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- EMDB-3727: RNA polymerase I pre-initiation complex -

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Basic information

Entry
Database: EMDB / ID: EMD-3727
TitleRNA polymerase I pre-initiation complex
Map data
Sample
  • Complex: RNA polymerase I pre-initiation complex with Core Factor, Rrn3 and transcription scaffold
    • Protein or peptide: x 18 types
    • DNA: x 2 types
  • Complex: RNA polymerase I pre-initiation complex with Core Factor, Rrn3 and transcription scaffold
  • Complex: RNA polymerase I pre-initiation complex with Core Factor, Rrn3 and transcription scaffold
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 / RNA polymerase III complex / transcription by RNA polymerase I / transcription by RNA polymerase III / RNA polymerase II, core complex / TBP-class protein binding / transcription elongation by RNA polymerase II / promoter-specific chromatin binding / 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 / 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. / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / 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-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 ...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 (brewer's yeast) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsSadian Y / Tafur L / Kosinski J / Jakobi AJ / Wetzel R / Buczak K / Hagen WJH / Beck M / Sachse C / Muller CW
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
DepositionMay 17, 2017-
Header (metadata) releaseMay 31, 2017-
Map releaseJul 26, 2017-
UpdateMar 28, 2018-
Current statusMar 28, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5oa1
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3727.png

Downloads & links

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Map

FileDownload / File: emd_3727.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.35 Å
Density
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.037984867 - 0.06979046
Average (Standard dev.)0.00024136012 (±0.0025315944)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 388.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z388.800388.800388.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.0380.0700.000

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Supplemental data

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Sample components

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Entire : RNA polymerase I pre-initiation complex with Core Factor, Rrn3 an...

EntireName: RNA polymerase I pre-initiation complex with Core Factor, Rrn3 and transcription scaffold
Components
  • Complex: RNA polymerase I pre-initiation complex with Core Factor, Rrn3 and transcription scaffold
    • Protein or peptide: RPA1_YEAST DNA-directed RNA polymerase I subunit RPA190
    • Protein or peptide: RPA2_YEAST DNA-directed RNA polymerase I subunit RPA135
    • Protein or peptide: RPA49_YEAST DNA-directed RNA polymerase I subunit
    • Protein or peptide: RPA43_YEAST DNA-directed RNA polymerase I subunit
    • Protein or peptide: RPAC1_YEAST DNA-directed RNA polymerases I and III subunit RPAC1
    • Protein or peptide: RPA34_YEAST DNA-directed RNA polymerase I subunit RPA34
    • Protein or peptide: RPAB1_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC1
    • Protein or peptide: RPAB2_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC2
    • Protein or peptide: RPAC2_YEAST DNA-directed RNA polymerases I and III subunit RPAC2
    • Protein or peptide: RPAB3_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC3
    • Protein or peptide: RPA14_YEAST DNA-directed RNA polymerase I subunit RPA14
    • Protein or peptide: RPA12_YEAST DNA-directed RNA polymerase I subunit RPA12
    • Protein or peptide: RPAB4_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC4
    • Protein or peptide: RPAB5_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC5
    • Protein or peptide: RRN3_YEAST RNA polymerase I-specific transcription initiation factor RRN3
    • Protein or peptide: RRN6_YEAST RNA polymerase I-specific transcription initiation factor RRN6
    • Protein or peptide: RRN7_YEAST RNA polymerase I-specific transcription initiation factor RRN7
    • Protein or peptide: RRN11_YEAST RNA polymerase I-specific transcription initiation factor RRN11
    • DNA: non-template DNA strand
    • DNA: template DNA strand
  • Complex: RNA polymerase I pre-initiation complex with Core Factor, Rrn3 and transcription scaffold
  • Complex: RNA polymerase I pre-initiation complex with Core Factor, Rrn3 and transcription scaffold

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Supramolecule #1: RNA polymerase I pre-initiation complex with Core Factor, Rrn3 an...

SupramoleculeName: RNA polymerase I pre-initiation complex with Core Factor, Rrn3 and transcription scaffold
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 875 MDa

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Supramolecule #2: RNA polymerase I pre-initiation complex with Core Factor, Rrn3 an...

