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- PDB-5oa1: RNA polymerase I pre-initiation complex -

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Basic information

Entry
Database: PDB / ID: 5oa1
TitleRNA polymerase I pre-initiation complex
Components
  • (ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA- ...) x 10
  • (DNA-directed RNA polymerase I subunit ...Polymerase) x 7
  • (DNA-directed RNA polymerases I and III subunit ...) x 2
  • (DNA-directed RNA polymerases I, II, and III subunit ...RNA polymerase) x 5
  • (RNA polymerase I-specific transcription initiation factor ...) x 4
  • ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA
  • DNA (49-MER)
  • DNA (56-MER)
KeywordsTRANSCRIPTION / RNA polymerase I / pre-initiation complex
Function / homology
Function and homology information


RNA polymerase I transcription regulatory region sequence-specific DNA binding / RNA polymerase I core factor complex / RNA polymerase I core promoter sequence-specific DNA binding / RNA polymerase I core binding / rDNA binding / RNA polymerase I general transcription initiation factor binding / RNA polymerase I general transcription initiation factor activity / RNA polymerase III activity / RNA polymerase I preinitiation complex assembly / RNA Polymerase I Transcription Initiation ...RNA polymerase I transcription regulatory region sequence-specific DNA binding / RNA polymerase I core factor complex / RNA polymerase I core promoter sequence-specific DNA binding / RNA polymerase I core binding / rDNA binding / RNA polymerase I general transcription initiation factor binding / RNA polymerase I general transcription initiation factor activity / RNA polymerase III activity / RNA polymerase I preinitiation complex assembly / RNA Polymerase I Transcription Initiation / 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 / regulation of cell size / Formation of the Early Elongation Complex / mRNA Capping / Formation of TC-NER Pre-Incision Complex / RNA polymerase II transcribes snRNA genes / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / Estrogen-dependent gene expression / 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-templated transcription / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / Dual incision in TC-NER / RNA polymerase I activity / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / tRNA transcription by RNA polymerase III / 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 / transcription elongation by RNA polymerase I / RNA polymerase I complex / transcription by RNA polymerase I / RNA polymerase III complex / transcription by RNA polymerase III / RNA polymerase II, core complex / TBP-class protein binding / promoter-specific chromatin binding / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / ribonucleoside binding / DNA-directed RNA polymerase / peroxisome / ribosome biogenesis / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / nucleic acid binding / protein dimerization activity / nucleolus / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
RNA polymerase I specific transcription initiation factor RRN3 / RNA polymerase I specific transcription initiation factor RRN3 / Transcription initiation factor Rrn11 / RNA polymerase I-specific transcription initiation factor Rrn6 / Transcription initiation factor Rrn11, budding yeast / RNA polymerase I-specific transcription initiation factor RRN6-like / : / : / : / RNA polymerase I-specific transcription initiation factor Rrn11 ...RNA polymerase I specific transcription initiation factor RRN3 / RNA polymerase I specific transcription initiation factor RRN3 / Transcription initiation factor Rrn11 / RNA polymerase I-specific transcription initiation factor Rrn6 / Transcription initiation factor Rrn11, budding yeast / RNA polymerase I-specific transcription initiation factor RRN6-like / : / : / : / RNA polymerase I-specific transcription initiation factor Rrn11 / Rrn6, beta-propeller / RRN6, K-rich C-terminal domain / Rrn6, helical bundle domain / Transcription initiation factor Rrn7, Zinc-finger / RNA polymerase I transcription initiation factor TAF1B/Rrn7 / : / : / Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7 / Rrn7/TAF1B, N-terminal cyclin domain / Rrn7/TAF1B, C-terminal cyclin domain / RNA polymerase I, subunit Rpa14, fungi / Yeast RNA polymerase I subunit RPA14 / DNA-directed RNA polymerase I, subunit RPA34.5 / DNA-directed RNA polymerase I subunit RPA34.5 / RNA polymerase I associated factor, A49-like / A49-like RNA polymerase I associated factor / Rpa43, N-terminal ribonucleoprotein (RNP) domain / RPA43, OB domain / RPA43 OB domain in RNA Pol I / DNA-directed RNA polymerase I subunit RPA2, domain 4 / DNA-directed RNA pol I, largest subunit / Pol I subunit A12, C-terminal zinc ribbon / : / RNA polymerase I, Rpa2 specific domain / DNA-directed RNA polymerases I and III subunit AC19 / DNA-directed RNA polymerases I and III subunit AC40 / Zinc finger TFIIS-type signature. / RNA polymerase subunit Rpb7-like / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / 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, 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 Rpo11 / 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. / RNA polymerase subunit CX / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RNA polymerases L / 13 to 16 Kd subunits signature. / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1 / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA-directed RNA polymerases I and III subunit RPAC1 / DNA-directed RNA polymerase I subunit RPA190 / 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 polymerase I subunit RPA135 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerases I and III subunit RPAC2 ...DNA / DNA (> 10) / DNA-directed RNA polymerases I and III subunit RPAC1 / DNA-directed RNA polymerase I subunit RPA190 / 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 polymerase I subunit RPA135 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerases I and III subunit RPAC2 / DNA-directed RNA polymerase I subunit RPA12 / RNA polymerase I-specific transcription initiation factor RRN6 / RNA polymerase I-specific transcription initiation factor RRN3 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase I-specific transcription initiation factor RRN7 / DNA-directed RNA polymerase I subunit RPA43 / DNA-directed RNA polymerase I subunit RPA34 / DNA-directed RNA polymerase I subunit RPA14 / DNA-directed RNA polymerase I subunit RPA49 / RNA polymerase I-specific transcription initiation factor RRN11
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Saccharomyces cerevisiae S288c (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsSadian, Y. / Tafur, L. / Kosinski, J. / Jakobi, A.J. / Muller, C.W.
CitationJournal: EMBO J / Year: 2017
Title: Structural insights into transcription initiation by yeast RNA polymerase I.
Authors: Yashar Sadian / Lucas Tafur / Jan Kosinski / Arjen J Jakobi / Rene Wetzel / Katarzyna Buczak / Wim Jh Hagen / Martin Beck / Carsten Sachse / Christoph W Müller /
Abstract: In eukaryotic cells, RNA polymerase I (Pol I) synthesizes precursor ribosomal RNA (pre-rRNA) that is subsequently processed into mature rRNA. To initiate transcription, Pol I requires the assembly of ...In eukaryotic cells, RNA polymerase I (Pol I) synthesizes precursor ribosomal RNA (pre-rRNA) that is subsequently processed into mature rRNA. To initiate transcription, Pol I requires the assembly of a multi-subunit pre-initiation complex (PIC) at the ribosomal RNA promoter. In yeast, the minimal PIC includes Pol I, the transcription factor Rrn3, and Core Factor (CF) composed of subunits Rrn6, Rrn7, and Rrn11. Here, we present the cryo-EM structure of the 18-subunit yeast Pol I PIC bound to a transcription scaffold. The cryo-EM map reveals an unexpected arrangement of the DNA and CF subunits relative to Pol I. The upstream DNA is positioned differently than in any previous structures of the Pol II PIC. Furthermore, the TFIIB-related subunit Rrn7 also occupies a different location compared to the Pol II PIC although it uses similar interfaces as TFIIB to contact DNA. Our results show that although general features of eukaryotic transcription initiation are conserved, Pol I and Pol II use them differently in their respective transcription initiation complexes.
History
DepositionJun 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Dec 6, 2017Group: Advisory / Database references
Category: citation / citation_author / pdbx_unobs_or_zero_occ_atoms
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.3Oct 24, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn

