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- EMDB-4148: Free monomeric RNA polymerase I at 4.0A resolution -

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Basic information

Entry
Database: EMDB / ID: EMD-4148
TitleFree monomeric RNA polymerase I at 4.0A resolution
Map dataSharpened map (B=-149A^2)
Sample
  • Complex: Yeast RNA polymerase I elongation complex
    • Protein or peptide: x 14 types
  • Ligand: x 2 types
KeywordsRNA polymerase I / transcription
Function / homology
Function and homology information


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 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 / regulation of cell size / Formation of TC-NER Pre-Incision Complex / RNA Polymerase I Promoter Escape / transcription initiation at RNA polymerase III promoter / 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 / Dual incision in TC-NER / transcription by RNA polymerase III / transcription by RNA polymerase I / 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 initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / promoter-specific chromatin binding / 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 / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
: / 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 / Pol I subunit A12, C-terminal zinc ribbon / RPA43, OB 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 / 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 / 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 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. / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / 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. / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, RBP11-like subunit / RNA polymerase, beta subunit, conserved site
Similarity search - Domain/homology
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 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 ...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 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / 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
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsNeyer S / Kunz M
CitationJournal: Nature / Year: 2016
Title: Structure of RNA polymerase I transcribing ribosomal DNA genes.
Authors: Simon Neyer / Michael Kunz / Christian Geiss / Merle Hantsche / Victor-Valentin Hodirnau / Anja Seybert / Christoph Engel / Margot P Scheffer / Patrick Cramer / Achilleas S Frangakis /
Abstract: RNA polymerase I (Pol I) is a highly processive enzyme that transcribes ribosomal DNA (rDNA) and regulates growth of eukaryotic cells. Crystal structures of free Pol I from the yeast Saccharomyces ...RNA polymerase I (Pol I) is a highly processive enzyme that transcribes ribosomal DNA (rDNA) and regulates growth of eukaryotic cells. Crystal structures of free Pol I from the yeast Saccharomyces cerevisiae have revealed dimers of the enzyme stabilized by a 'connector' element and an expanded cleft containing the active centre in an inactive conformation. The central bridge helix was unfolded and a Pol-I-specific 'expander' element occupied the DNA-template-binding site. The structure of Pol I in its active transcribing conformation has yet to be determined, whereas structures of Pol II and Pol III have been solved with bound DNA template and RNA transcript. Here we report structures of active transcribing Pol I from yeast solved by two different cryo-electron microscopy approaches. A single-particle structure at 3.8 Å resolution reveals a contracted active centre cleft with bound DNA and RNA, and a narrowed pore beneath the active site that no longer holds the RNA-cleavage-stimulating domain of subunit A12.2. A structure at 29 Å resolution that was determined from cryo-electron tomograms of Pol I enzymes transcribing cellular rDNA confirms contraction of the cleft and reveals that incoming and exiting rDNA enclose an angle of around 150°. The structures suggest a model for the regulation of transcription elongation in which contracted and expanded polymerase conformations are associated with active and inactive states, respectively.
History
DepositionOct 15, 2016-
Header (metadata) releaseNov 23, 2016-
Map releaseNov 23, 2016-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5m3m
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4148.png

Downloads & links

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Map

FileDownload / File: emd_4148.map.gz / Format: CCP4 / Size: 46.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map (B=-149A^2)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 230 pix.
= 241.5 Å		1.05 Å/pix.
x 230 pix.
= 241.5 Å		1.05 Å/pix.
x 230 pix.
= 241.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.03
Minimum - Maximum-0.09353096 - 0.15214713
Average (Standard dev.)-0.000035655336 (±0.0072155506)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions230230230
Spacing230230230
CellA=B=C: 241.49998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z230230230
origin x/y/z0.0000.0000.000
length x/y/z241.500241.500241.500
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ129141209
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS230230230
D min/max/mean-0.0940.152-0.000

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Supplemental data

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Additional map: Map filtered to 4.2A

Fileemd_4148_additional.map
AnnotationMap filtered to 4.2A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered half map1

Fileemd_4148_half_map_1.map
AnnotationUnfiltered half map1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered half map2

Fileemd_4148_half_map_2.map
AnnotationUnfiltered half map2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Yeast RNA polymerase I elongation complex