SupramoleculeName: RNA polymerase I pre-initiation complex with Core Factor, Rrn3 and transcription scaffold
type: complex / ID: 2 / Parent: 0 / Macromolecule list: #1-#18
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Supramolecule #3: RNA polymerase I pre-initiation complex with Core Factor, Rrn3 an...

SupramoleculeName: RNA polymerase I pre-initiation complex with Core Factor, Rrn3 and transcription scaffold
type: complex / ID: 3 / Parent: 0 / Macromolecule list: #19-#20
Recombinant expressionOrganism: synthetic construct (others)

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Macromolecule #1: RPA1_YEAST DNA-directed RNA polymerase I subunit RPA190

MacromoleculeName: RPA1_YEAST DNA-directed RNA polymerase I subunit RPA190
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MDISKPVGSE ITSVDFGILT AKEIRNLSAK QITNPTVLDN LGHPVSGGLY DLALGAFLRN LCSTCGLDE KFCPGHQGHI ELPVPCYNPL FFNQLYIYLR ASCLFCHHFR LKSVEVHRYA C KLRLLQYG LIDESYKLDE ITLGSLNSSM YTDDEAIEDN EDEMDGEGSK ...String:
MDISKPVGSE ITSVDFGILT AKEIRNLSAK QITNPTVLDN LGHPVSGGLY DLALGAFLRN LCSTCGLDE KFCPGHQGHI ELPVPCYNPL FFNQLYIYLR ASCLFCHHFR LKSVEVHRYA C KLRLLQYG LIDESYKLDE ITLGSLNSSM YTDDEAIEDN EDEMDGEGSK QSKDISSTLL NE LKSKRSE YVDMAIAKAL SDGRTTERGS FTATVNDERK KLVHEFHKKL LSRGKCDNCG MFS PKFRKD GFTKIFETAL NEKQITNNRV KGFIRQDMIK KQKQAKKLDG SNEASANDEE SFDV GRNPT TRPKTGSTYI LSTEVKNILD TVFRKEQCVL QYVFHSRPNL SRKLVKADSF FMDVL VVPP TRFRLPSKLG EEVHENSQNQ LLSKVLTTSL LIRDLNDDLS KLQKDKVSLE DRRVIF SRL MNAFVTIQND VNAFIDSTKA QGRTSGKVPI PGVKQALEKK EGLFRKHMMG KRVNYAA RS VISPDPNIET NEIGVPPVFA VKLTYPEPVT AYNIAELRQA VINGPDKWPG ATQIQNED G SLVSLIGMSV EQRKALANQL LTPSSNVSTH TLNKKVYRHI KNRDVVLMNR QPTLHKASM MGHKVRVLPN EKTLRLHYAN TGAYNADFDG DEMNMHFPQN ENARAEALNL ANTDSQYLTP TSGSPVRGL IQDHISAGVW LTSKDSFFTR EQYQQYIYGC IRPEDGHTTR SKIVTLPPTI F KPYPLWTG KQIITTVLLN VTPPDMPGIN LISKNKIKNE YWGKGSLENE VLFKDGALLC GI LDKSQYG ASKYGIVHSL HEVYGPEVAA KVLSVLGRLF TNYITATAFT CGMDDLRLTA EGN KWRTDI LKTSVDTGRE AAAEVTNLDK DTPADDPELL KRLQEILRDN NKSGILDAVT SSKV NAITS QVVSKCVPDG TMKKFPCNSM QAMALSGAKG SNVNVSQIMC LLGQQALEGR RVPVM VSGK TLPSFKPYET DAMAGGYVKG RFYSGIKPQE YYFHCMAGRE GLIDTAVKTS RSGYLQ RCL TKQLEGVHVS YDNSIRDADG TLVQFMYGGD AIDITKESHM TQFEFCLDNY YALLKKY NP SALIEHLDVE SALKYSKKTL KYRKKHSKEP HYKQSVKYDP VLAKYNPAKY LGSVSENF Q DKLESFLDKN SKLFKSSDGV NEKKFRALMQ LKYMRSLINP GEAVGIIASQ SVGEPSTQM TLNTFHFAGH GAANVTLGIP RLREIVMTAS AAIKTPQMTL PIWNDVSDEQ ADTFCKSISK VLLSEVIDK VIVTETTGTS NTAGGNAARS YVIHMRFFDN NEYSEEYDVS KEELQNVISN Q FIHLLEAA IVKEIKKQKR TTGPDIGVAV PRLQTDVANS SSNSKRLEED NDEEQSHKKT KQ AVSYDEP DEDEIETMRE AEKSSDEEGI DSDKESDSDS EDEDVDMNEQ INKSIVEANN NMN KVQRDR QSAIISHHRF ITKYNFDDES GKWCEFKLEL AADTEKLLMV NIVEEICRKS IIRQ IPHID RCVHPEPENG KRVLVTEGVN FQAMWDQEAF IDVDGITSND VAAVLKTYGV EAARN TIVN EINNVFSRYA ISVSFRHLDL IADMMTRQGT YLAFNRQGME TSTSSFMKMS YETTCQ FLT KAVLDNEREQ LDSPSARIVV GKLNNVGTGS FDVLAKVPNA A