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Structure visualization

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  • EMDB-3728
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Assembly

Deposited unit
A: DNA-directed RNA polymerase I subunit RPA190
B: DNA-directed RNA polymerase I subunit RPA135
C: DNA-directed RNA polymerases I and III subunit RPAC1
D: DNA-directed RNA polymerase I subunit RPA14
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 I subunit RPA43
H: DNA-directed RNA polymerases I, II, and III subunit RPABC3
I: DNA-directed RNA polymerase I subunit RPA12
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 I subunit RPA49
N: DNA-directed RNA polymerase I subunit RPA34
O: RNA polymerase I-specific transcription initiation factor RRN3
S: DNA (49-MER)
T: DNA (56-MER)
U: RNA polymerase I-specific transcription initiation factor RRN7
V: RNA polymerase I-specific transcription initiation factor RRN6
W: RNA polymerase I-specific transcription initiation factor RRN11
1: ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA
2: ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA
3: ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA
4: ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA
5: ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA
6: ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA
7: ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA
8: ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA
9: ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA
Q: ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA
P: ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA
Z: ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA
Y: ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA
R: ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)944,73141
Polymers944,27334
Non-polymers4587
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551
MethodPISA

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Components

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DNA-directed RNA polymerase I subunit ... , 7 types, 7 molecules ABDGIMN

#1: Protein DNA-directed RNA polymerase I subunit RPA190 / Polymerase / DNA-directed RNA polymerase I 190 kDa polypeptide / A190 / DNA-directed RNA polymerase I largest subunit


Mass: 186676.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P10964, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase I subunit RPA135 / Polymerase / DNA-directed RNA polymerase I 135 kDa polypeptide / A135 / DNA-directed RNA polymerase I ...DNA-directed RNA polymerase I 135 kDa polypeptide / A135 / DNA-directed RNA polymerase I polypeptide 2 / RNA polymerase I subunit 2


Mass: 135910.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P22138, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase I subunit RPA14 / Polymerase / A14 / DNA-directed RNA polymerase I 14 kDa polypeptide


