EMDB-11736: Cryo-EM structure of human RNA Polymerase III elongation complex 1

Basic information

• Entry: Database: EMDB / ID: EMD-11736
• Title: Cryo-EM structure of human RNA Polymerase III elongation complex 1
• Map data: Elongating Human Pol III complex Map B, unsharpened

Sample

• Complex: Human RNA Polymerase III Elongation Complex 1
  • Complex: Human RNA Polymerase
    • Protein or peptide: x 17 types
  • Complex: RNA, DNA
    • RNA: x 1 types
    • DNA: x 2 types
• Ligand: x 3 types

• Keywords: HUMAN / TRANSCRIPTION / SHORT RNAs

Function / homology

Function:

snRNA transcription by RNA polymerase III / RNA Polymerase III Chain Elongation / RNA Polymerase III Transcription Termination / calcitonin gene-related peptide receptor activity / DNA/RNA hybrid binding / regulation of transcription by RNA polymerase I / RPAP3/R2TP/prefoldin-like complex / regulation of transcription by RNA polymerase III / DNA polymerase III complex / Cytosolic sensors of pathogen-associated DNA / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / RNA Polymerase III Abortive And Retractive Initiation / RNA polymerase III activity / positive regulation of innate immune response / Abortive elongation of HIV-1 transcript in the absence of Tat / nucleobase-containing compound metabolic process / MicroRNA (miRNA) biogenesis / RNA Polymerase I Transcription Termination / FGFR2 alternative splicing / Viral Messenger RNA Synthesis / Signaling by FGFR2 IIIa TM / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / termination of RNA polymerase III transcription / PIWI-interacting RNA (piRNA) biogenesis / RNA polymerase I activity / mRNA Splicing - Minor Pathway / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / 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 / transcription initiation at RNA polymerase III promoter / tRNA transcription by RNA polymerase III / RNA Polymerase I Transcription Initiation / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / RNA polymerase II transcribes snRNA genes / Processing of Capped Intron-Containing Pre-mRNA / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / neuropeptide signaling pathway / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / RNA polymerase I complex / transcription by RNA polymerase I / RNA polymerase III complex / transcription by RNA polymerase III / Formation of HIV elongation complex in the absence of HIV Tat / RNA polymerase II, core complex / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / Inhibition of DNA recombination at telomere / positive regulation of interferon-beta production / mRNA Splicing - Major Pathway / acrosomal vesicle / protein-DNA complex / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / ribonucleoside binding / Formation of TC-NER Pre-Incision Complex / fibrillar center / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / single-stranded DNA binding / 4 iron, 4 sulfur cluster binding / double-stranded DNA binding / defense response to virus / Estrogen-dependent gene expression / cell population proliferation / transcription by RNA polymerase II / nucleic acid binding / protein stabilization / nuclear body / protein dimerization activity / nucleotide binding / intracellular membrane-bounded organelle / innate immune response / centrosome / DNA-templated transcription / chromatin binding / magnesium ion binding / DNA binding / zinc ion binding / nucleoplasm

Domain/homology:

DNA-directed RNA polymerase III subunit RPC5, C-terminal / DNA-directed RNA polymerase III subunit RPC5 C-terminal / 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 / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / Rpb4/RPC9 superfamily / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Zinc finger TFIIS-type signature. / RNA polymerase subunit Rpb7-like / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / HRDC-like superfamily / 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, 7 kDa subunit / DNA-directed RNA polymerase subunit Rpo11 / 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 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

Component:

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 polymerase III subunit RPC9 / DNA-directed RNA polymerase III subunit RPC4 / DNA-directed RNA polymerases I and III subunit RPAC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase III subunit RPC3 / DNA-directed RNA polymerase III subunit RPC6 / DNA-directed RNA polymerase III subunit RPC5 / DNA-directed RNA polymerase III subunit RPC2 / DNA-directed RNA polymerase III subunit RPC10 / DNA-directed RNA polymerase III subunit RPC8

