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- PDB-5fyw: Transcription initiation complex structures elucidate DNA opening (OC) -

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Basic information

Entry
Database: PDB / ID: 5fyw
TitleTranscription initiation complex structures elucidate DNA opening (OC)
Components
  • (DNA-DIRECTED RNA POLYMERASE II SUBUNIT ...) x 7
  • (DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC ...) x 5
  • (NONTEMPLATE 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


RNA polymerase II complex recruiting activity / transcription open complex formation at RNA polymerase II promoter / TFIIA-class transcription factor complex binding / RNA polymerase III transcription regulatory region sequence-specific DNA binding / RNA polymerase III preinitiation complex assembly / transcription factor TFIIIB complex / RNA polymerase I general transcription initiation factor binding / transcription factor TFIIE complex / regulation of transcription by RNA polymerase III / TFIIF-class transcription factor complex binding ...RNA polymerase II complex recruiting activity / transcription open complex formation at RNA polymerase II promoter / TFIIA-class transcription factor complex binding / RNA polymerase III transcription regulatory region sequence-specific DNA binding / RNA polymerase III preinitiation complex assembly / transcription factor TFIIIB complex / RNA polymerase I general transcription initiation factor binding / transcription factor TFIIE complex / regulation of transcription by RNA polymerase III / TFIIF-class transcription factor complex binding / transcriptional start site selection at RNA polymerase II promoter / transcription factor TFIIF complex / RPB4-RPB7 complex / transcription factor TFIIA complex / RNA polymerase I preinitiation complex assembly / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / transcription preinitiation complex / RNA Polymerase I Transcription Initiation / DNA binding, bending / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes / termination of RNA polymerase II transcription / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / RNA-templated transcription / Formation of TC-NER Pre-Incision Complex / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / RNA Polymerase I Promoter Escape / transcription initiation at RNA polymerase III promoter / termination of RNA polymerase I transcription / Gap-filling DNA repair synthesis and ligation in TC-NER / nucleolar large rRNA transcription by RNA polymerase I / transcription initiation at RNA polymerase I promoter / RNA polymerase II complex binding / Estrogen-dependent gene expression / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / nuclear-transcribed mRNA catabolic process / transcription by RNA polymerase III / positive regulation of translational initiation / Dual incision in TC-NER / protein phosphatase activator activity / positive regulation of transcription initiation by RNA polymerase II / translesion synthesis / RNA polymerase I complex / transcription elongation by RNA polymerase I / RNA polymerase III complex / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase II preinitiation complex assembly / tRNA transcription by RNA polymerase III / RNA polymerase II, core complex / transcription by RNA polymerase I / transcription-coupled nucleotide-excision repair / translation initiation factor binding / TBP-class protein binding / transcription coregulator activity / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / P-body / DNA-templated transcription initiation / positive regulation of transcription elongation by RNA polymerase II / ribonucleoside binding / mRNA processing / cytoplasmic stress granule / DNA-directed RNA polymerase / disordered domain specific binding / DNA-directed RNA polymerase activity / peroxisome / single-stranded DNA binding / ribosome biogenesis / transcription regulator complex / DNA-binding transcription factor binding / nucleic acid binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / protein dimerization activity / single-stranded RNA binding / nucleotide binding / negative regulation of DNA-templated transcription / mRNA binding / chromatin binding / regulation of DNA-templated transcription / nucleolus / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / metal ion binding
Similarity search - Function
: / Tfa2 E-tether / Transcription factor TFIIE beta subunit, DNA-binding domain / Transcription initiation factor TFIIE, beta subunit / TFA2, Winged helix domain 2 / TFIIE beta subunit core domain / TFA2 Winged helix domain 2 / TFIIE beta central core DNA-binding domain profile. / Transcription initiation factor IIE subunit alpha, N-terminal / Transcription factor TFE/TFIIEalpha HTH domain ...: / Tfa2 E-tether / Transcription factor TFIIE beta subunit, DNA-binding domain / Transcription initiation factor TFIIE, beta subunit / TFA2, Winged helix domain 2 / TFIIE beta subunit core domain / TFA2 Winged helix domain 2 / TFIIE beta central core DNA-binding domain profile. / Transcription initiation factor IIE subunit alpha, N-terminal / Transcription factor TFE/TFIIEalpha HTH domain / TFIIEalpha/SarR/Rpc3 HTH domain / Transcription factor E / TFIIE alpha subunit / TFE/IIEalpha-type HTH domain profile. / Transcription initiation factor IIE / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription initiation factor IIA, gamma subunit / Transcription factor IIA, alpha-helical domain / Transcription initiation factor IIA, gamma subunit, C-terminal / Transcription initiation factor IIA, gamma subunit, N-terminal / Transcription initiation factor IIA, gamma subunit, helical domain / Transcription initiation factor IIA, gamma subunit / Transcription factor IIA, beta-barrel / Transcription initiation factor IIF, beta subunit / TFIIF beta subunit, HTH domain / TFIIF, beta subunit, N-terminal / TFIIF, beta subunit HTH domain / TFIIF, beta subunit N-terminus / Transcription initiation factor IIF, alpha subunit / Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) / Transcription Factor IIF, Rap30/Rap74, interaction / Transcription factor TFIIB, cyclin-like domain / Transcription factor TFIIB, conserved site / Transcription factor TFIIB repeat / Transcription factor TFIIB repeat signature. / Zinc finger TFIIB-type profile. / Transcription factor TFIIB / Zinc finger, TFIIB-type / TFIIB zinc-binding / TATA-box binding protein, eukaryotic / TATA-box binding protein / TATA-box binding protein, conserved site / Transcription factor TFIID (or TATA-binding protein, TBP) / Transcription factor TFIID repeat signature. / TBP domain superfamily / DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb4/RPC9, core / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / DNA-directed RNA-polymerase II subunit / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / Rpb4/RPC9 superfamily / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Cyclin-like superfamily / Zinc finger TFIIS-type signature. / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase subunit Rpb7-like / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / HRDC-like superfamily / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S / : / RNA polymerase, Rpb8 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb8 / RNA polymerase subunit 8 / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase, subunit RPB6 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature.
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / TATA-box-binding protein / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 ...DNA / DNA (> 10) / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / TATA-box-binding protein / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB9 / Transcription initiation factor IIB / Transcription initiation factor IIA large subunit / Transcription initiation factor IIA subunit 2 / DNA-directed RNA polymerase II subunit RPB7 / Transcription initiation factor IIE subunit alpha / 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
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
SYNTHETIC CONSTRUCT (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.35 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.
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 2.0Oct 3, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / em_software ...atom_site / 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: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _em_software.image_processing_id / _em_software.name / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id
Revision 2.1May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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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Structure visualization

