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- EMDB-3957: Apo RNA Polymerase III - open conformation (oPOL3) -

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Basic information

Entry
Database: EMDB / ID: EMD-3957
TitleApo RNA Polymerase III - open conformation (oPOL3)
Map data
Sample
  • Complex: Apo RNA Polymerase III - Open Conformation
    • Protein or peptide: x 17 types
  • Ligand: x 2 types
KeywordsRNA Pol III / promoter opening / transcription
Function / homology
Function and homology information


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 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 / RNA Polymerase II Pre-transcription Events / RNA-templated transcription / termination of RNA polymerase III transcription / Formation of TC-NER Pre-Incision Complex / transcription initiation at RNA polymerase III promoter / RNA polymerase III activity / termination of RNA polymerase I transcription / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription by RNA polymerase I / transcription initiation at RNA polymerase I promoter / Estrogen-dependent gene expression / transcription by RNA polymerase III / Dual incision in TC-NER / transcription elongation by RNA polymerase I / tRNA transcription by RNA polymerase III / RNA polymerase I complex / RNA polymerase I activity / RNA polymerase III complex / RNA polymerase II, core complex / nucleotidyltransferase activity / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / peroxisome / ribosome biogenesis / single-stranded DNA binding / transcription by RNA polymerase II / nucleic acid binding / protein dimerization activity / nucleotide binding / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
DNA-directed RNA polymerase III subunit RPC4 / RNA polymerase III RPC4 / DNA-directed RNA polymerase III, subunit Rpc31 / DNA-directed RNA polymerase III subunit Rpc31 / Pol III subunit C11, C-terminal zinc ribbon / DNA-directed RNA polymerase III subunit Rpc5 / DNA-directed RNA polymerase III subunit RPC1, N-terminal / DNA-directed RNA polymerase III subunit RPC1, C-terminal / RPC5 protein / RNA polymerase III, subunit Rpc25 ...DNA-directed RNA polymerase III subunit RPC4 / RNA polymerase III RPC4 / DNA-directed RNA polymerase III, subunit Rpc31 / DNA-directed RNA polymerase III subunit Rpc31 / Pol III subunit C11, C-terminal zinc ribbon / DNA-directed RNA polymerase III subunit Rpc5 / DNA-directed RNA polymerase III subunit RPC1, N-terminal / DNA-directed RNA polymerase III subunit RPC1, C-terminal / RPC5 protein / RNA polymerase III, subunit Rpc25 / DNA-directed RNA polymerase III subunit RPC9 / RNA polymerase III subunit Rpc25 / RNA polymerase Rpc34 / RNA polymerase III Rpc82, C -terminal / RNA polymerase Rpc34-like / DNA-directed RNA polymerase III subunit RPC3 / RNA polymerase Rpc34 subunit / RNA polymerase III subunit RPC82 / DNA-directed RNA polymerase III subunit RPC3, helical hairpin domain / POLR3C, C-terminal winged-helix domain / RNA polymerase III subunit RPC82-related, helix-turn-helix / RNA polymerase III subunit RPC82 helix-turn-helix domain / DNA-directed RNA polymerase, subunit E/RPC8 / DNA-directed RNA polymerases I and III subunit AC19 / DNA-directed RNA polymerases I and III subunit AC40 / Rpb4/RPC9 superfamily / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / HRDC-like superfamily / 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 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / 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 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, subunit RPB6 / 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 / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / 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 / 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. / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / 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, alpha subunit
Similarity search - Domain/homology
DNA-directed RNA polymerase III subunit RPC1 / DNA-directed RNA polymerases I and III subunit RPAC1 / DNA-directed RNA polymerase III subunit RPC7 / 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 polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase III subunit RPC2 / DNA-directed RNA polymerase III subunit RPC4 / DNA-directed RNA polymerases I and III subunit RPAC2 ...DNA-directed RNA polymerase III subunit RPC1 / DNA-directed RNA polymerases I and III subunit RPAC1 / DNA-directed RNA polymerase III subunit RPC7 / 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 polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase III subunit RPC2 / DNA-directed RNA polymerase III subunit RPC4 / DNA-directed RNA polymerases I and III subunit RPAC2 / DNA-directed RNA polymerase III subunit RPC3 / DNA-directed RNA polymerase III subunit RPC6 / DNA-directed RNA polymerase III subunit RPC8 / DNA-directed RNA polymerase III subunit RPC5 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerase III subunit RPC9 / DNA-directed RNA polymerase III subunit RPC10
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsAbascal-Palacios G / Ramsay EP
Funding support United Kingdom, 4 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/K014390/1 United Kingdom
Cancer Research UK Programme FoundationCR-UK C47547/A21536 United Kingdom
Wellcome Trust200818/Z/16/Z United Kingdom
Marie Sklodowska-Curie Intra-European Fellowship655238 United Kingdom
CitationJournal: Nature / Year: 2018
Title: Structural basis of RNA polymerase III transcription initiation.
Authors: Guillermo Abascal-Palacios / Ewan Phillip Ramsay / Fabienne Beuron / Edward Morris / Alessandro Vannini /
Abstract: RNA polymerase (Pol) III transcribes essential non-coding RNAs, including the entire pool of transfer RNAs, the 5S ribosomal RNA and the U6 spliceosomal RNA, and is often deregulated in cancer cells. ...RNA polymerase (Pol) III transcribes essential non-coding RNAs, including the entire pool of transfer RNAs, the 5S ribosomal RNA and the U6 spliceosomal RNA, and is often deregulated in cancer cells. The initiation of gene transcription by Pol III requires the activity of the transcription factor TFIIIB to form a transcriptionally active Pol III preinitiation complex (PIC). Here we present electron microscopy reconstructions of Pol III PICs at 3.4-4.0 Å and a reconstruction of unbound apo-Pol III at 3.1 Å. TFIIIB fully encircles the DNA and restructures Pol III. In particular, binding of the TFIIIB subunit Bdp1 rearranges the Pol III-specific subunits C37 and C34, thereby promoting DNA opening. The unwound DNA directly contacts both sides of the Pol III cleft. Topologically, the Pol III PIC resembles the Pol II PIC, whereas the Pol I PIC is more divergent. The structures presented unravel the molecular mechanisms underlying the first steps of Pol III transcription and also the general conserved mechanisms of gene transcription initiation.
History
DepositionOct 27, 2017-
Header (metadata) releaseJan 17, 2018-
Map releaseJan 17, 2018-
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: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6eu2
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3957.png