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Macromolecule #2: RPA2_YEAST DNA-directed RNA polymerase I subunit RPA135

MacromoleculeName: RPA2_YEAST DNA-directed RNA polymerase I subunit RPA135
type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSKVIKPPGQ ARTADFRTLE RESRFINPPK DKSAFPLLQE AVQPHIGSFN ALTEGPDGGL LNLGVKDIG EKVIFDGKPL NSEDEISNSG YLGNKLSVSV EQVSIAKPMS NDGVSSAVER K VYPSESRQ RLTSYRGKLL LKLKWSVNNG EENLFEVRDC GGLPVMLQSN ...String:
MSKVIKPPGQ ARTADFRTLE RESRFINPPK DKSAFPLLQE AVQPHIGSFN ALTEGPDGGL LNLGVKDIG EKVIFDGKPL NSEDEISNSG YLGNKLSVSV EQVSIAKPMS NDGVSSAVER K VYPSESRQ RLTSYRGKLL LKLKWSVNNG EENLFEVRDC GGLPVMLQSN RCHLNKMSPY EL VQHKEES DEIGGYFIVN GIEKLIRMLI VQRRNHPMAI IRPSFANRGA SYSHYGIQIR SVR PDQTSQ TNVLHYLNDG QVTFRFSWRK NEYLVPVVMI LKALCHTSDR EIFDGIIGND VKDS FLTDR LELLLRGFKK RYPHLQNRTQ VLQYLGDKFR VVFQASPDQS DLEVGQEVLD RIVLV HLGK DGSQDKFRML LFMIRKLYSL VAGECSPDNP DATQHQEVLL GGFLYGMILK EKIDEY LQN IIAQVRMDIN RGMAINFKDK RYMSRVLMRV NENIGSKMQY FLSTGNLVSQ SGLDLQQ VS GYTVVAEKIN FYRFISHFRM VHRGSFFAQL KTTTVRKLLP ESWGFLCPVH TPDGSPCG L LNHFAHKCRI STQQSDVSRI PSILYSLGVA PASHTFAAGP SLCCVQIDGK IIGWVSHEQ GKIIADTLRY WKVEGKTPGL PIDLEIGYVP PSTRGQYPGL YLFGGHSRML RPVRYLPLDK EDIVGPFEQ VYMNIAVTPQ EIQNNVHTHV EFTPTNILSI LANLTPFSDF NQSPRNMYQC Q MGKQTMGT PGVALCHRSD NKLYRLQTGQ TPIVKANLYD DYGMDNFPNG FNAVVAVISY TG YDMDDAM IINKSADERG FGYGTMYKTE KVDLALNRNR GDPITQHFGF GNDEWPKEWL EKL DEDGLP YIGTYVEEGD PICAYFDDTL NKTKIKTYHS SEPAYIEEVN LIGDESNKFQ ELQT VSIKY RIRRTPQIGD KFSSRHGQKG VCSRKWPTID MPFSETGIQP DIIINPHAFP SRMTI GMFV ESLAGKAGAL HGIAQDSTPW IFNEDDTPAD YFGEQLAKAG YNYHGNEPMY SGATGE ELR ADIYVGVVYY QRLRHMVNDK FQVRSTGPVN SLTMQPVKGR KRHGGIRVGE MERDALI GH GTSFLLQDRL LNSSDYTQAS VCRECGSILT TQQSVPRIGS ISTVCCRRCS MRFEDAKK L LTKSEDGEKI FIDDSQIWED GQGNKFVGGN ETTTVAIPFV LKYLDSELSA MGIRLRYNV EPK

