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- EMDB-8777: Pol I Initial Transcribing Complex with a truncated scaffold at 6... -

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Basic information

Entry
Database: EMDB / ID: EMD-8777
TitlePol I Initial Transcribing Complex with a truncated scaffold at 6.9 angstrom
Map dataRNA polymerase I Initial Transcribing Complex with a truncated scaffold
Sample
  • Complex: RNA Polymerase I Initial Transcribing Complex with a truncated scaffold
    • Protein or peptide: x 17 types
    • RNA: x 1 types
    • DNA: x 3 types
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 general transcription initiation factor activity / RNA polymerase I general transcription initiation factor 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 ...RNA polymerase I transcription regulatory region sequence-specific DNA binding / RNA polymerase I core factor complex / RNA polymerase I general transcription initiation factor activity / RNA polymerase I general transcription initiation factor 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 / 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 / : / 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 / 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
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 ...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 / 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. / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / 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
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 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase I-specific transcription initiation factor RRN7 / DNA-directed RNA polymerase I subunit RPA43 / DNA-directed RNA polymerase I subunit RPA34 / DNA-directed RNA polymerase I subunit RPA14 / DNA-directed RNA polymerase I subunit RPA49 / RNA polymerase I-specific transcription initiation factor RRN11
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.9 Å
AuthorsHan Y / He Y
Funding support United States, 5 items
OrganizationGrant numberCountry
Northwestern UniversityCornew Innovation Award United States
National Institutes of Health/National Cancer Institute (NIH/NCI)NCI 5K22CA184235 United States
American Cancer SocietyIRG-15-173-21 United States
National Science Foundation (NSF, United States)MCB-1149521 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIGMS GM110387 United States
CitationJournal: Elife / Year: 2017
Title: Structural mechanism of ATP-independent transcription initiation by RNA polymerase I.
Authors: Yan Han / Chunli Yan / Thi Hoang Duong Nguyen / Ashleigh J Jackobel / Ivaylo Ivanov / Bruce A Knutson / Yuan He /
Abstract: Transcription initiation by RNA Polymerase I (Pol I) depends on the Core Factor (CF) complex to recognize the upstream promoter and assemble into a Pre-Initiation Complex (PIC). Here, we solve a ...Transcription initiation by RNA Polymerase I (Pol I) depends on the Core Factor (CF) complex to recognize the upstream promoter and assemble into a Pre-Initiation Complex (PIC). Here, we solve a structure of Pol I-CF-DNA to 3.8 Å resolution using single-particle cryo-electron microscopy. The structure reveals a bipartite architecture of Core Factor and its recognition of the promoter from -27 to -16. Core Factor's intrinsic mobility correlates well with different conformational states of the Pol I cleft, in addition to the stabilization of either Rrn7 N-terminal domain near Pol I wall or the tandem winged helix domain of A49 at a partially overlapping location. Comparison of the three states in this study with the Pol II system suggests that a ratchet motion of the Core Factor-DNA sub-complex at upstream facilitates promoter melting in an ATP-independent manner, distinct from a DNA translocase actively threading the downstream DNA in the Pol II PIC.
History
DepositionJun 16, 2017-
Header (metadata) releaseJul 5, 2017-
Map releaseJul 5, 2017-
UpdateDec 25, 2019-
Current statusDec 25, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.07
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8777.png

Downloads & links

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Map

FileDownload / File: emd_8777.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRNA polymerase I Initial Transcribing Complex with a truncated scaffold
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.36 Å/pix.
x 128 pix.
= 302.08 Å		2.36 Å/pix.
x 128 pix.
= 302.08 Å		2.36 Å/pix.
x 128 pix.
= 302.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07 / Movie #1: 0.07
Minimum - Maximum-0.10179037 - 0.23072258
Average (Standard dev.)0.0028788708 (±0.015079218)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 302.08 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.362.362.36
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z302.080302.080302.080
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ281156
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-0.1020.2310.003

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Supplemental data

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Sample components

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Entire : RNA Polymerase I Initial Transcribing Complex with a truncated sc...

EntireName: RNA Polymerase I Initial Transcribing Complex with a truncated scaffold
Components
  • Complex: RNA Polymerase I Initial Transcribing Complex with a truncated scaffold
    • 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 polymerase I subunit RPA14
    • 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 polymerase I subunit RPA43
    • 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: RNA polymerase I-specific transcription initiation factor RRN6
    • Protein or peptide: RNA polymerase I-specific transcription initiation factor RRN7
    • Protein or peptide: RNA polymerase I-specific transcription initiation factor RRN11
    • RNA: RNA
    • DNA: template strand DNA
    • DNA: upstream non-template strand DNA
    • DNA: downstream non-template strand DNA

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Supramolecule #1: RNA Polymerase I Initial Transcribing Complex with a truncated sc...