• Biological species: Homo sapiens (human) / synthetic construct (others)
• Method: single particle reconstruction / cryo EM / Resolution: 2.8 Å
• Authors: Girbig M / Misiaszek AD
• Citation: Journal: Nat Struct Mol Biol / Year: 2021; Title: Cryo-EM structures of human RNA polymerase III in its unbound and transcribing states.; Authors: Mathias Girbig / Agata D Misiaszek / Matthias K Vorländer / Aleix Lafita / Helga Grötsch / Florence Baudin / Alex Bateman / Christoph W Müller / ; Abstract: RNA polymerase III (Pol III) synthesizes transfer RNAs and other short, essential RNAs. Human Pol III misregulation is linked to tumor transformation, neurodegenerative and developmental disorders, and increased sensitivity to viral infections. Here, we present cryo-electron microscopy structures at 2.8 to 3.3 Å resolution of transcribing and unbound human Pol III. We observe insertion of the TFIIS-like subunit RPC10 into the polymerase funnel, providing insights into how RPC10 triggers transcription termination. Our structures resolve elements absent from Saccharomyces cerevisiae Pol III such as the winged-helix domains of RPC5 and an iron-sulfur cluster, which tethers the heterotrimer subcomplex to the core. The cancer-associated RPC7α isoform binds the polymerase clamp, potentially interfering with Pol III inhibition by tumor suppressor MAF1, which may explain why overexpressed RPC7α enhances tumor transformation. Finally, the human Pol III structure allows mapping of disease-related mutations and may contribute to the development of inhibitors that selectively target Pol III for therapeutic interventions.

History

Deposition	Sep 17, 2020	-
Header (metadata) release	Feb 3, 2021	-
Map release	Feb 3, 2021	-
Update	May 1, 2024	-
Current status	May 1, 2024	Processing site: PDBe / Status: Released

Map

• File: Download / File: emd_11736.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Annotation: Elongating Human Pol III complex Map B, unsharpened
• Voxel size: X=Y=Z: 1.05 Å

Density

Contour Level	By AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum	-0.017909722 - 0.06683617
Average (Standard dev.)	0.000025407966 (±0.002253317)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 336 336 336 Spacing 336 336 336
Cell	A=B=C: 352.8 Å α=β=γ: 90.0 °

CCP4 map header:

mode	Image stored as Reals
Å/pix. X/Y/Z	1.05	1.05	1.05
M x/y/z	336	336	336
origin x/y/z	0.000	0.000	0.000
length x/y/z	352.800	352.800	352.800
α/β/γ	90.000	90.000	90.000
MAP C/R/S	1	2	3
start NC/NR/NS	0	0	0
NC/NR/NS	336	336	336
D min/max/mean	-0.018	0.067	0.000

Supplemental data

Mask #1

• File: emd_11736_msk_1.map

Additional map: Elongating Human Pol III complex Map B, locally...

• File: emd_11736_additional_1.map
• Annotation: Elongating Human Pol III complex Map B, locally sharpened with LocalDeblur

Additional map: Elongating Human Pol III complex Map B1, from...

• File: emd_11736_additional_2.map
• Annotation: Elongating Human Pol III complex Map B1, from RELION multi-body refinement, body_001

Additional map: Elongating Human Pol III complex Map B2, from...

• File: emd_11736_additional_3.map
• Annotation: Elongating Human Pol III complex Map B2, from RELION multi-body refinement, body_002

Additional map: Elongating Human Pol III complex Map B1, from...

• File: emd_11736_additional_4.map
• Annotation: Elongating Human Pol III complex Map B1, from RELION multi-body refinement, body_001, sharpened with Density Modification

Additional map: Elongating Human Pol III complex Map B2, from...

• File: emd_11736_additional_5.map
• Annotation: Elongating Human Pol III complex Map B2, from RELION multi-body refinement, body_002, sharpened with Density Modification

Half map: #1

• File: emd_11736_half_map_1.map

Half map: #2

• File: emd_11736_half_map_2.map

Sample components

Entire : Human RNA Polymerase III Elongation Complex 1

• Entire: Name: Human RNA Polymerase III Elongation Complex 1

Components

• Complex: Human RNA Polymerase III Elongation Complex 1
  • Complex: Human RNA Polymerase
    • 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: RNA, DNA
    • RNA: RNA
    • DNA: Non-template DNA
    • DNA: Template-DNA
• Ligand: ZINC ION
• Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
• Ligand: MAGNESIUM ION

