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- PDB-6rql: RNA Polymerase I Closed Conformation 2 (CC2) -

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Entry
Database: PDB / ID: 6rql
TitleRNA Polymerase I Closed Conformation 2 (CC2)
Components
  • (DNA-directed RNA polymerase I subunit ...) x 7
  • (DNA-directed RNA polymerases I and III subunit ...) x 2
  • (DNA-directed RNA polymerases I, II, and III subunit ...) x 5
  • (RNA polymerase I-specific transcription initiation factor ...) x 4
  • Nontemplate strand
  • Template strand
KeywordsTRANSCRIPTION / RNA Polymerase I / Pre-initiation complex / PIC / Closed Complex / CC / Core Factor / CF / Rrn3
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 binding / RNA polymerase I general transcription initiation factor activity / RNA polymerase I general transcription initiation factor binding / rDNA binding / RNA polymerase I core promoter sequence-specific DNA binding / RNA polymerase I preinitiation complex assembly / RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA ...RNA polymerase I transcription regulatory region sequence-specific DNA binding / RNA polymerase I core factor complex / RNA polymerase I core binding / RNA polymerase I general transcription initiation factor activity / RNA polymerase I general transcription initiation factor binding / rDNA binding / RNA polymerase I core promoter sequence-specific DNA binding / 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 / 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 / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / RNA-templated transcription / Formation of TC-NER Pre-Incision Complex / regulation of cell size / 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 complex / tRNA transcription by RNA polymerase III / transcription by RNA polymerase I / TBP-class protein binding / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / promoter-specific chromatin binding / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / peroxisome / ribosome biogenesis / nucleic acid binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / protein dimerization activity / nucleolus / negative regulation of transcription by RNA polymerase II / mitochondrion / 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 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 / : / DNA-directed RNA polymerase I, subunit RPA34.5 / DNA-directed RNA polymerase I subunit RPA34.5 / RNA polymerase I, subunit Rpa14, fungi / Yeast RNA polymerase I subunit RPA14 / RNA polymerase I associated factor, A49-like / A49-like RNA polymerase I associated factor / Rpa43, N-terminal ribonucleoprotein (RNP) domain / RNA polymerase Rpb7-like, N-terminal domain / Pol I subunit A12, C-terminal zinc ribbon / 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 / : / RNA polymerase I, Rpa2 specific domain / Hypothetical Protein Ta0175; Chain: A, domain 2 - #20 / DCoH-like / RNA polymerase alpha subunit dimerisation domain / Hypothetical Protein Ta0175; Chain: A, domain 2 / 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 Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 / DNA-directed RNA polymerase, subunit 2, domain 6 / DNA-directed RNA polymerases I and III subunit AC19 / DNA-directed RNA polymerases I and III subunit AC40 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 / RNA polymerase Rpb2, domain 2 / RNA polymerase II, Rpb2 subunit, wall domain / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / RNA polymerase, RBP11-like subunit / Rubrerythrin, domain 2 / DNA-directed RNA polymerase, insert domain / RNA Polymerase Alpha Subunit; Chain A, domain 2 / Gyrase A; domain 2 / Homeodomain-like / 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 / 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. / RNA polymerase subunit CX / 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 Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo11 / RNA polymerases L / 13 to 16 Kd subunits signature. / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile.
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 speciessynthetic construct (others)
Saccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsMueller, C.W. / Sadian, Y. / Tafur, L.
Funding support1items
OrganizationGrant numberCountry
European Research CouncilERC-2013-AdG340964-POL1PIC
CitationJournal: Nat Commun / Year: 2019
Title: Molecular insight into RNA polymerase I promoter recognition and promoter melting.
Authors: Yashar Sadian / Florence Baudin / Lucas Tafur / Brice Murciano / Rene Wetzel / Felix Weis / Christoph W Müller /
Abstract: RNA polymerase I (Pol I) assembles with core factor (CF) and Rrn3 on the rDNA core promoter for transcription initiation. Here, we report cryo-EM structures of closed, intermediate and open Pol I ...RNA polymerase I (Pol I) assembles with core factor (CF) and Rrn3 on the rDNA core promoter for transcription initiation. Here, we report cryo-EM structures of closed, intermediate and open Pol I initiation complexes from 2.7 to 3.7 Å resolution to visualize Pol I promoter melting and to structurally and biochemically characterize the recognition mechanism of Pol I promoter DNA. In the closed complex, double-stranded DNA runs outside the DNA-binding cleft. Rotation of CF and upstream DNA with respect to Pol I and Rrn3 results in the spontaneous loading and opening of the promoter followed by cleft closure and positioning of the Pol I A49 tandem winged helix domain (tWH) onto DNA. Conformational rearrangement of A49 tWH leads to a clash with Rrn3 to initiate complex disassembly and promoter escape. Comprehensive insight into the Pol I transcription initiation cycle allows comparisons with promoter opening by Pol II and Pol III.
History
DepositionMay 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 22, 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
T: Template strand
U: Nontemplate strand
Q: RNA polymerase I-specific transcription initiation factor RRN7
S: RNA polymerase I-specific transcription initiation factor RRN6
R: RNA polymerase I-specific transcription initiation factor RRN11
M: DNA-directed RNA polymerase I subunit RPA49
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
N: DNA-directed RNA polymerase I subunit RPA34
O: RNA polymerase I-specific transcription initiation factor RRN3