SupramoleculeName: RNA Polymerase I Initial Transcribing Complex with a truncated scaffold
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
Molecular weightTheoretical: 900 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 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (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: DNA-directed RNA polymerase I subunit RPA135

MacromoleculeName: DNA-directed RNA polymerase I subunit RPA135 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (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: 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 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (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 #4: DNA-directed RNA polymerase I subunit RPA14

MacromoleculeName: DNA-directed RNA polymerase I subunit RPA14 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
SequenceString:
MMKGSRRTGN NTATTLNTPV VIHATQLPQH VSTDEVLQFL ESFIDEKENI IDSTTMNTIS GNAADADAA AVANTSLNID TNLSSSISQL KRIQRDFKGL PPAQDFSAAP IQVSTTEKKE T SIGVSATG GKKTTFADE

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Macromolecule #5: 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: 5 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (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 #6: 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: 6 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
SequenceString:
MSDYEEAFND GNENFEDFDV EHFSDEETYE EKPQFKDGET TDANGKTIVT GGNGPEDFQQ HEQIRRKTL KEKAIPKDQR ATTPYMTKYE RARILGTRAL QISMNAPVFV DLEGETDPLR I AMKELAEK KIPLVIRRYL PDGSFEDWSV EELIVDL

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Macromolecule #7: DNA-directed RNA polymerase I subunit RPA43

MacromoleculeName: DNA-directed RNA polymerase I subunit RPA43 / type: protein_or_peptide / ID: 7 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (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 #8: 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: 8 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
SequenceString:
MSNTLFDDIF QVSEVDPGRY NKVCRIEAAS TTQDQCKLTL DINVELFPVA AQDSLTVTIA SSLNLEDTP ANDSSATRSW RPPQAGDRSL ADDYDYVMYG TAYKFEEVSK DLIAVYYSFG G LLMRLEGN YRNLNNLKQE NAYLLIRR

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Macromolecule #9: DNA-directed RNA polymerase I subunit RPA12

MacromoleculeName: DNA-directed RNA polymerase I subunit RPA12 / type: protein_or_peptide / ID: 9 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
SequenceString:
MSVVGSLIFC LDCGDLLENP NAVLGSNVEC SQCKAIYPKS QFSNLKVVTT TADDAFPSSL RAKKSVVKT SLKKNELKDG ATIKEKCPQC GNEEMNYHTL QLRSADEGAT VFYTCTSCGY K FRTNN

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Macromolecule #10: 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: 10 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
SequenceString:
MIVPVRCFSC GKVVGDKWES YLNLLQEDEL DEGTALSRLG LKRYCCRRMI LTHVDLIEKF LRYNPLEKR D

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Macromolecule #11: DNA-directed RNA polymerases I and III subunit RPAC2

MacromoleculeName: DNA-directed RNA polymerases I and III subunit RPAC2 / type: protein_or_peptide / ID: 11 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
SequenceString:
MTEDIEQKKT ATEVTPQEPK HIQEEEEQDV DMTGDEEQEE EPDREKIKLL TQATSEDGTS ASFQIVEED HTLGNALRYV IMKNPDVEFC GYSIPHPSEN LLNIRIQTYG ETTAVDALQK G LKDLMDLC DVVESKFTEK IKSM

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Macromolecule #12: 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: 12 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
SequenceString:
MSREGFQIPT NLDAAAAGTS QARTATLKYI CAECSSKLSL SRTDAVRCKD CGHRILLKAR TKRLVQFEA R

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Macromolecule #13: DNA-directed RNA polymerase I subunit RPA49

MacromoleculeName: DNA-directed RNA polymerase I subunit RPA49 / type: protein_or_peptide / ID: 13 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (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 #14: DNA-directed RNA polymerase I subunit RPA34

MacromoleculeName: DNA-directed RNA polymerase I subunit RPA34 / type: protein_or_peptide / ID: 14 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (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 #15: RNA polymerase I-specific transcription initiation factor RRN6

MacromoleculeName: RNA polymerase I-specific transcription initiation factor RRN6
type: protein_or_peptide / ID: 15 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
Recombinant expressionOrganism: Escherichia coli (E. coli)
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

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Macromolecule #16: RNA polymerase I-specific transcription initiation factor RRN7

MacromoleculeName: RNA polymerase I-specific transcription initiation factor RRN7
type: protein_or_peptide / ID: 16 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
Recombinant expressionOrganism: Escherichia coli (E. coli)
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

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Macromolecule #17: RNA polymerase I-specific transcription initiation factor RRN11

MacromoleculeName: RNA polymerase I-specific transcription initiation factor RRN11
type: protein_or_peptide / ID: 17 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
Recombinant expressionOrganism: Escherichia coli (E. coli)
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

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Macromolecule #18: RNA

MacromoleculeName: RNA / type: rna / ID: 18
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
SequenceString:
AUGCGA

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Macromolecule #19: template strand DNA

MacromoleculeName: template strand DNA / type: dna / ID: 19 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
SequenceString:
TGTCTTCAAC TGCTTTCGCA TGAAGTACCT CCCAACTACT TTTCCTCACA CTTG

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Macromolecule #20: upstream non-template strand DNA

MacromoleculeName: upstream non-template strand DNA / type: dna / ID: 20 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
SequenceString:
TGAGGAAAAG TAGTTGGG

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Macromolecule #21: downstream non-template strand DNA

MacromoleculeName: downstream non-template strand DNA / type: dna / ID: 21 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
SequenceString:
GCAGTTGAAG ACA

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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

BufferpH: 7.6
GridModel: Quantifoil S7/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy

MicroscopeJEOL 3200FS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average exposure time: 12.0 sec. / Average electron dose: 17.2 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 5.0 µm / Calibrated defocus min: 2.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal magnification: 15000
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN

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Image processing

CTF correctionSoftware - Name: Gctf (ver. 0.5)
Details: CTF amplitude correction was performed following 3D auto refinement in relion.
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4c3i

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 43843
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 2.0)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.0)
Final 3D classificationNumber classes: 5 / Software - Name: RELION (ver. 2.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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