EntireName: Yeast RNA polymerase I elongation complex
Components
  • Complex: Yeast RNA polymerase I elongation complex
    • Protein or peptide: DNA-directed RNA polymerase I subunit RPA190
    • Protein or peptide: DNA-directed RNA polymerase I subunit RPA135
    • Protein or peptide: DNA-directed RNA polymerases I and III subunit RPAC1
    • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC1
    • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC2
    • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC3
    • Protein or peptide: DNA-directed RNA polymerase I subunit RPA12
    • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC5
    • Protein or peptide: DNA-directed RNA polymerases I and III subunit RPAC2
    • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC4
    • Protein or peptide: DNA-directed RNA polymerase I subunit RPA49
    • Protein or peptide: DNA-directed RNA polymerase I subunit RPA34
    • Protein or peptide: DNA-directed RNA polymerase I subunit RPA14
    • Protein or peptide: DNA-directed RNA polymerase I subunit RPA43
  • Ligand: ZINC ION
  • Ligand: SULFATE ION

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Supramolecule #1: Yeast RNA polymerase I elongation complex

SupramoleculeName: Yeast RNA polymerase I elongation complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#14
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 590 KDa

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Macromolecule #1: DNA-directed RNA polymerase I subunit RPA190

MacromoleculeName: DNA-directed RNA polymerase I subunit RPA190 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 186.676969 KDa
SequenceString: MDISKPVGSE ITSVDFGILT AKEIRNLSAK QITNPTVLDN LGHPVSGGLY DLALGAFLRN LCSTCGLDEK FCPGHQGHIE LPVPCYNPL FFNQLYIYLR ASCLFCHHFR LKSVEVHRYA CKLRLLQYGL IDESYKLDEI TLGSLNSSMY TDDEAIEDNE D EMDGEGSK ...String:
MDISKPVGSE ITSVDFGILT AKEIRNLSAK QITNPTVLDN LGHPVSGGLY DLALGAFLRN LCSTCGLDEK FCPGHQGHIE LPVPCYNPL FFNQLYIYLR ASCLFCHHFR LKSVEVHRYA CKLRLLQYGL IDESYKLDEI TLGSLNSSMY TDDEAIEDNE D EMDGEGSK QSKDISSTLL NELKSKRSEY VDMAIAKALS DGRTTERGSF TATVNDERKK LVHEFHKKLL SRGKCDNCGM FS PKFRKDG FTKIFETALN EKQITNNRVK GFIRQDMIKK QKQAKKLDGS NEASANDEES FDVGRNPTTR PKTGSTYILS TEV KNILDT VFRKEQCVLQ YVFHSRPNLS RKLVKADSFF MDVLVVPPTR FRLPSKLGEE VHENSQNQLL SKVLTTSLLI RDLN DDLSK LQKDKVSLED RRVIFSRLMN AFVTIQNDVN AFIDSTKAQG RTSGKVPIPG VKQALEKKEG LFRKHMMGKR VNYAA RSVI SPDPNIETNE IGVPPVFAVK LTYPEPVTAY NIAELRQAVI NGPDKWPGAT QIQNEDGSLV SLIGMSVEQR KALANQ LLT PSSNVSTHTL NKKVYRHIKN RDVVLMNRQP TLHKASMMGH KVRVLPNEKT LRLHYANTGA YNADFDGDEM NMHFPQN EN ARAEALNLAN TDSQYLTPTS GSPVRGLIQD HISAGVWLTS KDSFFTREQY QQYIYGCIRP EDGHTTRSKI VTLPPTIF K PYPLWTGKQI ITTVLLNVTP PDMPGINLIS KNKIKNEYWG KGSLENEVLF KDGALLCGIL DKSQYGASKY GIVHSLHEV YGPEVAAKVL SVLGRLFTNY ITATAFTCGM DDLRLTAEGN KWRTDILKTS VDTGREAAAE VTNLDKDTPA DDPELLKRLQ EILRDNNKS GILDAVTSSK VNAITSQVVS KCVPDGTMKK FPCNSMQAMA LSGAKGSNVN VSQIMCLLGQ QALEGRRVPV M VSGKTLPS FKPYETDAMA GGYVKGRFYS GIKPQEYYFH CMAGREGLID TAVKTSRSGY LQRCLTKQLE GVHVSYDNSI RD ADGTLVQ FMYGGDAIDI TKESHMTQFE FCLDNYYALL KKYNPSALIE HLDVESALKY SKKTLKYRKK HSKEPHYKQS VKY DPVLAK YNPAKYLGSV SENFQDKLES FLDKNSKLFK SSDGVNEKKF RALMQLKYMR SLINPGEAVG IIASQSVGEP STQM TLNTF HFAGHGAANV TLGIPRLREI VMTASAAIKT PQMTLPIWND VSDEQADTFC KSISKVLLSE VIDKVIVTET TGTSN TAGG NAARSYVIHM RFFDNNEYSE EYDVSKEELQ NVISNQFIHL LEAAIVKEIK KQKRTTGPDI GVAVPRLQTD VANSSS NSK RLEEDNDEEQ SHKKTKQAVS YDEPDEDEIE TMREAEKSSD EEGIDSDKES DSDSEDEDVD MNEQINKSIV EANNNMN KV QRDRQSAIIS HHRFITKYNF DDESGKWCEF KLELAADTEK LLMVNIVEEI CRKSIIRQIP HIDRCVHPEP ENGKRVLV T EGVNFQAMWD QEAFIDVDGI TSNDVAAVLK TYGVEAARNT IVNEINNVFS RYAISVSFRH LDLIADMMTR QGTYLAFNR QGMETSTSSF MKMSYETTCQ FLTKAVLDNE REQLDSPSAR IVVGKLNNVG TGSFDVLAKV PNAA

