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- PDB-6eu0: RNA Polymerase III open pre-initiation complex (OC-PIC) -

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Entry
Database: PDB / ID: 6eu0
TitleRNA Polymerase III open pre-initiation complex (OC-PIC)
Components
  • (DNA-directed RNA polymerase III subunit ...) x 10
  • (DNA-directed RNA polymerases I and III subunit ...) x 2
  • (DNA-directed RNA polymerases I, II, and III subunit ...) x 5
  • (Transcription factor ...) x 2
  • Non-Template
  • TATA-box-binding protein
  • Template
KeywordsTRANSCRIPTION / RNA Pol III / promoter opening
Function / homology
Function and homology information


RNA polymerase III core binding / TFIIA-class transcription factor complex binding / DNA-templated transcription open complex formation / RNA polymerase III transcription regulatory region sequence-specific DNA binding / RNA polymerase III preinitiation complex assembly / transcription factor TFIIIB complex / TFIIIC-class transcription factor complex binding / RNA polymerase I general transcription initiation factor binding / RNA polymerase III type 3 promoter sequence-specific DNA binding / regulation of transcription by RNA polymerase III ...RNA polymerase III core binding / TFIIA-class transcription factor complex binding / DNA-templated transcription open complex formation / RNA polymerase III transcription regulatory region sequence-specific DNA binding / RNA polymerase III preinitiation complex assembly / transcription factor TFIIIB complex / TFIIIC-class transcription factor complex binding / RNA polymerase I general transcription initiation factor binding / RNA polymerase III type 3 promoter sequence-specific DNA binding / regulation of transcription by RNA polymerase III / RNA polymerase III general transcription initiation factor activity / transcription factor TFIIA complex / RNA polymerase I preinitiation complex assembly / DNA binding, bending / RNA Polymerase I Transcription Initiation / transcription preinitiation complex / 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 / 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 / termination of RNA polymerase III transcription / transcription factor TFIID complex / RNA Polymerase II Pre-transcription Events / RNA-templated transcription / Formation of TC-NER Pre-Incision Complex / transcription initiation at RNA polymerase III promoter / RNA Polymerase I Promoter Escape / termination of RNA polymerase I transcription / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / Estrogen-dependent gene expression / transcription by RNA polymerase III / Dual incision in TC-NER / 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, core complex / tRNA transcription by RNA polymerase III / RNA polymerase II preinitiation complex assembly / transcription by RNA polymerase I / nucleotidyltransferase activity / TBP-class protein binding / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed RNA polymerase / disordered domain specific binding / DNA-directed RNA polymerase activity / peroxisome / ribosome biogenesis / single-stranded DNA binding / 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 / nucleotide binding / negative regulation of DNA-templated transcription / 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 / nucleus / cytoplasm / cytosol
Similarity search - Function
Transcription factor TFIIIB component B'', fungi / Brf1, TBP-binding domain / Brf1-like TBP-binding domain / Transcription factor TFIIIB component B'', Myb domain / Myb DNA-binding like / TATA-Binding Protein / RNA polymerase Rpb7-like, N-terminal domain / DNA-directed RNA polymerase III subunit RPC4 / RNA polymerase III RPC4 / DNA-directed RNA polymerase III, subunit Rpc31 ...Transcription factor TFIIIB component B'', fungi / Brf1, TBP-binding domain / Brf1-like TBP-binding domain / Transcription factor TFIIIB component B'', Myb domain / Myb DNA-binding like / TATA-Binding Protein / RNA polymerase Rpb7-like, N-terminal domain / DNA-directed RNA polymerase III subunit RPC4 / RNA polymerase III RPC4 / DNA-directed RNA polymerase III, subunit Rpc31 / DNA-directed RNA polymerase III subunit Rpc31 / Pol III subunit C11, C-terminal zinc ribbon / DNA-directed RNA polymerase III subunit Rpc5 / : / DNA-directed RNA polymerase III subunit RPC1, N-terminal / DNA-directed RNA polymerase III subunit RPC1, C-terminal / RPC5 protein / RNA polymerase III, subunit Rpc25 / DNA-directed RNA polymerase III subunit RPC9 / RNA polymerase III subunit Rpc25 / RNA polymerase Rpc34 / RNA polymerase III Rpc82, C -terminal / RNA polymerase Rpc34-like / DNA-directed RNA polymerase III subunit RPC3 / : / RNA polymerase Rpc34 subunit / RNA polymerase III subunit RPC82 / DNA-directed RNA polymerase III subunit RPC3, helical hairpin domain / POLR3C, C-terminal winged-helix domain / RNA polymerase III subunit RPC82-related, helix-turn-helix / RNA polymerase III subunit RPC82 helix-turn-helix domain / DNA-directed RNA polymerase, subunit E/RPC8 / Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1 / RNA polymerase, Rpb5, N-terminal domain / RNA polymerase ii, chain L / RPB5-like RNA polymerase subunit / DNA-directed RNA polymerases I and III