFIIE complex / go:0001186: / TFIIA-class transcription factor complex binding / dephosphorylation of RNA polymerase II C-terminal domain / transcriptional open complex formation at RNA polymerase II promoter / transcription factor TFIIF complex / TFIIH-class transcription factor complex binding / transcriptional start site selection at RNA polymerase II promoter / RNA polymerase II complex recruiting activity ...promoter clearance from RNA polymerase II promoter / transcription factor TFIIE complex / go:0001186: / TFIIA-class transcription factor complex binding / dephosphorylation of RNA polymerase II C-terminal domain / transcriptional open complex formation at RNA polymerase II promoter / transcription factor TFIIF complex / TFIIH-class transcription factor complex binding / 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 / RNA polymerase III regulatory region DNA binding / regulation of protein serine/threonine phosphatase activity / 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 / transcription factor TFIID complex / DNA binding, bending / 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
TFA2 Winged helix domain 2 / Transcription factor TFIIB, conserved site / DNA-directed RNA polymerase, subunit 2 / Transcription initiation factor IIA, gamma subunit, C-terminal / Transcription initiation factor IIA, gamma subunit, N-terminal / Transcription initiation factor TFIIE, beta subunit / Transcription factor TFE/TFIIEalpha HTH domain / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerase, subunit H/Rpb5, conserved site / Archaeal RpoH /eukaryotic RPB5 RNA polymerase subunit ...TFA2 Winged helix domain 2 / Transcription factor TFIIB, conserved site / DNA-directed RNA polymerase, subunit 2 / Transcription initiation factor IIA, gamma subunit, C-terminal / Transcription initiation factor IIA, gamma subunit, N-terminal / Transcription initiation factor TFIIE, beta subunit / Transcription factor TFE/TFIIEalpha HTH domain / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerase, subunit H/Rpb5, conserved site / Archaeal RpoH /eukaryotic RPB5 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases, subunit N, zinc binding site / RNA-binding domain, S1 / RNA polymerase subunit RPB10 / DNA-directed RNA polymerase RPB5 subunit, eukaryote/virus / TFIIEalpha/SarR/Rpc3 HTH domain / 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 / Winged helix-like DNA-binding domain superfamily / Winged helix DNA-binding domain superfamily / RNA polymerase, RBP11-like subunit / RNA polymerase Rpb2, OB-fold / Cyclin-like / RNA polymerase Rpb5, N-terminal domain superfamily / Transcription initiation factor IIF, alpha subunit / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 5 / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase, RBP11-like dimerisation domain / Transcription factor TFIIB, cyclin-like 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 / RNA polymerase subunit, RPB6/omega / TBP domain superfamily / Nucleic acid-binding, OB-fold / Zinc finger, RING/FYVE/PHD-type / Zinc finger, TFIIB-type / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb3/Rpb11 dimerisation 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 / RNA polymerase Rpb8 / Transcription factor S-II (TFIIS) / RNA polymerases M/15 Kd subunit / RNA polymerases N / 8 kDa subunit / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase Rpb2, domain 5 / 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 factor IIA, alpha/beta subunit / Transcription initiation factor IIA, gamma subunit, helical domain / Transcription initiation factor IIA, gamma subunit / TFIIE alpha subunit / TFIIE beta subunit core domain / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb2, domain 4 / Cyclin-like superfamily / TFIIF, beta subunit, N-terminal / 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 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / Transcription factor E / TFIIF beta subunit, HTH domain / TFA2, Winged helix domain 2 / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb2, domain 3
DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB9 / Transcription initiation factor IIE subunit alpha / Transcription initiation factor IIB / Transcription initiation factor IIA large subunit / Transcription initiation factor IIA subunit 2 / DNA-directed RNA polymerase II subunit RPB7 / DNA-directed RNA polymerase II subunit RPB1 / Transcription initiation factor IIE subunit beta / DNA-directed RNA polymerase II subunit RPB11 ...DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB9 / Transcription initiation factor IIE subunit alpha / Transcription initiation factor IIB / Transcription initiation factor IIA large subunit / Transcription initiation factor IIA subunit 2 / DNA-directed RNA polymerase II subunit RPB7 / DNA-directed RNA polymerase II subunit RPB1 / Transcription initiation factor IIE subunit beta / 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 polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerase II subunit RPB3 / TATA-box-binding protein / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC2