UniProtKB: DNA-directed RNA polymerase I subunit RPA190

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Macromolecule #2: DNA-directed RNA polymerase I subunit RPA135

MacromoleculeName: DNA-directed RNA polymerase I subunit RPA135 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 135.910328 KDa
SequenceString: MSKVIKPPGQ ARTADFRTLE RESRFINPPK DKSAFPLLQE AVQPHIGSFN ALTEGPDGGL LNLGVKDIGE KVIFDGKPLN SEDEISNSG YLGNKLSVSV EQVSIAKPMS NDGVSSAVER KVYPSESRQR LTSYRGKLLL KLKWSVNNGE ENLFEVRDCG G LPVMLQSN ...String:
MSKVIKPPGQ ARTADFRTLE RESRFINPPK DKSAFPLLQE AVQPHIGSFN ALTEGPDGGL LNLGVKDIGE KVIFDGKPLN SEDEISNSG YLGNKLSVSV EQVSIAKPMS NDGVSSAVER KVYPSESRQR LTSYRGKLLL KLKWSVNNGE ENLFEVRDCG G LPVMLQSN RCHLNKMSPY ELVQHKEESD EIGGYFIVNG IEKLIRMLIV QRRNHPMAII RPSFANRGAS YSHYGIQIRS VR PDQTSQT NVLHYLNDGQ VTFRFSWRKN EYLVPVVMIL KALCHTSDRE IFDGIIGNDV KDSFLTDRLE LLLRGFKKRY PHL QNRTQV LQYLGDKFRV VFQASPDQSD LEVGQEVLDR IVLVHLGKDG SQDKFRMLLF MIRKLYSLVA GECSPDNPDA TQHQ EVLLG GFLYGMILKE KIDEYLQNII AQVRMDINRG MAINFKDKRY MSRVLMRVNE NIGSKMQYFL STGNLVSQSG LDLQQ VSGY TVVAEKINFY RFISHFRMVH RGSFFAQLKT TTVRKLLPES WGFLCPVHTP DGSPCGLLNH FAHKCRISTQ QSDVSR IPS ILYSLGVAPA SHTFAAGPSL CCVQIDGKII GWVSHEQGKI IADTLRYWKV EGKTPGLPID LEIGYVPPST RGQYPGL YL FGGHSRMLRP VRYLPLDKED IVGPFEQVYM NIAVTPQEIQ NNVHTHVEFT PTNILSILAN LTPFSDFNQS PRNMYQCQ M GKQTMGTPGV ALCHRSDNKL YRLQTGQTPI VKANLYDDYG MDNFPNGFNA VVAVISYTGY DMDDAMIINK SADERGFGY GTMYKTEKVD LALNRNRGDP ITQHFGFGND EWPKEWLEKL DEDGLPYIGT YVEEGDPICA YFDDTLNKTK IKTYHSSEPA YIEEVNLIG DESNKFQELQ TVSIKYRIRR TPQIGDKFSS RHGQKGVCSR KWPTIDMPFS ETGIQPDIII NPHAFPSRMT I GMFVESLA GKAGALHGIA QDSTPWIFNE DDTPADYFGE QLAKAGYNYH GNEPMYSGAT GEELRADIYV GVVYYQRLRH MV NDKFQVR STGPVNSLTM QPVKGRKRHG GIRVGEMERD ALIGHGTSFL LQDRLLNSSD YTQASVCREC GSILTTQQSV PRI GSISTV CCRRCSMRFE DAKKLLTKSE DGEKIFIDDS QIWEDGQGNK FVGGNETTTV AIPFVLKYLD SELSAMGIRL RYNV EPK