Downloads & links

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Map

FileDownload / File: emd_3957.map.gz / Format: CCP4 / Size: 111.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 308 pix.
= 323.4 Å		1.05 Å/pix.
x 308 pix.
= 323.4 Å		1.05 Å/pix.
x 308 pix.
= 323.4 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: 0.04
Minimum - Maximum-0.16812992 - 0.35569736
Average (Standard dev.)0.0006596678 (±0.008511955)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions308308308
Spacing308308308
CellA=B=C: 323.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z308308308
origin x/y/z0.0000.0000.000
length x/y/z323.400323.400323.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS308308308
D min/max/mean-0.1680.3560.001

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Supplemental data

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Sample components

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Entire : Apo RNA Polymerase III - Open Conformation

EntireName: Apo RNA Polymerase III - Open Conformation
Components
  • Complex: Apo RNA Polymerase III - Open Conformation
    • Protein or peptide: DNA-directed RNA polymerase III subunit RPC1
    • Protein or peptide: DNA-directed RNA polymerase III subunit RPC2
    • Protein or peptide: DNA-directed RNA polymerases I and III subunit RPAC1
    • Protein or peptide: DNA-directed RNA polymerase III subunit RPC9
    • 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 III subunit RPC8
    • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC3
    • Protein or peptide: DNA-directed RNA polymerase III subunit RPC10
    • 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 III subunit RPC5
    • Protein or peptide: DNA-directed RNA polymerase III subunit RPC4
    • Protein or peptide: DNA-directed RNA polymerase III subunit RPC3
    • Protein or peptide: DNA-directed RNA polymerase III subunit RPC6
    • Protein or peptide: DNA-directed RNA polymerase III subunit RPC7
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Apo RNA Polymerase III - Open Conformation

SupramoleculeName: Apo RNA Polymerase III - Open Conformation / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#17
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

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Macromolecule #1: DNA-directed RNA polymerase III subunit RPC1