Biological speciesSACCHAROMYCES CEREVISIAE (baker's yeast)
SYNTHETIC (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.8 Å
AuthorsPlaschka, C. / Hantsche, M. / Dienemann, C. / Burzinski, C. / Plitzko, J. / Cramer, P.
CitationJournal: Nature / Year: 2016
Title: Transcription initiation complex structures elucidate DNA opening.
Authors: C Plaschka / M Hantsche / C Dienemann / C Burzinski / J Plitzko / P Cramer /
Abstract: Transcription of eukaryotic protein-coding genes begins with assembly of the RNA polymerase (Pol) II initiation complex and promoter DNA opening. Here we report cryo-electron microscopy (cryo-EM) ...Transcription of eukaryotic protein-coding genes begins with assembly of the RNA polymerase (Pol) II initiation complex and promoter DNA opening. Here we report cryo-electron microscopy (cryo-EM) structures of yeast initiation complexes containing closed and open DNA at resolutions of 8.8 Å and 3.6 Å, respectively. DNA is positioned and retained over the Pol II cleft by a network of interactions between the TATA-box-binding protein TBP and transcription factors TFIIA, TFIIB, TFIIE, and TFIIF. DNA opening occurs around the tip of the Pol II clamp and the TFIIE 'extended winged helix' domain, and can occur in the absence of TFIIH. Loading of the DNA template strand into the active centre may be facilitated by movements of obstructing protein elements triggered by allosteric binding of the TFIIE 'E-ribbon' domain. The results suggest a unified model for transcription initiation with a key event, the trapping of open promoter DNA by extended protein-protein and protein-DNA contacts.
Validation Report
SummaryFull reportAbout validation report
History
DepositionMar 10, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Database references
Revision 1.2Jun 1, 2016Group: Database references
Revision 1.3Apr 19, 2017Group: Other
Revision 1.4Oct 3, 2018Group: Advisory / Data collection / Derived calculations
Category: em_software / ndb_struct_conf_na ...em_software / ndb_struct_conf_na / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _em_software.image_processing_id / _em_software.name
Revision 1.5Jan 23, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_seq_map_depositor_info / pdbx_unobs_or_zero_occ_atoms ...pdbx_seq_map_depositor_info / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _pdbx_seq_map_depositor_info.one_letter_code_mod
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AM" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AM" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "GB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "QC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "UA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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 RPABC 1
F: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2
G: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7
H: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3
I: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9
J: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5
K: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11
L: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4
M: TRANSCRIPTION INITIATION FACTOR IIB
N: SYNTHETIC CLOSED PROMOTER DNA CONSTRUCT
O: TATA-BOX-BINDING PROTEIN
Q: TRANSCRIPTION INITIATION FACTOR IIF SUBUNIT ALPHA
R: TRANSCRIPTION INITIATION FACTOR IIF SUBUNIT BETA
T: SYNTHETIC CLOSED PROMOTER DNA CONSTRUCT
U: TRANSCRIPTION INITIATION FACTOR IIA LARGE SUBUNIT
V: TRANSCRIPTION INITIATION FACTOR IIA SUBUNIT 2
W: TRANSCRIPTION INITIATION FACTOR IIE SUBUNIT ALPHA
X: TRANSCRIPTION INITIATION FACTOR IIE SUBUNIT BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)890,12733
Polymers889,44922
Non-polymers67811
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 1 / RNA POLYMERASE II SUBUNIT B1 / DNA-DIRECTED RNA POLYMERASE III ...RNA POLYMERASE II SUBUNIT 1 / 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 (baker's yeast) / Strain: BJ5464 RPB3 HIS-BIO / 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 (baker's yeast) / Strain: BJ5464 RPB3 HIS-BIO / References: UniProt: P08518, DNA-directed RNA polymerase
#3: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 / Polymerase / RNA POLYMERASE II SUBUNIT 3 / RNA POLYMERASE II SUBUNIT B3 / B44.5 / DNA-DIRECTED RNA POLYMERASE II ...RNA POLYMERASE II SUBUNIT 3 / 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 (baker's yeast) / Strain: BJ5464 RPB3 HIS-BIO / 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: 25451.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / Strain: BJ5464 RPB3 HIS-BIO / 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 (baker's yeast) / Strain: BJ5464 RPB3 HIS-BIO / 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 (baker's yeast) / Strain: BJ5464 RPB3 HIS-BIO / 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 (baker's yeast) / Strain: BJ5464 RPB3 HIS-BIO / References: UniProt: P38902

