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- EMDB-10595: Cryo-EM structure of the RNA Polymerase III-Maf1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-10595
TitleCryo-EM structure of the RNA Polymerase III-Maf1 complex
Map dataSharpened and locally filtered EM map
Sample
  • Complex: RNA Polymerase III - Maf1 complex
    • Complex: DNA-directed RNA polymerase IIIPolymerase
      • Protein or peptide: x 17 types
    • Complex: Repressor of RNA polymerase III transcription MAF1
      • Protein or peptide: x 1 types
  • Ligand: x 1 types
Function / homology
Function and homology information


Regulation of PTEN gene transcription / : / negative regulation of transcription by RNA polymerase III / RNA polymerase III core binding / RNA polymerase III activity / 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 PTEN gene transcription / : / negative regulation of transcription by RNA polymerase III / RNA polymerase III core binding / RNA polymerase III activity / 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 / 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 / transcription by RNA polymerase I / RNA polymerase III complex / transcription by RNA polymerase III / RNA polymerase II, core complex / nucleotidyltransferase activity / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / peroxisome / single-stranded DNA binding / ribosome biogenesis / transcription by RNA polymerase II / nucleic acid binding / protein dimerization activity / nucleotide binding / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Repressor of RNA polymerase III transcription Maf1 / Repressor of RNA polymerase III transcription Maf1 superfamily / Maf1 regulator / 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 ...Repressor of RNA polymerase III transcription Maf1 / Repressor of RNA polymerase III transcription Maf1 superfamily / Maf1 regulator / 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 / 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 / RNA polymerase subunit Rpb7-like / HRDC-like superfamily / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / 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, 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. / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / 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. / 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 / RNA polymerase Rpb1, domain 4 / RNA polymerase, N-terminal
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 / Repressor of RNA polymerase III transcription MAF1 / DNA-directed RNA polymerase III subunit RPC9 / DNA-directed RNA polymerase III subunit RPC10
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsVorlaender MK / Hagen WJH / Mueller CW
Funding support Germany, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-2013-AdG340964-POL1PIC Germany
CitationJournal: Nat Struct Mol Biol / Year: 2020
Title: Structural basis for RNA polymerase III transcription repression by Maf1.
Authors: Matthias K Vorländer / Florence Baudin / Robyn D Moir / René Wetzel / Wim J H Hagen / Ian M Willis / Christoph W Müller /
Abstract: Maf1 is a conserved inhibitor of RNA polymerase III (Pol III) that influences phenotypes ranging from metabolic efficiency to lifespan. Here, we present a 3.3-Å-resolution cryo-EM structure of yeast ...Maf1 is a conserved inhibitor of RNA polymerase III (Pol III) that influences phenotypes ranging from metabolic efficiency to lifespan. Here, we present a 3.3-Å-resolution cryo-EM structure of yeast Maf1 bound to Pol III, establishing that Maf1 sequesters Pol III elements involved in transcription initiation and binds the mobile C34 winged helix 2 domain, sealing off the active site. The Maf1 binding site overlaps with that of TFIIIB in the preinitiation complex.
History
DepositionJan 8, 2020-
Header (metadata) releaseFeb 19, 2020-
Map releaseFeb 19, 2020-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.075
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.075
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6tut
  • Surface level: 0.075
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10595.png

Downloads & links

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Map

FileDownload / File: emd_10595.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened and locally filtered EM map
Voxel sizeX=Y=Z: 1.041 Å
Density
Contour LevelBy AUTHOR: 0.075 / Movie #1: 0.075
Minimum - Maximum-0.23891374 - 0.4194077
Average (Standard dev.)0.00001267956 (±0.010117584)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 374.76 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0411.0411.041
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z374.760374.760374.760
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.2390.4190.000

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Supplemental data

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Half map: Half map 1, generated by relion refine

Fileemd_10595_half_map_1.map
AnnotationHalf map 1, generated by relion_refine
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2, generated by relion refine