Mass: 14599.128 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P50106
#7: Protein DNA-directed RNA polymerase I subunit RPA43 / Polymerase / A43 / DNA-directed DNA-dependent RNA polymerase 36 kDa polypeptide


Mass: 36264.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P46669
#9: Protein DNA-directed RNA polymerase I subunit RPA12 / Polymerase / A12 / A12.2 / DNA-directed RNA polymerase I 13.7 kDa polypeptide


Mass: 13676.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P32529
#13: Protein DNA-directed RNA polymerase I subunit RPA49 / Polymerase / A49 / DNA-directed RNA polymerase I 49 kDa polypeptide


Mass: 46721.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: Q01080
#14: Protein DNA-directed RNA polymerase I subunit RPA34 / Polymerase / A34 / DNA-directed DNA-dependent RNA polymerase 34.5 kDa polypeptide / A34.5


Mass: 26933.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P47006

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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 S288C (yeast) / 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 S288C (yeast) / 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 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 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: 17931.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae 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 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 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 S288C (yeast) / References: UniProt: P40422

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RNA polymerase I-specific transcription initiation factor ... , 4 types, 4 molecules OUVW

#15: Protein RNA polymerase I-specific transcription initiation factor RRN3


Mass: 72458.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P36070
#18: Protein RNA polymerase I-specific transcription initiation factor RRN7


Mass: 60435.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: RRN7, YJL025W, J1273 / Production host: Escherichia coli (E. coli) / References: UniProt: P40992
#19: Protein RNA polymerase I-specific transcription initiation factor RRN6


Mass: 102163.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: RRN6, YBL014C, YBL0311, YBL0312 / Production host: Escherichia coli (E. coli) / References: UniProt: P32786
#20: Protein RNA polymerase I-specific transcription initiation factor RRN11


Mass: 59334.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: RRN11, YML043C, YM9827.09C / Production host: Escherichia coli (E. coli) / References: UniProt: Q04712

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DNA chain , 2 types, 2 molecules ST

#16: DNA chain DNA (49-MER)


Mass: 22000.131 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae S288c (yeast)
#17: DNA chain DNA (56-MER)


Mass: 21216.605 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae S288c (yeast)

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ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA- ... , 10 types, 12 molecules 1245Q687PZYR

#21: Protein/peptide ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA


Mass: 942.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Production host: Escherichia coli (E. coli)
#22: Protein/peptide ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA


Mass: 1368.494 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Production host: Escherichia coli (E. coli)
#24: Protein/peptide ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA


Mass: 1723.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Production host: Escherichia coli (E. coli)
#25: Protein/peptide ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA


Mass: 1155.260 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Production host: Escherichia coli (E. coli)
#26: Protein/peptide ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA


Mass: 728.793 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Production host: Escherichia coli (E. coli)
#27: Protein/peptide ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA


Mass: 1794.960 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Production host: Escherichia coli (E. coli)
#28: Protein/peptide ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA


Mass: 1581.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Production host: Escherichia coli (E. coli)
#29: Protein/peptide ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA


Mass: 1084.182 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Production host: Escherichia coli (E. coli)
#30: Protein/peptide ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA


Mass: 870.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Production host: Escherichia coli (E. coli)
#31: Protein/peptide ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA


Mass: 1937.116 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Production host: Escherichia coli (E. coli)

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Protein/peptide / Non-polymers , 2 types, 9 molecules 39

#23: Protein/peptide ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA


Mass: 657.715 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Production host: Escherichia coli (E. coli)
#32: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn

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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 I pre-initiation complexCOMPLEX#1-#310MULTIPLE SOURCES
2RNA polymerase I pre-initiation complexCOMPLEX#1-#151NATURAL
3RNA polymerase I pre-initiation complexCOMPLEX#16-#171RECOMBINANT
4RNA polymerase I pre-initiation complexCOMPLEX#18-#311RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Saccharomyces cerevisiae S288C (yeast)559292
23Saccharomyces cerevisiae S288C (yeast)559292
34Saccharomyces cerevisiae S288C (yeast)559292
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
14Escherichia coli (E. coli)562
23synthetic construct (others)32630
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in.
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen 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: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 2 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 38589 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT
Details: PLEASE NOTE: This entry represents a model built based on a 4.4 Angstrom cryo-EM map. Due to the limited resolution, the sequence in several regions of Rrn6, Rrn7, and Rrn11 subunits is only ...Details: PLEASE NOTE: This entry represents a model built based on a 4.4 Angstrom cryo-EM map. Due to the limited resolution, the sequence in several regions of Rrn6, Rrn7, and Rrn11 subunits is only tentatively assigned and may contain sequence register shifts. To account for these uncertainties, the coordinates of the Core Factor subunits Rrn6, Rrn7, and Rrn11 subunits in this entry only contain backbone atoms and unassigned helices located in the EM density are built as poly-alanines. For more details regarding the model and its limitations please refer to the publication (Sadian et al., EMBO J, 2017) associated with this entry.

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