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Macromolecule #3: RPA49_YEAST DNA-directed RNA polymerase I subunit

MacromoleculeName: RPA49_YEAST DNA-directed RNA polymerase I subunit / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSVKRSVSEI EIESVQDQPS VAVGSFFKGF RAPSDTTFDL YKKKKSEKDE FVLHGENERL EYEGYTDSS SQASNQYVVG LFNPEKKSIQ LYKAPVLVSK VVSKSSKNLR GPKIKSKSDT R PSALRNAL GEAFGTKKAK KAIADLERNR IDSDKLTDSA IDIVDSVRTA ...String:
MSVKRSVSEI EIESVQDQPS VAVGSFFKGF RAPSDTTFDL YKKKKSEKDE FVLHGENERL EYEGYTDSS SQASNQYVVG LFNPEKKSIQ LYKAPVLVSK VVSKSSKNLR GPKIKSKSDT R PSALRNAL GEAFGTKKAK KAIADLERNR IDSDKLTDSA IDIVDSVRTA SKDLPTRAQL DE ITSNDRP TPLANIDATD VEQIYPIESI IPKKELQFIR VSSILKEADK EKKLELFPYQ NNS KYVAKK LDSLTQPSQM TKLQLLYYLS LLLGVYENRR VNNKTKLLER LNSPPEILVD GILS RFTVI KPGQFGRSKD RSYFIDPQNE DKILCYILAI IMHLDNFIVE ITPLAHELNL KPSKV VSLF RVLGAIVKGA TVAQAEAFGI PKSTAASYKI ATMKVPFKLP EMTRRGRGPR R

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Macromolecule #4: RPA43_YEAST DNA-directed RNA polymerase I subunit

MacromoleculeName: RPA43_YEAST DNA-directed RNA polymerase I subunit / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSQVKRANEN RETARFIKKH KKQVTNPIDE KNGTSNCIVR VPIALYVSLA PMYLENPLQG VMKQHLNPL VMKYNNKVGG VVLGYEGLKI LDADPLSKED TSEKLIKITP DTPFGFTWCH V NLYVWQPQ VGDVLEGYIF IQSASHIGLL IHDAFNASIK KNNIPVDWTF ...String:
MSQVKRANEN RETARFIKKH KKQVTNPIDE KNGTSNCIVR VPIALYVSLA PMYLENPLQG VMKQHLNPL VMKYNNKVGG VVLGYEGLKI LDADPLSKED TSEKLIKITP DTPFGFTWCH V NLYVWQPQ VGDVLEGYIF IQSASHIGLL IHDAFNASIK KNNIPVDWTF VHNDVEEDAD VI NTDENNG NNNNEDNKDS NGGSNSLGKF SFGNRSLGHW VDSNGEPIDG KLRFTVRNVH TTG RVVSVD GTLISDADEE GNGYNSSRSQ AESLPIVSNK KIVFDDEVSI ENKESHKELD LPEV KEDNG SEIVYEENTS ESNDGESSDS D

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Macromolecule #5: RPAC1_YEAST DNA-directed RNA polymerases I and III subunit RPAC1