subunit AC19 / DNA-directed RNA polymerases I and III subunit AC40 / 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-Binding Protein / 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. / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / RNA polymerase Rpb1, domain 3 / RNA polymerase, RBP11-like subunit / Enzyme I; Chain A, domain 2 / Rubrerythrin, domain 2 / Myb-like DNA-binding domain / TBP domain superfamily / DNA-directed RNA polymerase, insert domain / RNA Polymerase Alpha Subunit; Chain A, domain 2 / Gyrase A; domain 2 / Rpb4/RPC9 superfamily / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / Homeodomain-like / Cyclin-like superfamily / SANT/Myb domain / HRDC-like superfamily / 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 / 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
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA-directed RNA polymerase III subunit RPC1 / DNA-directed RNA polymerases I and III subunit RPAC1 / TATA-box-binding protein / DNA-directed RNA polymerase III subunit RPC7 / 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 / DNA (> 10) / DNA-directed RNA polymerase III subunit RPC1 / DNA-directed RNA polymerases I and III subunit RPAC1 / TATA-box-binding protein / DNA-directed RNA polymerase III subunit RPC7 / 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 III subunit RPC2 / DNA-directed RNA polymerase III subunit RPC4 / DNA-directed RNA polymerases I and III subunit RPAC2 / Transcription factor IIIB 70 kDa subunit / DNA-directed RNA polymerase III subunit RPC3 / DNA-directed RNA polymerase III subunit RPC6 / DNA-directed RNA polymerase III subunit RPC8 / DNA-directed RNA polymerase III subunit RPC5 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / Transcription factor TFIIIB component B'' / DNA-directed RNA polymerase III subunit RPC9 / DNA-directed RNA polymerase III subunit RPC10
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Saccharomyces cerevisiae S288c (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsAbascal-Palacios, G. / Ramsay, E.P. / Beuron, F. / Morris, E. / Vannini, A.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/K014390/1 United Kingdom
Cancer Research UK Programme FoundationCR-UK C47547/A21536 United Kingdom
Wellcome Trust200818/Z/16/Z United Kingdom
Marie Sklodowska-Curie Intra-European Fellowship655238 United Kingdom
CitationJournal: Nature / Year: 2018
Title: Structural basis of RNA polymerase III transcription initiation.
Authors: Guillermo Abascal-Palacios / Ewan Phillip Ramsay / Fabienne Beuron / Edward Morris / Alessandro Vannini /
Abstract: RNA polymerase (Pol) III transcribes essential non-coding RNAs, including the entire pool of transfer RNAs, the 5S ribosomal RNA and the U6 spliceosomal RNA, and is often deregulated in cancer cells. ...RNA polymerase (Pol) III transcribes essential non-coding RNAs, including the entire pool of transfer RNAs, the 5S ribosomal RNA and the U6 spliceosomal RNA, and is often deregulated in cancer cells. The initiation of gene transcription by Pol III requires the activity of the transcription factor TFIIIB to form a transcriptionally active Pol III preinitiation complex (PIC). Here we present electron microscopy reconstructions of Pol III PICs at 3.4-4.0 Å and a reconstruction of unbound apo-Pol III at 3.1 Å. TFIIIB fully encircles the DNA and restructures Pol III. In particular, binding of the TFIIIB subunit Bdp1 rearranges the Pol III-specific subunits C37 and C34, thereby promoting DNA opening. The unwound DNA directly contacts both sides of the Pol III cleft. Topologically, the Pol III PIC resembles the Pol II PIC, whereas the Pol I PIC is more divergent. The structures presented unravel the molecular mechanisms underlying the first steps of Pol III transcription and also the general conserved mechanisms of gene transcription initiation.
History
DepositionOct 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 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]
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: DNA-directed RNA polymerase III subunit RPC1
B: DNA-directed RNA polymerase III subunit RPC2
C: DNA-directed RNA polymerases I and III subunit RPAC1
D: DNA-directed RNA polymerase III subunit RPC9
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 III subunit RPC8
H: DNA-directed RNA polymerases I, II, and III subunit RPABC3
I: DNA-directed RNA polymerase III subunit RPC10
J: DNA-directed RNA polymerases I, II, and III subunit RPABC5
K: DNA-directed RNA polymerases I and III subunit RPAC2
L: DNA-directed RNA polymerases I, II, and III subunit RPABC4
M: DNA-directed RNA polymerase III subunit RPC5
N: DNA-directed RNA polymerase III subunit RPC4
O: DNA-directed RNA polymerase III subunit RPC3
P: DNA-directed RNA polymerase III subunit RPC6
Q: DNA-directed RNA polymerase III subunit RPC7
R: Non-Template
S: Template
V: Transcription factor TFIIIB component B''
Y: TATA-box-binding protein
Z: Transcription factor IIIB 70 kDa subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)899,60330
Polymers899,12122
Non-polymers4828
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area125010 Å2
ΔGint-630 kcal/mol
Surface area286180 Å2
MethodPISA