Supramolecule #1: Human RNA Polymerase III Elongation Complex 1

• Supramolecule: Name: Human RNA Polymerase III Elongation Complex 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#20
• Molecular weight: Theoretical: 776 KDa

Supramolecule #2: Human RNA Polymerase

• Supramolecule: Name: Human RNA Polymerase / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#17
• Source (natural): Organism: Homo sapiens (human) / Strain: HEK293F

Supramolecule #3: RNA, DNA

• Supramolecule: Name: RNA, DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #18-#20
• Source (natural): Organism: synthetic construct (others)

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

• Macromolecule: Name: 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: Homo sapiens (human)
• Molecular weight: Theoretical: 155.860125 KDa

Sequence

String:

MVKEQFRETD VAKKISHICF GMKSPEEMRQ QAHIQVVSKN LYSQDNQHAP LLYGVLDHRM GTSEKDRPCE TCGKNLADCL GHYGYIDLE LPCFHVGYFR AVIGILQMIC KTCCHIMLSQ EEKKQFLDYL KRPGLTYLQK RGLKKKISDK CRKKNICHHC G AFNGTVKK CGLLKIIHEK YKTNKKVVDP IVSNFLQSFE TAIEHNKEVE PLLGRAQENL NPLVVLNLFK RIPAEDVPLL LM NPEAGKP SDLILTRLLV PPLCIRPSVV SDLKSGTNED DLTMKLTEII FLNDVIKKHR ISGAKTQMIM EDWDFLQLQC ALY INSELS GIPLNMAPKK WTRGFVQRLK GKQGRFRGNL SGKRVDFSGR TVISPDPNLR IDEVAVPVHV AKILTFPEKV NKAN INFLR KLVQNGPEVH PGANFIQQRH TQMKRFLKYG NREKMAQELK YGDIVERHLI DGDVVLFNRQ PSLHKLSIMA HLARV KPHR TFRFNECVCT PYNADFDGDE MNLHLPQTEE AKAEALVLMG TKANLVTPRN GEPLIAAIQD FLTGAYLLTL KDTFFD RAK ACQIIASILV GKDEKIKVRL PPPTILKPVT LWTGKQIFSV ILRPSDDNPV RANLRTKGKQ YCGKGEDLCA NDSYVTI QN SELMSGSMDK GTLGSGSKNN IFYILLRDWG QNEAADAMSR LARLAPVYLS NRGFSIGIGD VTPGQGLLKA KYELLNAG Y KKCDEYIEAL NTGKLQQQPG CTAEETLEAL ILKELSVIRD HAGSACLREL DKSNSPLTMA LCGSKGSFIN ISQMIACVG QQAISGSRVP DGFENRSLPH FEKHSKLPAA KGFVANSFYS GLTPTEFFFH TMAGREGLVD TAVKTAETGY MQRRLVKSLE DLCSQYDLT VRSSTGDIIQ FIYGGDGLDP AAMEGKDEPL EFKRVLDNIK AVFPCPSEPA LSKNELILTT ESIMKKSEFL C CQDSFLQE IKKFIKGVSE KIKKTRDKYG INDNGTTEPR VLYQLDRITP TQVEKFLETC RDKYMRAQME PGSAVGALCA QS IGEPGTQ MTLKTFHFAG VASMNITLGV PRIKEIINAS KAISTPIITA QLDKDDDADY ARLVKGRIEK TLLGEISEYI EEV FLPDDC FILVKLSLER IRLLRLEVNA ETVRYSICTS KLRVKPGDVA VHGEAVVCVT PRENSKSSMY YVLQFLKEDL PKVV VQGIP EVSRAVIHID EQSGKEKYKL LVEGDNLRAV MATHGVKGTR TTSNNTYEVE KTLGIEAART TIINEIQYTM VNHGM SIDR RHVMLLSDLM TYKGEVLGIT RFGLAKMKES VLMLASFEKT ADHLFDAAYF GQKDSVCGVS ECIIMGIPMN IGTGLF KLL HKADRDPNPP KRPLIFDTNE FHIPLVT