MacromoleculeName: RPAC1_YEAST DNA-directed RNA polymerases I and III subunit RPAC1
type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSNIVGIEYN RVTNTTSTDF PGFSKDAENE WNVEKFKKDF EVNISSLDAR EANFDLINID TSIANAFRR IMISEVPSVA AEYVYFFNNT SVIQDEVLAH RIGLVPLKVD PDMLTWVDSN L PDDEKFTD ENTIVLSLNV KCTRNPDAPK GSTDPKELYN NAHVYARDLK ...String:
MSNIVGIEYN RVTNTTSTDF PGFSKDAENE WNVEKFKKDF EVNISSLDAR EANFDLINID TSIANAFRR IMISEVPSVA AEYVYFFNNT SVIQDEVLAH RIGLVPLKVD PDMLTWVDSN L PDDEKFTD ENTIVLSLNV KCTRNPDAPK GSTDPKELYN NAHVYARDLK FEPQGRQSTT FA DCPVVPA DPDILLAKLR PGQEISLKAH CILGIGGDHA KFSPVSTASY RLLPQINILQ PIK GESARR FQKCFPPGVI GIDEGSDEAY VKDARKDTVS REVLRYEEFA DKVKLGRVRN HFIF NVESA GAMTPEEIFF KSVRILKNKA EYLKNCPITQ

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Macromolecule #6: RPA34_YEAST DNA-directed RNA polymerase I subunit RPA34

MacromoleculeName: RPA34_YEAST DNA-directed RNA polymerase I subunit RPA34
type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSKLSKDYVS DSDSDDEVIS NEFSIPDGFK KCKHLKNFPL NGDNKKKAKQ QQVWLIKFPS NVDISKLKS LPVDFESSTT MTIDKHDYKI MDDTDIESSL TQDNLSNMTL LVPSESKESL K IASTAKDN APLQFDKVFS VSETAKIPAI DYSKVRVPRK DVPKVEGLKL ...String:
MSKLSKDYVS DSDSDDEVIS NEFSIPDGFK KCKHLKNFPL NGDNKKKAKQ QQVWLIKFPS NVDISKLKS LPVDFESSTT MTIDKHDYKI MDDTDIESSL TQDNLSNMTL LVPSESKESL K IASTAKDN APLQFDKVFS VSETAKIPAI DYSKVRVPRK DVPKVEGLKL EHFATGYDAE DF HVAEEVK ENKKEPKKRS HHDDEEESSE KKKKKKEKRE KREKKDKKDK KKKHRD

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Macromolecule #7: RPAB1_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC1

MacromoleculeName: RPAB1_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC1
type: protein_or_peptide / ID: 7 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MDQENERNIS RLWRAFRTVK EMVKDRGYFI TQEEVELPLE DFKAKYCDSM GRPQRKMMSF QANPTEESI SKFPDMGSLW VEFCDEPSVG VKTMKTFVIH IQEKNFQTGI FVYQNNITPS A MKLVPSIP PATIETFNEA ALVVNITHHE LVPKHIRLSS DEKRELLKRY ...String:
MDQENERNIS RLWRAFRTVK EMVKDRGYFI TQEEVELPLE DFKAKYCDSM GRPQRKMMSF QANPTEESI SKFPDMGSLW VEFCDEPSVG VKTMKTFVIH IQEKNFQTGI FVYQNNITPS A MKLVPSIP PATIETFNEA ALVVNITHHE LVPKHIRLSS DEKRELLKRY RLKESQLPRI QR ADPVALY LGLKRGEVVK IIRKSETSGR YASYRICM

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Macromolecule #8: RPAB2_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC2

MacromoleculeName: RPAB2_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC2
type: protein_or_peptide / ID: 8 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
MSDYEEAFND GNENFEDFDV EHFSDEETYE EKPQFKDGET TDANGKTIVT GGNGPEDFQQ HEQIRRKTL KEKAIPKDQR ATTPYMTKYE RARILGTRAL QISMNAPVFV DLEGETDPLR I AMKELAEK KIPLVIRRYL PDGSFEDWSV EELIVDL

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Macromolecule #9: RPAC2_YEAST DNA-directed RNA polymerases I and III subunit RPAC2