MacromoleculeName: DNA-directed RNA polymerase III subunit RPC1 / 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: 162.517812 KDa
SequenceString: MKEVVVSETP KRIKGLEFSA LSAADIVAQS EVEVSTRDLF DLEKDRAPKA NGALDPKMGV SSSSLECATC HGNLASCHGH FGHLKLALP VFHIGYFKAT IQILQGICKN CSAILLSETD KRQFLHELRR PGVDNLRRMG ILKKILDQCK KQRRCLHCGA L NGVVKKAA ...String:
MKEVVVSETP KRIKGLEFSA LSAADIVAQS EVEVSTRDLF DLEKDRAPKA NGALDPKMGV SSSSLECATC HGNLASCHGH FGHLKLALP VFHIGYFKAT IQILQGICKN CSAILLSETD KRQFLHELRR PGVDNLRRMG ILKKILDQCK KQRRCLHCGA L NGVVKKAA AGAGSAALKI IHDTFRWVGK KSAPEKDIWV GEWKEVLAHN PELERYVKRC MDDLNPLKTL NLFKQIKSAD CE LLGIDAT VPSGRPETYI WRYLPAPPVC IRPSVMMQDS PASNEDDLTV KLTEIVWTSS LIKAGLDKGI SINNMMEHWD YLQ LTVAMY INSDSVNPAM LPGSSNGGGK VKPIRGFCQR LKGKQGRFRG NLSGKRVDFS GRTVISPDPN LSIDEVAVPD RVAK VLTYP EKVTRYNRHK LQELIVNGPN VHPGANYLLK RNEDARRNLR YGDRMKLAKN LQIGDVVERH LEDGDVVLFN RQPSL HRLS ILSHYAKIRP WRTFRLNECV CTPYNADFDG DEMNLHVPQT EEARAEAINL MGVKNNLLTP KSGEPIIAAT QDFITG SYL ISHKDSFYDR ATLTQLLSMM SDGIEHFDIP PPAIMKPYYL WTGKQVFSLL IKPNHNSPVV INLDAKNKVF VPPKSKS LP NEMSQNDGFV IIRGSQILSG VMDKSVLGDG KKHSVFYTIL RDYGPQEAAN AMNRMAKLCA RFLGNRGFSI GINDVTPA D DLKQKKEELV EIAYHKCDEL ITLFNKGELE TQPGCNEEQT LEAKIGGLLS KVREEVGDVC INELDNWNAP LIMATCGSK GSTLNVSQMV AVVGQQIISG NRVPDGFQDR SLPHFPKNSK TPQSKGFVRN SFFSGLSPPE FLFHAISGRE GLVDTAVKTA ETGYMSRRL MKSLEDLSCQ YDNTVRTSAN GIVQFTYGGD GLDPLEMEGN AQPVNFNRSW DHAYNITFNN QDKGLLPYAI M ETANEILG PLEERLVRYD NSGCLVKRED LNKAEYVDQY DAERDFYHSL REYINGKATA LANLRKSRGM LGLLEPPAKE LQ GIDPDET VPDNVKTSVS QLYRISEKSV RKFLEIALFK YRKARLEPGT AIGAIGAQSI GEPGTQMTLK TFHFAGVASM NVT LGVPRI KEIINASKVI STPIINAVLV NDNDERAARV VKGRVEKTLL SDVAFYVQDV YKDNLSFIQV RIDLGTIDKL QLEL TIEDI AVAITRASKL KIQASDVNII GKDRIAINVF PEGYKAKSIS TSAKEPSEND VFYRMQQLRR ALPDVVVKGL PDISR AVIN IRDDGKRELL VEGYGLRDVM CTDGVIGSRT TTNHVLEVFS VLGIEAARYS IIREINYTMS NHGMSVDPRH IQLLGD VMT YKGEVLGITR FGLSKMRDSV LQLASFEKTT DHLFDAAFYM KKDAVEGVSE CIILGQTMSI GTGSFKVVKG TNISEKD LV PKRCLFESLS NEAALKAN

UniProtKB: DNA-directed RNA polymerase III subunit RPC1

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Macromolecule #2: DNA-directed RNA polymerase III subunit RPC2