Theoretical massNumber of molelcules
Total (without water)927,82820
Polymers927,82820
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area123160 Å2
ΔGint-600 kcal/mol
Surface area269080 Å2
MethodPISA

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Components

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DNA chain , 2 types, 2 molecules TU

#1: DNA chain Template strand


Mass: 21216.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#2: DNA chain Nontemplate strand


Mass: 21942.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)

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

#3: 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 (brewer's yeast)
Gene: RRN7, YJL025W, J1273 / Production host: Escherichia coli (E. coli) / References: UniProt: P40992
#4: 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 (brewer's yeast)
Gene: RRN6, YBL014C, YBL0311, YBL0312 / Production host: Escherichia coli (E. coli) / References: UniProt: P32786
#5: 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 (brewer's yeast)
Gene: RRN11, YML043C, YM9827.09C / Production host: Escherichia coli (E. coli) / References: UniProt: Q04712
#20: Protein RNA polymerase I-specific transcription initiation factor RRN3


Mass: 72458.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RRN3, YKL125W / Production host: Escherichia coli (E. coli) / References: UniProt: P36070

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

#6: Protein DNA-directed RNA polymerase I subunit RPA49 / A49 / DNA-directed RNA polymerase I 49 kDa polypeptide


Mass: 46721.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RPA49, RRN13, YNL248C, N0880 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q01080
#7: Protein DNA-directed RNA polymerase I subunit RPA190 / 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 genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RPA190, RPA1, RRN1, YOR341W, O6276 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P10964, DNA-directed RNA polymerase
#8: Protein DNA-directed RNA polymerase I subunit RPA135 / 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 genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RPA135, RPA2, RRN2, SRP3, YPR010C, YP9531.03C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P22138, DNA-directed RNA polymerase
#10: Protein DNA-directed RNA polymerase I subunit RPA14 / A14 / DNA-directed RNA polymerase I 14 kDa polypeptide


Mass: 14599.128 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RPA14, YDR156W, YD8358.11 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P50106
#13: Protein DNA-directed RNA polymerase I subunit RPA43 / A43 / DNA-directed DNA-dependent RNA polymerase 36 kDa polypeptide


Mass: 36264.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RPA43, RRN12, YOR340C, O6271 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P46669
#15: Protein DNA-directed RNA polymerase I subunit RPA12 / 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 genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RPA12, RRN4, YJR063W, J1747 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32529
#19: Protein DNA-directed RNA polymerase I subunit RPA34 / 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 genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RPA34, YJL148W, J0637 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P47006

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

#9: 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 genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RPC40, RPA5, RPC5, YPR110C, P8283.18 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P07703
#17: 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 genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RPC19, YNL113W, N1937 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P28000

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DNA-directed RNA polymerases I, II, and III subunit ... , 5 types, 5 molecules EFHJL

#11: 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 genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RPB5, RPA7, RPC9, YBR154C, YBR1204 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P20434
#12: 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 genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RPO26, RPB6, YPR187W, P9677.8 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P20435
#14: 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 genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RPB8, YOR224C, YOR50-14 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P20436
#16: 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 genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RPB10, YOR210W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P22139
#18: 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 genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RPC10, RPB12, YHR143W-A, YHR143BW / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40422

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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 Closed Complex conformation 2 (CC2)COMPLEXall0MULTIPLE SOURCES
2Nucleic acidCOMPLEX#1-#21RECOMBINANT
3transcription initiation factorCOMPLEX#3-#5, #201RECOMBINANT
4RNA Polymerase ICOMPLEX#6-#191RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12synthetic construct (others)32630
23Saccharomyces cerevisiae (brewer's yeast)4932
34Saccharomyces cerevisiae (brewer's yeast)4932
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12synthetic construct (others)32630
23Escherichia coli (E. coli)562
34Saccharomyces cerevisiae (brewer's yeast)4932
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 4 K

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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: 1.1075 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategory
2SerialEMimage acquisition
4GctfCTF correction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 24482 / Symmetry type: POINT

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