Fileemd_10595_half_map_2.map
AnnotationHalf map 2, generated by relion_refine
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RNA Polymerase III - Maf1 complex

EntireName: RNA Polymerase III - Maf1 complex
Components
  • Complex: RNA Polymerase III - Maf1 complex
    • Complex: DNA-directed RNA polymerase IIIPolymerase
      • Protein or peptide: DNA-directed RNA polymerase III subunit RPC1Polymerase
      • Protein or peptide: DNA-directed RNA polymerase III subunit RPC2Polymerase
      • Protein or peptide: DNA-directed RNA polymerases I and III subunit RPAC1
      • Protein or peptide: DNA-directed RNA polymerase III subunit RPC9Polymerase
      • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC1RNA polymerase
      • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC2RNA polymerase
      • Protein or peptide: DNA-directed RNA polymerase III subunit RPC8Polymerase
      • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC3RNA polymerase
      • Protein or peptide: DNA-directed RNA polymerase III subunit RPC10Polymerase
      • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC5RNA polymerase
      • Protein or peptide: DNA-directed RNA polymerases I and III subunit RPAC2
      • Protein or peptide: DNA-directed RNA polymerases I, II, and III subunit RPABC4RNA polymerase
      • Protein or peptide: DNA-directed RNA polymerase III subunit RPC5Polymerase
      • Protein or peptide: DNA-directed RNA polymerase III subunit RPC4Polymerase
      • Protein or peptide: DNA-directed RNA polymerase III subunit RPC3Polymerase
      • Protein or peptide: DNA-directed RNA polymerase III subunit RPC6Polymerase
      • Protein or peptide: DNA-directed RNA polymerase III subunit RPC7Polymerase
    • Complex: Repressor of RNA polymerase III transcription MAF1
      • Protein or peptide: Repressor of RNA polymerase III transcription MAF1,Repressor of RNA polymerase III transcription MAF1
  • Ligand: ZINC ION

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Supramolecule #1: RNA Polymerase III - Maf1 complex

SupramoleculeName: RNA Polymerase III - Maf1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#18
Molecular weightTheoretical: 720 KDa

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Supramolecule #2: DNA-directed RNA polymerase III

SupramoleculeName: DNA-directed RNA polymerase III / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#17
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)

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Supramolecule #3: Repressor of RNA polymerase III transcription MAF1

SupramoleculeName: Repressor of RNA polymerase III transcription MAF1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #18
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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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 S288C (yeast)
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

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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 S288C (yeast)
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

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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 S288C (yeast)
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

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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 S288C (yeast)
Molecular weightTheoretical: 18.623123 KDa
SequenceString:
MKVLEERNAF LSDYEVLKFL TDLEKKHLWD QKSLAALKKS RSKGKQNRPY NHPELQGITR NVVNYLSINK NFINQEDEGE ERESSGAKD AEKSGISKMS DESFAELMTK LNSFKLFKAE KLQIVNQLPA NMVHLYSIVE ECDARFDEKT IEEMLEIISG Y A

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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 S288C (yeast)
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

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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 S288C (yeast)
Molecular weightTheoretical: 17.931834 KDa
SequenceString:
MSDYEEAFND GNENFEDFDV EHFSDEETYE EKPQFKDGET TDANGKTIVT GGNGPEDFQQ HEQIRRKTLK EKAIPKDQRA TTPYMTKYE RARILGTRAL QISMNAPVFV DLEGETDPLR IAMKELAEKK IPLVIRRYLP DGSFEDWSVE ELIVDL

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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 S288C (yeast)
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

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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 S288C (yeast)
Molecular weightTheoretical: 16.525363 KDa
SequenceString:
MSNTLFDDIF QVSEVDPGRY NKVCRIEAAS TTQDQCKLTL DINVELFPVA AQDSLTVTIA SSLNLEDTPA NDSSATRSWR PPQAGDRSL ADDYDYVMYG TAYKFEEVSK DLIAVYYSFG GLLMRLEGNY RNLNNLKQEN AYLLIRR