MacromoleculeName: DNA-directed RNA polymerase III subunit RPC2 / 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: 129.629383 KDa
SequenceString: MVAATKRRKT HIHKHVKDEA FDDLLKPVYK GKKLTDEINT AQDKWHLLPA FLKVKGLVKQ HLDSFNYFVD TDLKKIIKAN QLILSDVDP EFYLKYVDIR VGKKSSSSTK DYLTPPHECR LRDMTYSAPI YVDIEYTRGR NIIMHKDVEI GRMPIMLRSN K CILYDADE ...String:
MVAATKRRKT HIHKHVKDEA FDDLLKPVYK GKKLTDEINT AQDKWHLLPA FLKVKGLVKQ HLDSFNYFVD TDLKKIIKAN QLILSDVDP EFYLKYVDIR VGKKSSSSTK DYLTPPHECR LRDMTYSAPI YVDIEYTRGR NIIMHKDVEI GRMPIMLRSN K CILYDADE SKMAKLNECP LDPGGYFIVN GTEKVILVQE QLSKNRIIVE ADEKKGIVQA SVTSSTHERK SKTYVITKNG KI YLKHNSI AEEIPIAIVL KACGILSDLE IMQLVCGNDS SYQDIFAVNL EESSKLDIYT QQQALEYIGA KVKTMRRQKL TIL QEGIEA IATTVIAHLT VEALDFREKA LYIAMMTRRV VMAMYNPKMI DDRDYVGNKR LELAGQLISL LFEDLFKKFN NDFK LSIDK VLKKPNRAME YDALLSINVH SNNITSGLNR AISTGNWSLK RFKMERAGVT HVLSRLSYIS ALGMMTRISS QFEKS RKVS GPRALQPSQF GMLCTADTPE GEACGLVKNL ALMTHITTDD EEEPIKKLCY VLGVEDITLI DSASLHLNYG VYLNGT LIG SIRFPTKFVT QFRHLRRTGK VSEFISIYSN SHQMAVHIAT DGGRICRPLI IVSDGQSRVK DIHLRKLLDG ELDFDDF LK LGLVEYLDVN EENDSYIALY EKDIVPSMTH LEIEPFTILG AVAGLIPYPH HNQSPRNTYQ CAMGKQAIGA IAYNQFKR I DTLLYLMTYP QQPMVKTKTI ELIDYDKLPA GQNATVAVMS YSGYDIEDAL VLNKSSIDRG FGRCETRRKT TTVLKRYAN HTQDIIGGMR VDENGDPIWQ HQSLGPDGLG EVGMKVQSGQ IYINKSVPTN SADAPNPNNV NVQTQYREAP VIYRGPEPSH IDQVMMSVS DNDQALIKVL LRQNRRPELG DKFSSRHGQK GVCGIIVKQE DMPFNDQGIV PDIIMNPHGF PSRMTVGKMI E LISGKAGV LNGTLEYGTC FGGSKLEDMS KILVDQGFNY SGKDMLYSGI TGECLQAYIF FGPIYYQKLK HMVLDKMHAR AR GPRAVLT RQPTEGRSRD GGLRLGEMER DCVIAYGASQ LLLERLMISS DAFEVDVCDK CGLMGYSGWC TTCKSAENII KMT IPYAAK LLFQELLSMN IAPRLRLEDI FQQ

UniProtKB: DNA-directed RNA polymerase III subunit RPC2

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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 polymerase III subunit RPC9

MacromoleculeName: DNA-directed RNA polymerase III subunit RPC9 / 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: 18.623123 KDa
SequenceString:
MKVLEERNAF LSDYEVLKFL TDLEKKHLWD QKSLAALKKS RSKGKQNRPY NHPELQGITR NVVNYLSINK NFINQEDEGE ERESSGAKD AEKSGISKMS DESFAELMTK LNSFKLFKAE KLQIVNQLPA NMVHLYSIVE ECDARFDEKT IEEMLEIISG Y A

UniProtKB: DNA-directed RNA polymerase III subunit RPC9

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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 / 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 #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 / 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 #7: DNA-directed RNA polymerase III subunit RPC8

MacromoleculeName: DNA-directed RNA polymerase III subunit RPC8 / 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: 24.34977 KDa
SequenceString: MFILSKIADL VRIPPDQFHR DTISAITHQL NNKFANKIIP NVGLCITIYD LLTVEEGQLK PGDGSSYINV TFRAVVFKPF LGEIVTGWI SKCTAEGIKV SLLGIFDDIF IPQNMLFEGC YYTPEESAWI WPMDEETKLY FDVNEKIRFR IEREVFVDVK P KSPKEREL ...String:
MFILSKIADL VRIPPDQFHR DTISAITHQL NNKFANKIIP NVGLCITIYD LLTVEEGQLK PGDGSSYINV TFRAVVFKPF LGEIVTGWI SKCTAEGIKV SLLGIFDDIF IPQNMLFEGC YYTPEESAWI WPMDEETKLY FDVNEKIRFR IEREVFVDVK P KSPKEREL EERAQLENEI EGKNEETPQN EKPPAYALLG SCQTDGMGLV SWWE

UniProtKB: DNA-directed RNA polymerase III subunit RPC8

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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 / 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 #9: DNA-directed RNA polymerase III subunit RPC10