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DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC ... , 5 types, 5 molecules EFHJL

#5: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1 / RNA polymerase / RNA POLYMERASES I / II / AND III SUBUNIT ABC1 / ABC27 / DNA-DIR ECTED RNA POLYMERASES I / II / AND ...RNA POLYMERASES I / II / AND III SUBUNIT ABC1 / ABC27 / DNA-DIR ECTED RNA POLYMERASES I / II / AND III 27 KDA POLYPEPTIDE / DNA-DIRECTED RNA POLYMERASES I / II / AND III SUBUNIT RPABC 1


Mass: 25117.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / Strain: BJ5464 RPB3 HIS-BIO / References: UniProt: P20434
#6: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2 / RNA polymerase / RNA POLYMERASES I / II / AND III SUBUNIT ABC2 / ABC23 / DNA-DIRECTED RNA POLYMERASES I / II / AND ...RNA POLYMERASES I / II / AND III SUBUNIT ABC2 / ABC23 / DNA-DIRECTED RNA POLYMERASES I / II / AND III 23 KDA POLYPEPTIDE / DNA-DIRECTED RNA POLYMERASES I / II / AND III SUBUNIT RPABC 2


Mass: 17931.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / Strain: BJ5464 RPB3 HIS-BIO / References: UniProt: P20435
#8: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3 / 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 / II / AND III 14.5 KDA POLYPEPTIDE / DNA-DIRECTED RNA POLYMERASES I / II / AND III SUBUNIT RPABC 3


Mass: 16525.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / Strain: BJ5464 RPB3 HIS-BIO / References: UniProt: P20436
#10: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5 / RNA polymerase / RNA POLYMERASES I / II / AND III SUBUNIT ABC5 / ABC10-BETA / AB C8 / DNA-DIRECTED RNA POLYMERASES I ...RNA POLYMERASES I / II / AND III SUBUNIT ABC5 / ABC10-BETA / AB C8 / DNA-DIRECTED RNA POLYMERASES I / II / AND III 8.3 KDA POLYPEPTID E / DNA-DIRECTED RNA POLYMERASES I / II / AND III SUBUNIT RPABC 5


Mass: 8290.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / Strain: BJ5464 RPB3 HIS-BIO / References: UniProt: P22139
#12: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4 / RNA polymerase / RNA POLYMERASES I / II / AND III SUBUNIT ABC4 / ABC10-ALPHA / D NA-DIRECTED RNA POLYMERASES I / II ...RNA POLYMERASES I / II / AND III SUBUNIT ABC4 / ABC10-ALPHA / D NA-DIRECTED RNA POLYMERASES I / II / AND III SUBUNIT RPABC 4


Mass: 7729.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / Strain: BJ5464 RPB3 HIS-BIO / 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 / TRANSCRIPTION FACTOR IIB


Mass: 38257.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (baker's yeast)
Plasmid: POPINE / 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 (baker's yeast)
Plasmid: PET21B / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P13393

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SYNTHETIC CLOSED PROMOTER DNA ... , 2 types, 2 molecules NT