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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: NONTEMPLATE DNA
O: TATA-BOX-BINDING PROTEIN
Q: TRANSCRIPTION INITIATION FACTOR IIF SUBUNIT ALPHA
R: TRANSCRIPTION INITIATION FACTOR IIF SUBUNIT BETA
T: NONTEMPLATE DNA
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)891,26833
Polymers890,59022
Non-polymers67811
Water00
1


  • Idetical with deposited unit
  • defined by author
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 / 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 / RPB1


Mass: 191821.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: BJ5464 RPB3 HIS-BIO / References: UniProt: P04050, DNA-directed RNA polymerase
#2: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 / RNA POLYMERASE II SUBUNIT 2 / B150 / DNA-DIRECTED RNA POLYMERASE II 140 KDA POLYPEPTIDE / RPB2


Mass: 138937.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: BJ5464 RPB3 HIS-BIO / References: UniProt: P08518, DNA-directed RNA polymerase
#3: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 / 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 / RPB3


Mass: 35330.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: BJ5464 RPB3 HIS-BIO / References: UniProt: P16370
#4: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 / RNA POLYMERASE II SUBUNIT B4 / B32 / DNA-DIRECTED RNA POLYMERASE II 32 KDA POLYPEPTIDE / RPB4


Mass: 25451.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: BJ5464 RPB3 HIS-BIO / References: UniProt: P20433
#7: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 / RNA POLYMERASE II SUBUNIT B7 / B16 / RPB7


Mass: 19081.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: BJ5464 RPB3 HIS-BIO / References: UniProt: P34087
#9: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 / 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 / RPB9


Mass: 14308.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: BJ5464 RPB3 HIS-BIO / References: UniProt: P27999
#11: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 / RNA POLYMERASE II SUBUNIT B11 / B13.6 / DNA-DIRECTED RNA POLYMERASE II 13.6 KDA POLYPEPTIDE / RPB11


Mass: 13633.493 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer'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 POLYMERASES I / II / AND III SUBUNIT ABC1 / ABC27 / DNA-DIRECTED RNA POLYMERASES I / II / AND ...RNA POLYMERASES I / II / AND III SUBUNIT ABC1 / ABC27 / DNA-DIRECTED RNA POLYMERASES I / II / AND III 27 KDA POLYPEPTIDE / RPB5


Mass: 25117.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: BJ5464 RPB3 HIS-BIO / References: UniProt: P20434
#6: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2 / 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 / RPB6


Mass: 17931.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: BJ5464 RPB3 HIS-BIO / References: UniProt: P20435
#8: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3 / 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 / RPB8


Mass: 16525.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: BJ5464 RPB3 HIS-BIO / References: UniProt: P20436
#10: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5 / 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 POLYPEPTIDE / RPB10


Mass: 8290.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain: BJ5464 RPB3 HIS-BIO / References: UniProt: P22139
#12: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4 / RNA POLYMERASES I / II / AND III SUBUNIT ABC4 / ABC10-ALPHA / R PB12


Mass: 7729.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer'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 / TFIIB