MacromoleculeName: DNA-directed RNA polymerase III subunit RPC10 / 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: 12.525109 KDa
SequenceString:
MLSFCPSCNN MLLITSGDSG VYTLACRSCP YEFPIEGIEI YDRKKLPRKE VDDVLGGGWD NVDQTKTQCP NYDTCGGESA YFFQLQIRS ADEPMTTFYK CVNCGHRWKE N

UniProtKB: DNA-directed RNA polymerase III subunit RPC10

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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 / 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 #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 / 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 #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 / 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 #13: DNA-directed RNA polymerase III subunit RPC5

MacromoleculeName: DNA-directed RNA polymerase III subunit RPC5 / 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: 32.178115 KDa
SequenceString: MSIDNKLFVT EEDEEDRTQD RADVEDESND IDMIADENGT NSAIANEQEE KSEEVKAEDD TGEEEEDDPV IEEFPLKISG EEESLHVFQ YANRPRLVGR KPAEHPFISA ARYKPKSHLW EIDIPLDEQA FYNKDKAESE WNGVNVQTLK GVGVENNGQY A AFVKDMQV ...String:
MSIDNKLFVT EEDEEDRTQD RADVEDESND IDMIADENGT NSAIANEQEE KSEEVKAEDD TGEEEEDDPV IEEFPLKISG EEESLHVFQ YANRPRLVGR KPAEHPFISA ARYKPKSHLW EIDIPLDEQA FYNKDKAESE WNGVNVQTLK GVGVENNGQY A AFVKDMQV YLVPIERVAQ LKPFFKYIDD ANVTRKQEDA RRNPNPSSQR AQVVTMSVKS VNDPSQNRLT GSLLAHKVAD EE ANIELTW AEGTFEQFKD TIVKEAEDKT LVALEKQEDY IDNLV

UniProtKB: DNA-directed RNA polymerase III subunit RPC5

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Macromolecule #14: DNA-directed RNA polymerase III subunit RPC4

MacromoleculeName: DNA-directed RNA polymerase III subunit RPC4 / 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: 46.751469 KDa
SequenceString: MSSNKGNGRL PSLKDSSSNG GGSAKPSLKF KPKAVARKSK EEREAAASKV KLEEESKRGN DKKHFNNKNK RVTGAGGQQR RMAKYLNNT HVISSGPLAA GNFVSEKGDL RRGFIKSEGS GSSLVQKGLE TIDNGAESSE NEAEDDDNEG VASKSKKKFN M GKEFEARN ...String:
MSSNKGNGRL PSLKDSSSNG GGSAKPSLKF KPKAVARKSK EEREAAASKV KLEEESKRGN DKKHFNNKNK RVTGAGGQQR RMAKYLNNT HVISSGPLAA GNFVSEKGDL RRGFIKSEGS GSSLVQKGLE TIDNGAESSE NEAEDDDNEG VASKSKKKFN M GKEFEARN LIEDEDDGES EKSSDVDMDD EEWRSKRIEQ LFPVRPVRVR HEDVETVKRE IQEALSEKPT REPTPSVKTE PV GTGLQSY LEERERQVNE KLADLGLEKE FQSVDGKEAA AELELLNADH QHILRKLKKM NNKPERFMVF QLPTRLPAFE RPA VKEEKE DMETQASDPS KKKKNIKKKD TKDALSTREL AGKVGSIRVH KSGKLSVKIG NVVMDIGKGA ETTFLQDVIA LSIA DDASS AELLGRVDGK IVVTPQI

UniProtKB: DNA-directed RNA polymerase III subunit RPC4

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Macromolecule #15: DNA-directed RNA polymerase III subunit RPC3