MacromoleculeName: RPAC2_YEAST DNA-directed RNA polymerases I and III subunit RPAC2
type: protein_or_peptide / ID: 9 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
MTEDIEQKKT ATEVTPQEPK HIQEEEEQDV DMTGDEEQEE EPDREKIKLL TQATSEDGTS ASFQIVEED HTLGNALRYV IMKNPDVEFC GYSIPHPSEN LLNIRIQTYG ETTAVDALQK G LKDLMDLC DVVESKFTEK IKSM

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Macromolecule #10: RPAB3_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC3

MacromoleculeName: RPAB3_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC3
type: protein_or_peptide / ID: 10 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
MSNTLFDDIF QVSEVDPGRY NKVCRIEAAS TTQDQCKLTL DINVELFPVA AQDSLTVTIA SSLNLEDTP ANDSSATRSW RPPQAGDRSL ADDYDYVMYG TAYKFEEVSK DLIAVYYSFG G LLMRLEGN YRNLNNLKQE NAYLLIRR

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Macromolecule #11: RPA14_YEAST DNA-directed RNA polymerase I subunit RPA14

MacromoleculeName: RPA14_YEAST DNA-directed RNA polymerase I subunit RPA14
type: protein_or_peptide / ID: 11 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
MMKGSRRTGN NTATTLNTPV VIHATQLPQH VSTDEVLQFL ESFIDEKENI IDSTTMNTIS GNAADADAA AVANTSLNID TNLSSSISQL KRIQRDFKGL PPAQDFSAAP IQVSTTEKKE T SIGVSATG GKKTTFADE

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Macromolecule #12: RPA12_YEAST DNA-directed RNA polymerase I subunit RPA12

MacromoleculeName: RPA12_YEAST DNA-directed RNA polymerase I subunit RPA12
type: protein_or_peptide / ID: 12 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
MSVVGSLIFC LDCGDLLENP NAVLGSNVEC SQCKAIYPKS QFSNLKVVTT TADDAFPSSL RAKKSVVKT SLKKNELKDG ATIKEKCPQC GNEEMNYHTL QLRSADEGAT VFYTCTSCGY K FRTNN

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Macromolecule #13: RPAB4_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC4

MacromoleculeName: RPAB4_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC4
type: protein_or_peptide / ID: 13 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
MSREGFQIPT NLDAAAAGTS QARTATLKYI CAECSSKLSL SRTDAVRCKD CGHRILLKAR TKRLVQFEA R

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Macromolecule #14: RPAB5_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC5

MacromoleculeName: RPAB5_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC5
type: protein_or_peptide / ID: 14 / Enantiomer: DEXTRO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
MIVPVRCFSC GKVVGDKWES YLNLLQEDEL DEGTALSRLG LKRYCCRRMI LTHVDLIEKF LRYNPLEKR D

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Macromolecule #15: RRN3_YEAST RNA polymerase I-specific transcription initiation fac...

MacromoleculeName: RRN3_YEAST RNA polymerase I-specific transcription initiation factor RRN3
type: protein_or_peptide / ID: 15 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MMAFENTSKR PPQDFVAPID QKKRKVQFSD STGLVTLQPE EIKDEVFSAA MYSRFVKSAL DDLDKNDST QIGIIANQVA LPSKNPERIN DKNLNILLDI LSSNINRIES SRGTFLIQSI I NFEKWWEL PPHTLSKYIY FIKILCSSIP KWWQDVSMIL VSCFILPIKQ ...String:
MMAFENTSKR PPQDFVAPID QKKRKVQFSD STGLVTLQPE EIKDEVFSAA MYSRFVKSAL DDLDKNDST QIGIIANQVA LPSKNPERIN DKNLNILLDI LSSNINRIES SRGTFLIQSI I NFEKWWEL PPHTLSKYIY FIKILCSSIP KWWQDVSMIL VSCFILPIKQ TVCHHDMLKY FL RMIPSSM GFIDTYLAKF FPNKNDTRRK LVNYTSNLLK LRGYCSELGF QIWSLLIEKI ISI DVELQN ELDELDDDVD DDDLEEVDLE DDDDLDDDSG DDDDENCGNS NEELRSGAAD GSQS DSEDM DIIEGMDGTE EYNVELTQGI KELSTKLDSI LTLVSTHVEE QVTPESLESG EGVGV FNTL TTLFKTHVLP TYYTRSIQYI MFHVSQQQLE LMDSFLVTLI DISFAVNEAA EKKIKS LQY LGSYIARAKK LSRTQIIFVA SYLTSWLNRY VIEREEEVDQ RGGMERFKHF YAAFQAL CY IFCFRHNIFR DTDGNWECEL DKFFQRMVIS KFNPLKFCNE NVMLMFARIA QQESVAYC F SIIENNNNER LRGIIGKADS DKKENSAQAN TTSSSWSLAT RQQFIDLQSY FPYDPLFLK NYKILMKEYY IEWSEASGEY ESDGSDD