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Components

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DNA-directed RNA polymerase III subunit ... , 10 types, 10 molecules ABDGIMNOPQ

#1: Protein DNA-directed RNA polymerase III subunit RPC1 / RNA polymerase III subunit C1 / DNA-directed RNA polymerase III largest subunit / RNA polymerase ...RNA polymerase III subunit C1 / DNA-directed RNA polymerase III largest subunit / RNA polymerase III subunit C160


Mass: 162517.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P04051, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase III subunit RPC2 / RNA polymerase III subunit C2 / C128 / DNA-directed RNA polymerase III 130 kDa polypeptide


Mass: 129629.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P22276, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase III subunit RPC9 / RNA polymerase III subunit C9 / RNA polymerase III subunit C17


Mass: 18623.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P47076
#7: Protein DNA-directed RNA polymerase III subunit RPC8 / RNA polymerase III subunit C8 / DNA-directed RNA polymerase III 25 kDa polypeptide / RNA polymerase ...RNA polymerase III subunit C8 / DNA-directed RNA polymerase III 25 kDa polypeptide / RNA polymerase III subunit C25


Mass: 24349.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P35718
#9: Protein DNA-directed RNA polymerase III subunit RPC10 / RNA polymerase III subunit C10 / DNA-directed RNA polymerases III 12.5 kDa polypeptide / RNA ...RNA polymerase III subunit C10 / DNA-directed RNA polymerases III 12.5 kDa polypeptide / RNA polymerase III subunit C11


Mass: 12525.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q04307
#13: Protein DNA-directed RNA polymerase III subunit RPC5 / RNA polymerase III subunit C5 / DNA-directed RNA polymerase III 37 kDa polypeptide / RNA polymerase ...RNA polymerase III subunit C5 / DNA-directed RNA polymerase III 37 kDa polypeptide / RNA polymerase III subunit C37


Mass: 32178.115 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P36121
#14: Protein DNA-directed RNA polymerase III subunit RPC4 / RNA polymerase III subunit C4 / C53 / DNA-directed RNA polymerase III 47 kDa polypeptide


Mass: 46751.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P25441
#15: Protein DNA-directed RNA polymerase III subunit RPC3 / RNA polymerase III subunit C3 / C82 / DNA-directed III 74 kDa polypeptide / C74