MacromoleculeName: DNA-directed RNA polymerase III subunit RPC3 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 74.11282 KDa
SequenceString: MDELLGEALS AENQTGESTV ESEKLVTPED VMTISSLEQR TLNPDLFLYK ELVKAHLGER AASVIGMLVA LGRLSVRELV EKIDGMDVD SVKTTLVSLT QLRCVKYLQE TAISGKKTTY YYYNEEGIHI LLYSGLIIDE IITQMRVNDE EEHKQLVAEI V QNVISLGS ...String:
MDELLGEALS AENQTGESTV ESEKLVTPED VMTISSLEQR TLNPDLFLYK ELVKAHLGER AASVIGMLVA LGRLSVRELV EKIDGMDVD SVKTTLVSLT QLRCVKYLQE TAISGKKTTY YYYNEEGIHI LLYSGLIIDE IITQMRVNDE EEHKQLVAEI V QNVISLGS LTVEDYLSSV TSDSMKYTIS SLFVQLCEMG YLIQISKLHY TPIEDLWQFL YEKHYKNIPR NSPLSDLKKR SQ AKMNAKT DFAKIINKPN ELSQILTVDP KTSLRIVKPT VSLTINLDRF MKGRRSKQLI NLAKTRVGSV TAQVYKIALR LTE QKSPKI RDPLTQTGLL QDLEEAKSFQ DEAELVEEKT PGLTFNAIDL ARHLPAELDL RGSLLSRKPS DNKKRSGSNA AASL PSKKL KTEDGFVIPA LPAAVSKSLQ ESGDTQEEDE EEEDLDADTE DPHSASLINS HLKILASSNF PFLNETKPGV YYVPY SKLM PVLKSSVYEY VIASTLGPSA MRLSRCIRDN KLVSEKIINS TALMKEKDIR STLASLIRYN SVEIQEVPRT ADRSAS RAV FLFRCKETHS YNFMRQNLEW NMANLLFKKE KLKQENSTLL KKANRDDVKG RENELLLPSE LNQLKMVNER ELNVFAR LS RLLSLWEVFQ MA

UniProtKB: DNA-directed RNA polymerase III subunit RPC3

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Macromolecule #16: DNA-directed RNA polymerase III subunit RPC6

MacromoleculeName: DNA-directed RNA polymerase III subunit RPC6 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 36.17416 KDa
SequenceString: MSGMIENGLQ LSDNAKTLHS QMMSKGIGAL FTQQELQKQM GIGSLTDLMS IVQELLDKNL IKLVKQNDEL KFQGVLESEA QKKATMSAE EALVYSYIEA SGREGIWSKT IKARTNLHQH VVLKCLKSLE SQRYVKSVKS VKFPTRKIYM LYSLQPSVDI T GGPWFTDG ...String:
MSGMIENGLQ LSDNAKTLHS QMMSKGIGAL FTQQELQKQM GIGSLTDLMS IVQELLDKNL IKLVKQNDEL KFQGVLESEA QKKATMSAE EALVYSYIEA SGREGIWSKT IKARTNLHQH VVLKCLKSLE SQRYVKSVKS VKFPTRKIYM LYSLQPSVDI T GGPWFTDG ELDIEFINSL LTIVWRFISE NTFPNGFKNF ENGPKKNVFY APNVKNYSTT QEILEFITAA QVANVELTPS NI RSLCEVL VYDDKLEKVT HDCYRVTLES ILQMNQGEGE PEAGNKALED EEEFSIFNYF KMFPASKHDK EVVYFDEWTI

UniProtKB: DNA-directed RNA polymerase III subunit RPC6

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Macromolecule #17: DNA-directed RNA polymerase III subunit RPC7

MacromoleculeName: DNA-directed RNA polymerase III subunit RPC7 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 27.752971 KDa
SequenceString: MSSYRGGSRG GGSNYMSNLP FGLGYGDVGK NHITEFPSIP LPINGPITNK ERSLAVKYIN FGKTVKDGPF YTGSMSLIID QQENSKSGK RKPNIILDED DTNDGIERYS DKYLKKRKIG ISIDDHPYNL NLFPNELYNV MGINKKKLLA ISKFNNADDV F TGTGLQDE ...String:
MSSYRGGSRG GGSNYMSNLP FGLGYGDVGK NHITEFPSIP LPINGPITNK ERSLAVKYIN FGKTVKDGPF YTGSMSLIID QQENSKSGK RKPNIILDED DTNDGIERYS DKYLKKRKIG ISIDDHPYNL NLFPNELYNV MGINKKKLLA ISKFNNADDV F TGTGLQDE NIGLSMLAKL KELAEDVDDA STGDGAAKGS KTGEGEDDDL ADDDFEEDED EEDDDDYNAE KYFNNGDDDD YG DEEDPNE EAAF

UniProtKB: DNA-directed RNA polymerase III subunit RPC7

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Macromolecule #18: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 18 / Number of copies: 6 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #19: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 19 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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: 8
GridModel: Quantifoil R2/2 / Material: MOLYBDENUM / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 40.0 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: EMDB MAP
EMDB ID:

3179

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0.2) / Number images used: 54213
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.0.2)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.0.2)
FSC plot (resolution estimation)

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