+
Macromolecule #16: RRN6_YEAST RNA polymerase I-specific transcription initiation fac...

MacromoleculeName: RRN6_YEAST RNA polymerase I-specific transcription initiation factor RRN6
type: protein_or_peptide / ID: 16 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSEGQIPSSD VLGSQLGVGV QGASLYCPQE NYTTKKQEKP QWLRPVDDTL AEDALDLHIV VKSLLCDTA IRYISDDKVL QESDADDDLI TSDIDEDTDN QGDTSIVVNP VIPVVPKDVH F FKKVDVGN DSMFGVNCDT PVSFQDYIPS DLLRNLDDTL QESTNSSRPM ...String:
MSEGQIPSSD VLGSQLGVGV QGASLYCPQE NYTTKKQEKP QWLRPVDDTL AEDALDLHIV VKSLLCDTA IRYISDDKVL QESDADDDLI TSDIDEDTDN QGDTSIVVNP VIPVVPKDVH F FKKVDVGN DSMFGVNCDT PVSFQDYIPS DLLRNLDDTL QESTNSSRPM QDAFFWDPTV AN RLDSQYI QTASDLRNYR DGTEIIAYAS GKTGSVLNIA VLTRQNTLHL NRHNNVTSIE LHS PIKSIK IPGASESIGR RSNLVGIITE NSFQIFRIES VHSRSCDVMV SSSEPLYFVE IDDL QVVDF AFNPWDLQQF AIIDIKGNWS IGRIPKNFNN NNKRKLQLID NLHGTIFDPE ELSSW KRIE WFSHFQKILV FDRSKMIEID FMNNWQTEVV QAKAWSNIRD YKRIDDKNGI LLTSRE III VGASESNDPV RRISWKHDLD PDDTTLRITV QKVKKPDHIL LVAFVYSMRH KRIYMHV FS HRKANLFQSL GCSTVLEIPG GTPTGIETIL TLDHIDDESR REEDADENFE LVVDFLVK L RNSSEVYYYA LSNTQNSEPN KQETPIIVDH PEWASLFNNA DEREKESIGA LVSQIKLKE RERISRVQNL IEHENSHDED KYLQDLGYRL SIATNELLES WQKTKDESIL SGSLSHSKLK NLLENSDSF ASIPEFSSLL DQFFQYYQDQ DVTFIGFEKL LHLFLHEDVP GLDIFYNKLL Q CWVLVSPQ AELLTKEIVK DIIWSLARLE KPSLFEPIQN EISRSLSGPY QDIISSWDMD DI NEEDESN EFNFDSQFSA PFNGRPPFNL NSQSQIPTIK SSQSSGLARR KRILKTQSQK ATP LSQSTQ NLSVLPDSMT PAFTLMQPPS SQISFVNDSQ PRNSQKAKKK KKRIRGFG

+
Macromolecule #17: RRN7_YEAST RNA polymerase I-specific transcription initiation fac...