#14: DNA chain SYNTHETIC CLOSED PROMOTER DNA CONSTRUCT


Mass: 17254.084 Da / Num. of mol.: 1 / Details: NON-TEMPLATE STRAND / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast)
#18: DNA chain SYNTHETIC CLOSED PROMOTER DNA CONSTRUCT


Mass: 26172.779 Da / Num. of mol.: 1 / Details: TEMPLATE STRAND / Source method: obtained synthetically / Source: (synth.) SYNTHETIC (others)

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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 10 5 KDA SUBUNIT / P105


Mass: 82320.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (baker's yeast)
Plasmid: PET21 / 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 (baker's yeast)
Plasmid: PETDUET-1 / 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 / TFIIA LARGE SUBUNIT / TFIIA 32 KDA SUBUNIT


Mass: 32230.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (baker's yeast)
Strain: BJ5464 RPB3 HIS-BIO / 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 / TRANSCRI PTION INITIATION FACTOR IIA SMALL SUBUNIT


Mass: 13473.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (baker's yeast)
Plasmid: POPINE / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P32774

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TRANSCRIPTION INITIATION FACTOR IIE SUBUNIT ... , 2 types, 2 molecules WX

#21: Protein TRANSCRIPTION INITIATION FACTOR IIE SUBUNIT ALPHA / TFIIE-ALPHA / FACTOR A 66 KDA SUBUNIT / TRANSCRIPTION FACTOR A LARGE SUBUNIT


Mass: 54804.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (baker's yeast)
Plasmid: POPINE / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P36100
#22: Protein 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 method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (baker's yeast)
Plasmid: PET21 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P36145

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Non-polymers , 2 types, 11 molecules

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


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#24: 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

ComponentName: YEAST POL II TRANSCRIPTION INITIATION COMPLEX (CLOSED DNA)
Type: COMPLEX
Buffer solutionName: 25 MM HEPES-KOH PH 7.5, 150 MM POTASSIUM ACETATE, 2 MM MGCL2, 5 MM DTT
pH: 7.5
Details: 25 MM HEPES-KOH PH 7.5, 150 MM POTASSIUM ACETATE, 2 MM MGCL2, 5 MM DTT
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Details: LIQUID ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Jun 20, 2016
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 37000 X / Calibrated magnification: 37037 X / Nominal defocus max: 5000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansNum. digital images: 959

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Processing

EM softwareName: RELION / Category: 3D reconstruction
CTF correctionDetails: EACH PARTICLE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: RELION 1.3 / Resolution: 8.8 Å / Num. of particles: 5690
Details: THE MODEL FOR THE CLOSED COMPLEX WAS DERIVED FROM THE OPEN COMPLEX MODEL (5FYW). THREE RIGID-BODY GROUPS (1. POL II, TFIIA, TFIIB, TBP, TFIIE E-RIBBON AND TFIIF DIMERIZATION DOMAIN, 2. TFIIE ...Details: THE MODEL FOR THE CLOSED COMPLEX WAS DERIVED FROM THE OPEN COMPLEX MODEL (5FYW). THREE RIGID-BODY GROUPS (1. POL II, TFIIA, TFIIB, TBP, TFIIE E-RIBBON AND TFIIF DIMERIZATION DOMAIN, 2. TFIIE DOMAINS TFA1 AND TFA2 WH, 3.TFIIE TFA2 WH1 AND TFIIF TFG2 WH) WERE INDIVIDUALLY FITTED INTO THE CLOSED COMPLEX EM DENSITY BY AN AUTOMATED CORRELATION SEARCH IN SITUS. TO MODEL CLOSED PROMOTER DNA, UPSTREAM DNA WAS EXTENDED WITH CANONICAL DUPLEX B-FORM DNA IN COOT AND RIGID-BODY FITTED IN UCSF CHIMERA TO REFLECT THE DENSITY. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3383. (DEPOSITION ID: 14367).
Symmetry type: POINT
RefinementHighest resolution: 8.8 Å
Refinement stepCycle: LAST / Highest resolution: 8.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39865 2268 11 0 42144

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