Mass: 74112.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P32349
#16: Protein DNA-directed RNA polymerase III subunit RPC6 / RNA polymerase III subunit C6 / C34 / DNA-directed RNA polymerase III 36 kDa polypeptide


Mass: 36174.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P32910
#17: Protein DNA-directed RNA polymerase III subunit RPC7 / RNA polymerase III subunit C7 / DNA-directed RNA polymerase III 31 kDa polypeptide / C31


Mass: 27752.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P17890

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DNA-directed RNA polymerases I and III subunit ... , 2 types, 2 molecules CK

#3: Protein DNA-directed RNA polymerases I and III subunit RPAC1 / RNA polymerases I and III subunit AC1 / C37 / DNA-directed RNA polymerases I and III 40 kDa polypeptide / C40


Mass: 37732.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P07703
#11: Protein DNA-directed RNA polymerases I and III subunit RPAC2 / RNA polymerases I and III subunit AC2 / AC19 / DNA-directed RNA polymerases I and III 16 kDa ...RNA polymerases I and III subunit AC2 / AC19 / DNA-directed RNA polymerases I and III 16 kDa polypeptide / RPA19


Mass: 16167.860 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P28000

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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 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)
Strain: ATCC 204508 / S288c / References: UniProt: P20434
#6: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC2 / 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: 17931.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P20435
#8: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC3 / 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)
Strain: ATCC 204508 / S288c / References: UniProt: P20436
#10: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC5 / 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)
Strain: ATCC 204508 / S288c / References: UniProt: P22139
#12: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC4 / 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)
Strain: ATCC 204508 / S288c / References: UniProt: P40422

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DNA chain , 2 types, 2 molecules RS

#18: DNA chain Non-Template


Mass: 21445.754 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae S288c (yeast)
#19: DNA chain Template


Mass: 21708.973 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae S288c (yeast)

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Transcription factor ... , 2 types, 2 molecules VZ

#20: Protein Transcription factor TFIIIB component B'' / TFIIIB90


Mass: 67801.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: BDP1, TFC5, YNL039W, N2682 / Production host: Escherichia coli (E. coli) / References: UniProt: P46678
#22: Protein Transcription factor IIIB 70 kDa subunit / TFIIIB / B-related factor 1 / BRF-1


Mass: 67011.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: BRF1, PCF4, TDS4, YGR246C / Production host: Escherichia coli (E. coli) / References: UniProt: P29056

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Protein , 1 types, 1 molecules Y

#21: 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)
Strain: ATCC 204508 / S288c / Gene: SPT15, BTF1, TBP1, YER148W / Production host: Escherichia coli (E. coli) / References: UniProt: P13393

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Non-polymers , 2 types, 8 molecules

#23: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / 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

Component
IDNameTypeEntity IDParent-IDSource
1RNA Polymerase III open pre-initiation complexCOMPLEX#1-#220MULTIPLE SOURCES
2RNA Polymerase IIICOMPLEX#1-#191NATURAL
3Nucleic acidCOMPLEX#18-#191RECOMBINANT
4transcription factorsCOMPLEX#20-#221RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)559292
23Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)559292
34Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)559292
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
13synthetic construct (others)32630
24Escherichia coli (E. coli)562
Buffer solutionpH: 8
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 %

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 39 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
EM software
IDNameVersionCategory
1RELION2.0.2particle selection
2EPU1.4.4image acquisition
4CTFFIND4.1.5CTF correction
7Coot0.8.8model fitting
9RELION2.0.2initial Euler assignment
10RELION2.0.2final Euler assignment
11RELION2.0.2classification
12RELION2.0.23D reconstruction
13PHENIX1.12-2829model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 40847 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00450017
ELECTRON MICROSCOPYf_angle_d1.04767906
ELECTRON MICROSCOPYf_dihedral_angle_d12.70530155
ELECTRON MICROSCOPYf_chiral_restr0.0587580
ELECTRON MICROSCOPYf_plane_restr0.0078414

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Jul 12, 2017. Major update of PDB

Major update of PDB

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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