MacromoleculeName: RRN7_YEAST RNA polymerase I-specific transcription initiation factor RRN7
type: protein_or_peptide / ID: 17 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSTFIRGPIC GTDNCPSRLW RIIDGRRTCQ YGHVMEGDVE FNDDEDDLNG LGAGVITRRL NLTTNATGS FQSSQLTNSQ LLQQQQRQSH KKFKKLIGHE AKLLFLKSFQ FILKRQIRWL I TEMRFPKE FEHVAKIIWL KILKTINDQP QEELKLQLHM TSTISILYLA ...String:
MSTFIRGPIC GTDNCPSRLW RIIDGRRTCQ YGHVMEGDVE FNDDEDDLNG LGAGVITRRL NLTTNATGS FQSSQLTNSQ LLQQQQRQSH KKFKKLIGHE AKLLFLKSFQ FILKRQIRWL I TEMRFPKE FEHVAKIIWL KILKTINDQP QEELKLQLHM TSTISILYLA STHLSLPVYT CD YIKWICT AKMPYFQASE ILPKSWRIQL PNYYVSILEG SISPFNGQLY NKIALTCGMI HFK EFFNSE ISCQGLLLKL VMQCALPPEF YFYTKQVIEF EETDIRNLTL WERTDERHTG RVSN HAELR VLSYFMLTIN WMLSFDRDRQ YPLKWILSLT ESLTQRTTTS ESIGRNIVKV VYPDK PTSS DYFQWSEEET LEFLKWMEKQ FLPTQTKSLH NENGSMEMTI DQKIARRKLY KIFPLD REA NHDGEFNDST HQLTFIEDLQ ERYAKQTPFF ESNKIRDSLN YQEANPPARK EAIGRLL TH IASQLLVDFA ISKEQLKDCI SRIKNACLHR MN

+
Macromolecule #18: RRN11_YEAST RNA polymerase I-specific transcription initiation fa...

MacromoleculeName: RRN11_YEAST RNA polymerase I-specific transcription initiation factor RRN11
type: protein_or_peptide / ID: 18 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MFEVPITLTN RKFAQRRKLK YQYINYISRR FDRISKKSTT TDSLPTPENS AAENNDEEEG QNSEAGTYR RSVLQQKKRR RERHWRSVVG EIYSTTESET DSQEEETEEG GEHDTGIDKE D SDEERKFW KKYEKPEKSF EIWRTVSSQN KQPINKQKMT YHNFKKIEKI ...String:
MFEVPITLTN RKFAQRRKLK YQYINYISRR FDRISKKSTT TDSLPTPENS AAENNDEEEG QNSEAGTYR RSVLQQKKRR RERHWRSVVG EIYSTTESET DSQEEETEEG GEHDTGIDKE D SDEERKFW KKYEKPEKSF EIWRTVSSQN KQPINKQKMT YHNFKKIEKI PLRKMEIPLL HC TKENKLY FQSISRGLEP LKTSTSEVRN YRTRHIVTLT DLLHLNVSRH NWSLAYKIFA TLI RIPGVQ IKSLWGIGVE ILDNLSNSSS GLDFLQWMCQ IYSSKSRFVQ NINYRSIVPP FQTG SRTHT AKFAITYLWS SLINCQKSME PSSNIIDKPF DTENDLLQEL IDKISEWVLT PPFME DAEV WFIYASCHLL KADTLSRQFV NDNKNNDLIG LDRDIKINQV IKHIHYVRTF LKICLD KGG FAVPSRLIEN QLKSFESRLY GEAQDIQERD VANVYDSIDN SSVENSFGDV YETNAEF LD TQLMDLSPED NGLDEMHYSD EDSSE

+
Macromolecule #19: non-template DNA strand

MacromoleculeName: non-template DNA strand / type: dna / ID: 19 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
SequenceString:
GGTTTAGTCA TGGAGTACAA GTGTGAGGAA AAGTAGTTGG CGTAGCAGGA GAAGTAAAGC AGTTGAAGAC

+
Macromolecule #20: template DNA strand

MacromoleculeName: template DNA strand / type: dna / ID: 20 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
SequenceString:
CCAAATCAGT ACCTCATGTT CACACTCCTT TTCATCAACC CTCCATGAAG TACGCTTTCG TCAACTTCTG

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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

Concentration0.2 mg/mL
BufferpH: 7.5
GridMaterial: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 105000
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 4235 / Average exposure time: 20.0 sec. / Average electron dose: 2.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4)
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 38589

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