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

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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 / transcription
Function / homologyRNA polymerases, subunit N, zinc binding site / DNA-directed RNA polymerase, insert domain superfamily / DNA-directed RNA polymerases I and III subunit AC19 / DNA-directed RNA polymerases I and III subunit AC40 / Pol I subunit A12, C-terminal zinc ribbon / RPB5-like RNA polymerase subunit / RPB6/omega subunit-like superfamily / RNA polymerase, RBP11-like subunit / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 ...RNA polymerases, subunit N, zinc binding site / DNA-directed RNA polymerase, insert domain superfamily / DNA-directed RNA polymerases I and III subunit AC19 / DNA-directed RNA polymerases I and III subunit AC40 / Pol I subunit A12, C-terminal zinc ribbon / RPB5-like RNA polymerase subunit / RPB6/omega subunit-like superfamily / RNA polymerase, RBP11-like subunit / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / RNA polymerase Rpb7-like, N-terminal domain superfamily / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase Rpb2, domain 6 / RNA polymerase Rpb1, domain 2 / RNA polymerase I transcription initiation factor TAF1B/Rrn7 / DNA-directed RNA polymerase, subunit RPB6 / Transcription factor S-II (TFIIS) / RNA polymerase I-specific transcription initiation factor Rrn6 / RNA polymerase I, subunit Rpa14, fungi / DNA-directed RNA polymerase I, subunit RPA34.5 / DNA-directed RNA polymerase RPB5 subunit, eukaryote/virus / RNA polymerase Rpb2, OB-fold / DNA-directed RNA pol I, largest subunit / DNA-directed RNA polymerase, subunit 2 / Transcription initiation factor Rrn11, budding yeast / RNA polymerase subunit RPB10 / RNA polymerase I-specific transcription initiation factor RRN6-like / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerase, subunit H/Rpb5, conserved site / Archaeal RpoH /eukaryotic RPB5 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / Formation of TC-NER Pre-Incision Complex / Transcription initiation factor Rrn7, Zinc-finger / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb5, C-terminal domain / RNA polymerase subunit, RPB6/omega / Zinc finger TFIIS-type signature. / Yeast RNA polymerase I subunit RPA14 / DNA-directed RNA polymerase I subunit RPA34.5 / RNA polymerase I-specific transcription-initiation factor / Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7 / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / 30 to 40 Kd subunits signature. / RNA polymerases M / 15 Kd subunits signature. / A49-like RNA polymerase I associated factor / RNA polymerases H / 23 Kd subunits signature. / RNA polymerases K / 14 to 18 Kd subunits signature. / RNA polymerases N / 8 Kd subunits signature. / RNA polymerases L / 13 to 16 Kd subunits signature. / RNA polymerases beta chain signature. / Zinc finger TFIIS-type profile. / RNA polymerase I, Rpa2 specific domain / RNA polymerase I specific transcription initiation factor RRN3 / RNA polymerase Rpb6 / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases N / 8 kDa subunit / RNA polymerases M/15 Kd subunit / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase Rpb8 / RNA polymerase Rpb5, N-terminal domain / RNA polymerase I specific initiation factor / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 2 / RNA polymerase beta subunit / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 5 / Nucleic acid-binding, OB-fold / DNA-directed RNA polymerase subunit/transcription factor S / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / DNA-directed RNA polymerase, M/15kDa subunit / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / Zinc finger, TFIIS-type / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerase, alpha subunit / DNA-directed RNA polymerase, subunit N/Rpb10 / Dual incision in TC-NER / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase II transcribes snRNA genes / RNA polymerase, Rpb5, N-terminal / mRNA Capping / mRNA Splicing - Minor Pathway / RNA Polymerase I Transcription Initiation / 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 Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression / RNA polymerase, Rpb8 / Gap-filling DNA repair synthesis and ligation in TC-NER / RNA polymerase Rpb7, N-terminal / Transcription initiation factor Rrn11 / DNA-directed RNA polymerase, insert domain
Function and homology information
Specimen sourceSaccharomyces cerevisiae S288C (yeast)
Saccharomyces cerevisiae S288c (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.4 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 20, 2017 / Release: Jul 26, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jul 26, 2017Structure modelrepositoryInitial release
1.1Aug 2, 2017Structure modelDatabase referencescitation_author_citation_author.name
1.2Dec 6, 2017Structure modelAdvisory / Database referencescitation / citation_author / pdbx_unobs_or_zero_occ_atoms_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

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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
Polyers944,27334
Non-polymers4587
Water0
1


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/peptide 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: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P10964, DNA-directed RNA polymerase
#2: Protein/peptide DNA-directed RNA polymerase I subunit RPA135 / Polymerase / 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: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P22138, DNA-directed RNA polymerase
#4: Protein/peptide 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: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P50106
#7: Protein/peptide 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: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P46669
#9: Protein/peptide 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: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P32529
#13: Protein/peptide 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: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: Q01080
#14: Protein/peptide 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: (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/peptide 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: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P07703
#11: Protein/peptide 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 polypeptide / RPA19


Mass: 16167.860 Da / Num. of mol.: 1 / 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/peptide 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 kDa polypeptide


Mass: 25117.094 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P20434
#6: Protein/peptide 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 kDa polypeptide


Mass: 17931.834 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P20435
#8: Protein/peptide 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 / and III 14.5 kDa polypeptide


Mass: 16525.363 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P20436
#10: Protein/peptide 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 / and III 8.3 kDa polypeptide


Mass: 8290.732 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P22139
#12: Protein/peptide 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: (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/peptide RNA polymerase I-specific transcription initiation factor RRN3


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


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


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


Mass: 59334.262 Da / Num. of mol.: 1 / 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: (synth.) Saccharomyces cerevisiae S288c (yeast)
#17: DNA chain DNA (56-MER)


Mass: 21216.605 Da / Num. of mol.: 1 / 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: (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: (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: (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: (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: (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: (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: (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: (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: (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: (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: (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 / Formula: Zn / Zinc

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent IDSource
1RNA polymerase I pre-initiation complexCOMPLEX1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 310MULTIPLE SOURCES
2RNA polymerase I pre-initiation complexCOMPLEX1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 151NATURAL
3RNA polymerase I pre-initiation complexCOMPLEX16, 171RECOMBINANT
4RNA polymerase I pre-initiation complexCOMPLEX18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 311RECOMBINANT
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
12559292Saccharomyces cerevisiae S288C (yeast)
23559292Saccharomyces cerevisiae S288C (yeast)
34559292Saccharomyces cerevisiae S288C (yeast)
Source (recombinant)
IDEntity assembly IDNcbi tax IDOrganism
14562Escherichia coli (E. coli)
2332630synthetic construct (others)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: 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 / Number of particles: 38589 / Symmetry type: POINT
Atomic model buildingDetails: 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.
Ref protocol: FLEXIBLE FIT

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