UniProtKB: DNA-directed RNA polymerase I subunit RPA135

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Macromolecule #3: DNA-directed RNA polymerases I and III subunit RPAC1

MacromoleculeName: DNA-directed RNA polymerases I and III subunit RPAC1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 37.732613 KDa
SequenceString: MSNIVGIEYN RVTNTTSTDF PGFSKDAENE WNVEKFKKDF EVNISSLDAR EANFDLINID TSIANAFRRI MISEVPSVAA EYVYFFNNT SVIQDEVLAH RIGLVPLKVD PDMLTWVDSN LPDDEKFTDE NTIVLSLNVK CTRNPDAPKG STDPKELYNN A HVYARDLK ...String:
MSNIVGIEYN RVTNTTSTDF PGFSKDAENE WNVEKFKKDF EVNISSLDAR EANFDLINID TSIANAFRRI MISEVPSVAA EYVYFFNNT SVIQDEVLAH RIGLVPLKVD PDMLTWVDSN LPDDEKFTDE NTIVLSLNVK CTRNPDAPKG STDPKELYNN A HVYARDLK FEPQGRQSTT FADCPVVPAD PDILLAKLRP GQEISLKAHC ILGIGGDHAK FSPVSTASYR LLPQINILQP IK GESARRF QKCFPPGVIG IDEGSDEAYV KDARKDTVSR EVLRYEEFAD KVKLGRVRNH FIFNVESAGA MTPEEIFFKS VRI LKNKAE YLKNCPITQ

UniProtKB: DNA-directed RNA polymerases I and III subunit RPAC1

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Macromolecule #4: DNA-directed RNA polymerases I, II, and III subunit RPABC1

MacromoleculeName: DNA-directed RNA polymerases I, II, and III subunit RPABC1
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 25.117094 KDa
SequenceString: MDQENERNIS RLWRAFRTVK EMVKDRGYFI TQEEVELPLE DFKAKYCDSM GRPQRKMMSF QANPTEESIS KFPDMGSLWV EFCDEPSVG VKTMKTFVIH IQEKNFQTGI FVYQNNITPS AMKLVPSIPP ATIETFNEAA LVVNITHHEL VPKHIRLSSD E KRELLKRY ...String:
MDQENERNIS RLWRAFRTVK EMVKDRGYFI TQEEVELPLE DFKAKYCDSM GRPQRKMMSF QANPTEESIS KFPDMGSLWV EFCDEPSVG VKTMKTFVIH IQEKNFQTGI FVYQNNITPS AMKLVPSIPP ATIETFNEAA LVVNITHHEL VPKHIRLSSD E KRELLKRY RLKESQLPRI QRADPVALYL GLKRGEVVKI IRKSETSGRY ASYRICM

UniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC1

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Macromolecule #5: DNA-directed RNA polymerases I, II, and III subunit RPABC2

MacromoleculeName: DNA-directed RNA polymerases I, II, and III subunit RPABC2
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 17.931834 KDa
SequenceString:
MSDYEEAFND GNENFEDFDV EHFSDEETYE EKPQFKDGET TDANGKTIVT GGNGPEDFQQ HEQIRRKTLK EKAIPKDQRA TTPYMTKYE RARILGTRAL QISMNAPVFV DLEGETDPLR IAMKELAEKK IPLVIRRYLP DGSFEDWSVE ELIVDL

UniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC2

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Macromolecule #6: DNA-directed RNA polymerases I, II, and III subunit RPABC3

MacromoleculeName: DNA-directed RNA polymerases I, II, and III subunit RPABC3
type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 16.525363 KDa
SequenceString:
MSNTLFDDIF QVSEVDPGRY NKVCRIEAAS TTQDQCKLTL DINVELFPVA AQDSLTVTIA SSLNLEDTPA NDSSATRSWR PPQAGDRSL ADDYDYVMYG TAYKFEEVSK DLIAVYYSFG GLLMRLEGNY RNLNNLKQEN AYLLIRR

UniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC3

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Macromolecule #7: DNA-directed RNA polymerase I subunit RPA12

MacromoleculeName: DNA-directed RNA polymerase I subunit RPA12 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 13.676566 KDa
SequenceString:
MSVVGSLIFC LDCGDLLENP NAVLGSNVEC SQCKAIYPKS QFSNLKVVTT TADDAFPSSL RAKKSVVKTS LKKNELKDGA TIKEKCPQC GNEEMNYHTL QLRSADEGAT VFYTCTSCGY KFRTNN

UniProtKB: DNA-directed RNA polymerase I subunit RPA12

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Macromolecule #8: DNA-directed RNA polymerases I, II, and III subunit RPABC5

MacromoleculeName: DNA-directed RNA polymerases I, II, and III subunit RPABC5
type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 8.290732 KDa
SequenceString:
MIVPVRCFSC GKVVGDKWES YLNLLQEDEL DEGTALSRLG LKRYCCRRMI LTHVDLIEKF LRYNPLEKRD

UniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC5

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Macromolecule #9: DNA-directed RNA polymerases I and III subunit RPAC2

MacromoleculeName: DNA-directed RNA polymerases I and III subunit RPAC2 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 16.16786 KDa
SequenceString:
MTEDIEQKKT ATEVTPQEPK HIQEEEEQDV DMTGDEEQEE EPDREKIKLL TQATSEDGTS ASFQIVEEDH TLGNALRYVI MKNPDVEFC GYSIPHPSEN LLNIRIQTYG ETTAVDALQK GLKDLMDLCD VVESKFTEKI KSM

UniProtKB: DNA-directed RNA polymerases I and III subunit RPAC2

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Macromolecule #10: DNA-directed RNA polymerases I, II, and III subunit RPABC4

MacromoleculeName: DNA-directed RNA polymerases I, II, and III subunit RPABC4
type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 7.729969 KDa
SequenceString:
MSREGFQIPT NLDAAAAGTS QARTATLKYI CAECSSKLSL SRTDAVRCKD CGHRILLKAR TKRLVQFEAR

UniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC4

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Macromolecule #11: DNA-directed RNA polymerase I subunit RPA49

MacromoleculeName: DNA-directed RNA polymerase I subunit RPA49 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 46.721707 KDa
SequenceString: MSVKRSVSEI EIESVQDQPS VAVGSFFKGF RAPSDTTFDL YKKKKSEKDE FVLHGENERL EYEGYTDSSS QASNQYVVGL FNPEKKSIQ LYKAPVLVSK VVSKSSKNLR GPKIKSKSDT RPSALRNALG EAFGTKKAKK AIADLERNRI DSDKLTDSAI D IVDSVRTA ...String:
MSVKRSVSEI EIESVQDQPS VAVGSFFKGF RAPSDTTFDL YKKKKSEKDE FVLHGENERL EYEGYTDSSS QASNQYVVGL FNPEKKSIQ LYKAPVLVSK VVSKSSKNLR GPKIKSKSDT RPSALRNALG EAFGTKKAKK AIADLERNRI DSDKLTDSAI D IVDSVRTA SKDLPTRAQL DEITSNDRPT PLANIDATDV EQIYPIESII PKKELQFIRV SSILKEADKE KKLELFPYQN NS KYVAKKL DSLTQPSQMT KLQLLYYLSL LLGVYENRRV NNKTKLLERL NSPPEILVDG ILSRFTVIKP GQFGRSKDRS YFI DPQNED KILCYILAII MHLDNFIVEI TPLAHELNLK PSKVVSLFRV LGAIVKGATV AQAEAFGIPK STAASYKIAT MKVP FKLPE MTRRGRGPRR