Mass: 38257.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: P29055
#15: Protein TATA-BOX-BINDING PROTEIN / TATA SEQUENCE-BINDING PROTEIN / TBP / TATA-BINDING FACTOR / TA TA-BOX FACTOR / TRANSCRIPTION FACTOR ...TATA SEQUENCE-BINDING PROTEIN / TBP / TATA-BINDING FACTOR / TA TA-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 (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: P13393

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DNA chain , 2 types, 2 molecules NT

#14: DNA chain NONTEMPLATE DNA


Mass: 22424.338 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#18: DNA chain NONTEMPLATE DNA


Mass: 22143.199 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (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 / TFG1


Mass: 82320.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / 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 / TFG2


Mass: 46684.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / 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 / TOA1


Mass: 32230.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / 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 / TOA2


Mass: 13473.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / 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 / TFA1


Mass: 54804.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: P36100
#22: Protein TRANSCRIPTION INITIATION FACTOR IIE SUBUNIT BETA / TFIIE-BETA / FACTOR A 43 KDA SUBUNIT / TRANSCRIPTION FACTOR A SMALL SUBUNIT / TFA2


Mass: 37050.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: P36145

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Non-polymers , 2 types, 11 molecules

#23: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#24: Chemical ChemComp-MG / MAGNESIUM ION


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 (OPEN 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: CRYOGEN - ETHANE. INSTRUMENT - FEI VITROBOT MARK IV. QUANTIFOIL R 3.5- 1 HOLEY CARBON GRIDS WERE GLOW-DISCHARGED BEFORE DEPOSITION OF 4.5 MICROLITERS OF SAMPLE. GRIDS WERE THEN BLOTTED FOR 8. ...Details: CRYOGEN - ETHANE. INSTRUMENT - FEI VITROBOT MARK IV. QUANTIFOIL R 3.5- 1 HOLEY CARBON GRIDS WERE GLOW-DISCHARGED BEFORE DEPOSITION OF 4.5 MICROLITERS OF SAMPLE. GRIDS WERE THEN BLOTTED FOR 8.5 S AND PLUNGE- FROZEN IN LIQUID ETHANE.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Apr 26, 2016
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 37000 X / Calibrated magnification: 37037 X / Nominal defocus max: 4200 nm / Nominal defocus min: 700 nm / Cs: 2.3 mm
Image recordingElectron dose: 33 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansNum. digital images: 1756

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Processing

EM softwareName: RELION / Version: 1.3 / Category: 3D reconstruction
CTF correctionDetails: EACH PARTICLE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.35 Å / Num. of particles: 11231 / Actual pixel size: 1.35 Å
Details: RESIDUES INDICATED AS POLY-ALANINE ARE OF UNCERTAIN AMINO ACID REGISTER. THE FOLLOWING REGIONS WERE MODELED INTO THE INDICATED UNSHARPENED MAP DUE TO WEAKER DENSITY. RPB2 RESIDUES 919-932 ...Details: RESIDUES INDICATED AS POLY-ALANINE ARE OF UNCERTAIN AMINO ACID REGISTER. THE FOLLOWING REGIONS WERE MODELED INTO THE INDICATED UNSHARPENED MAP DUE TO WEAKER DENSITY. RPB2 RESIDUES 919-932 (OC1, EMD-3375). TFIIF SUBUNIT TFG1 RESIDUES 327-330 (POLY-ALANINE) AND 404-415 (POLY-ALANINE) (OC4, EMD-3380). TFIIF SUBUNIT TFG2 RESIDUES 233-244 (POLY- ALANINE) (OC4, EMD-3380). TFIIE SUBUNITS TFA1 (POLY- ALANINE) AND TFA2 (POLY-ALANINE) AND TFIIF SUBUNIT TFG2 WINGED HELIX DOMAIN RESIDUES 294-352 (POLY-ALANINE) (OC3, EMD-3378 AND OC3-FOCUSED, EMD-3379). TFIIF SUBUNIT TFG2 WINGED HELIX DOMAIN RESIDUES 359-370 (UNK) WERE PUTATIVELY ASSIGNED TO TFG2 (OC3-FOCUSED, EMD-3379). TFIIE SUBUNIT TFA2 RESIDUES 256-280 SHOW UNCERTAIN CONNECTIVITY. THE SEQUENCE OF THE TFIIF TFG2 LINKER (RESIDUES 249-280) WAS ASSIGNED BASED ON THE STRONG SIDECHAIN DENSITY OF RESIDUES I252, L255, F277, L278 AND THEIR FIT TO THE LOCAL CHEMICAL ENVIRONMENT. TFIIF SUBUNIT TFG1 RESIDUES 21-35 WERE MODELED BASED ON A SEPARATE X-RAY ANALYSIS (PDB 5IP7) AND FITTED (OC4 ROUND 2 CLASS 2). SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3378. (DEPOSITION ID: 14360).
Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Details: REFINEMENT PROTOCOL--CRYO-EM
RefinementHighest resolution: 4.35 Å
Refinement stepCycle: LAST / Highest resolution: 4.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39871 1828 11 0 41710

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