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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 S288C (yeast)
Molecular weightTheoretical: 12.525109 KDa
SequenceString:
MLSFCPSCNN MLLITSGDSG VYTLACRSCP YEFPIEGIEI YDRKKLPRKE VDDVLGGGWD NVDQTKTQCP NYDTCGGESA YFFQLQIRS ADEPMTTFYK CVNCGHRWKE N

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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 S288C (yeast)
Molecular weightTheoretical: 8.290732 KDa
SequenceString:
MIVPVRCFSC GKVVGDKWES YLNLLQEDEL DEGTALSRLG LKRYCCRRMI LTHVDLIEKF LRYNPLEKRD

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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 S288C (yeast)
Molecular weightTheoretical: 16.16786 KDa
SequenceString:
MTEDIEQKKT ATEVTPQEPK HIQEEEEQDV DMTGDEEQEE EPDREKIKLL TQATSEDGTS ASFQIVEEDH TLGNALRYVI MKNPDVEFC GYSIPHPSEN LLNIRIQTYG ETTAVDALQK GLKDLMDLCD VVESKFTEKI KSM

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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 S288C (yeast)
Molecular weightTheoretical: 7.729969 KDa
SequenceString:
MSREGFQIPT NLDAAAAGTS QARTATLKYI CAECSSKLSL SRTDAVRCKD CGHRILLKAR TKRLVQFEAR

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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 S288C (yeast)
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

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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 S288C (yeast)
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

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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 S288C (yeast)
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

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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 S288C (yeast)
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

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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 S288C (yeast)
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

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Macromolecule #18: Repressor of RNA polymerase III transcription MAF1,Repressor of R...

MacromoleculeName: Repressor of RNA polymerase III transcription MAF1,Repressor of RNA polymerase III transcription MAF1
type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 30.493762 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GAMGKFIDEL DIERVNQTLN FETNDCKIVG SCDIFTTKAV ASDRKLYKTI DQHLDTILQE NENYNASSGT ATNNVNKRRK SSINERPSN LSLGPFGPIN EPSSRKIFAY LIAILNASYP DHDFSSVEPT DFVKTSLKTF ISKFENTLYS LGRQPEEWVW E VINSHMTL ...String:
GAMGKFIDEL DIERVNQTLN FETNDCKIVG SCDIFTTKAV ASDRKLYKTI DQHLDTILQE NENYNASSGT ATNNVNKRRK SSINERPSN LSLGPFGPIN EPSSRKIFAY LIAILNASYP DHDFSSVEPT DFVKTSLKTF ISKFENTLYS LGRQPEEWVW E VINSHMTL SDCVLFQYSP SNSFLEDEPG YLWNLIGFLY NRKRKRVAYL YLICSRLNSS TGEVEDALAK KPQGKLIIDD GS NEYEGEY DFTYDENVID DKSDQEESLQ

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Macromolecule #19: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 19 / Number of copies: 7 / Formula: ZN
Molecular weightTheoretical: 65.409 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

Concentration0.15 mg/mL
BufferpH: 7.5 / Details: 15 mM HEPES, 150 mM (NH4)2SO4, 5 mM DTT
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2.0 nm / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV / Details: Blot time 6, blot force 2.
Detailscrosslinked with BS3

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 130000
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Number grids imaged: 1 / Number real images: 10520 / Average exposure time: 14.0 sec. / Average electron dose: 60.5 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1688795
CTF correctionSoftware:
Namedetails
Warp (ver. 1.05)
RELION (ver. 3.0)CTF refinement
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6eu3

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationSoftware - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 117442
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER / Overall B value: 64
Output model

PDB-6tut:
Cryo-EM structure of the RNA Polymerase III-Maf1 complex

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