UniProtKB: DNA-directed RNA polymerase I subunit RPA49

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Macromolecule #12: DNA-directed RNA polymerase I subunit RPA34

MacromoleculeName: DNA-directed RNA polymerase I subunit RPA34 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 26.933518 KDa
SequenceString: MSKLSKDYVS DSDSDDEVIS NEFSIPDGFK KCKHLKNFPL NGDNKKKAKQ QQVWLIKFPS NVDISKLKSL PVDFESSTTM TIDKHDYKI MDDTDIESSL TQDNLSNMTL LVPSESKESL KIASTAKDNA PLQFDKVFSV SETAKIPAID YSKVRVPRKD V PKVEGLKL ...String:
MSKLSKDYVS DSDSDDEVIS NEFSIPDGFK KCKHLKNFPL NGDNKKKAKQ QQVWLIKFPS NVDISKLKSL PVDFESSTTM TIDKHDYKI MDDTDIESSL TQDNLSNMTL LVPSESKESL KIASTAKDNA PLQFDKVFSV SETAKIPAID YSKVRVPRKD V PKVEGLKL EHFATGYDAE DFHVAEEVKE NKKEPKKRSH HDDEEESSEK KKKKKEKREK REKKDKKDKK KKHRD

UniProtKB: DNA-directed RNA polymerase I subunit RPA34

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Macromolecule #13: DNA-directed RNA polymerase I subunit RPA14

MacromoleculeName: DNA-directed RNA polymerase I subunit RPA14 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 14.599128 KDa
SequenceString:
MMKGSRRTGN NTATTLNTPV VIHATQLPQH VSTDEVLQFL ESFIDEKENI IDSTTMNTIS GNAADADAAA VANTSLNIDT NLSSSISQL KRIQRDFKGL PPAQDFSAAP IQVSTTEKKE TSIGVSATGG KKTTFADE

UniProtKB: DNA-directed RNA polymerase I subunit RPA14

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Macromolecule #14: DNA-directed RNA polymerase I subunit RPA43

MacromoleculeName: DNA-directed RNA polymerase I subunit RPA43 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 36.264852 KDa
SequenceString: MSQVKRANEN RETARFIKKH KKQVTNPIDE KNGTSNCIVR VPIALYVSLA PMYLENPLQG VMKQHLNPLV MKYNNKVGGV VLGYEGLKI LDADPLSKED TSEKLIKITP DTPFGFTWCH VNLYVWQPQV GDVLEGYIFI QSASHIGLLI HDAFNASIKK N NIPVDWTF ...String:
MSQVKRANEN RETARFIKKH KKQVTNPIDE KNGTSNCIVR VPIALYVSLA PMYLENPLQG VMKQHLNPLV MKYNNKVGGV VLGYEGLKI LDADPLSKED TSEKLIKITP DTPFGFTWCH VNLYVWQPQV GDVLEGYIFI QSASHIGLLI HDAFNASIKK N NIPVDWTF VHNDVEEDAD VINTDENNGN NNNEDNKDSN GGSNSLGKFS FGNRSLGHWV DSNGEPIDGK LRFTVRNVHT TG RVVSVDG TLISDADEEG NGYNSSRSQA ESLPIVSNKK IVFDDEVSIE NKESHKELDL PEVKEDNGSE IVYEENTSES NDG ESSDSD

UniProtKB: DNA-directed RNA polymerase I subunit RPA43

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Macromolecule #15: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 15 / Number of copies: 7 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #16: SULFATE ION

MacromoleculeName: SULFATE ION / type: ligand / ID: 16 / Number of copies: 1 / Formula: SO4
Molecular weightTheoretical: 96.063 Da
Chemical component information

ChemComp-SO4:
SULFATE ION

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 7.8
Component:
ConcentrationName
5.0 mMHepes
150.0 mMPotassium acetate
1.0 mMMagnesium chloride
0.01 mMZinc chloride
0.01 mMbeta-mercaptoethanol
GridModel: Quantifoil, UltrAuFoil, R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot force 13, blotting time 8.5s.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 56.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4c2m

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 94000
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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