UniProtKB: DNA-directed RNA polymerase III subunit RPC1

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

• Macromolecule: Name: 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: Homo sapiens (human)
• Molecular weight: Theoretical: 127.953891 KDa

Sequence

String:

MDVLAEEFGN LTPEQLAAPI PTVEEKWRLL PAFLKVKGLV KQHIDSFNYF INVEIKKIMK ANEKVTSDAD PMWYLKYLNI YVGLPDVEE SFNVTRPVSP HECRLRDMTY SAPITVDIEY TRGSQRIIRN ALPIGRMPIM LRSSNCVLTG KTPAEFAKLN E CPLDPGGY FIVKGVEKVI LIQEQLSKNR IIVEADRKGA VGASVTSSTH EKKSRTNMAV KQGRFYLRHN TLSEDIPIVI IF KAMGVES DQEIVQMIGT EEHVMAAFGP SLEECQKAQI FTQMQALKYI GNKVRRQRMW GGGPKKTKIE EARELLASTI LTH VPVKEF NFRAKCIYTA VMVRRVILAQ GDNKVDDRDY YGNKRLELAG QLLSLLFEDL FKKFNSEMKK IADQVIPKQR AAQF DVVKH MRQDQITNGM VNAISTGNWS LKRFKMDRQG VTQVLSRLSY ISALGMMTRI SSQFEKTRKV SGPRSLQPSQ WGMLC PSDT PEGEACGLVK NLALMTHITT DMEDGPIVKL ASNLGVEDVN LLCGEELSYP NVFLVFLNGN ILGVIRDHKK LVNTFR LMR RAGYINEFVS ISTNLTDRCV YISSDGGRLC RPYIIVKKQK PAVTNKHMEE LAQGYRNFED FLHESLVEYL DVNEEND CN IALYEHTINK DTTHLEIEPF TLLGVCAGLI PYPHHNQSPR NTYQCAMGKQ AMGTIGYNQR NRIDTLMYLL AYPQKPMV K TKTIELIEFE KLPAGQNATV AVMSYSGYDI EDALVLNKAS LDRGFGRCLV YKNAKCTLKR YTNQTFDKVM GPMLDAATR KPIWRHEILD ADGICSPGEK VENKQVLVNK SMPTVTQIPL EGSNVPQQPQ YKDVPITYKG ATDSYIEKVM ISSNAEDAFL IKMLLRQTR RPEIGDKFSS RHGQKGVCGL IVPQEDMPFC DSGICPDIIM NPHGFPSRMT VGKLIELLAG KAGVLDGRFH Y GTAFGGSK VKDVCEDLVR HGYNYLGKDY VTSGITGEPL EAYIYFGPVY YQKLKHMVLD KMHARARGPR AVLTRQPTEG RS RDGGLRL GEMERDCLIG YGASMLLLER LMISSDAFEV DVCGQCGLLG YSGWCHYCKS SCHVSSLRIP YACKLLFQEL QSM NIIPRL KLSKYNE

UniProtKB: DNA-directed RNA polymerase III subunit RPC2

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

• Macromolecule: Name: DNA-directed RNA polymerases I and III subunit RPAC1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 39.301672 KDa

Sequence

String:

MAASQAVEEM RSRVVLGEFG VRNVHTTDFP GNYSGYDDAW DQDRFEKNFR VDVVHMDENS LEFDMVGIDA AIANAFRRIL LAEVPTMAV EKVLVYNNTS IVQDEILAHR LGLIPIHADP RLFEYRNQGD EEGTEIDTLQ FRLQVRCTRN PHAAKDSSDP N ELYVNHKV YTRHMTWIPL GNQADLFPEG TIRPVHDDIL IAQLRPGQEI DLLMHCVKGI GKDHAKFSPV ATASYRLLPD IT LLEPVEG EAAEELSRCF SPGVIEVQEV QGKKVARVAN PRLDTFSREI FRNEKLKKVV RLARVRDHYI FSVESTGVLP PDV LVSEAI KVLMGKCRRF LDELDAVQMD

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

Macromolecule #4: DNA-directed RNA polymerase III subunit RPC9

• Macromolecule: Name: DNA-directed RNA polymerase III subunit RPC9 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 16.89399 KDa

Sequence

String:

MEVKDANSAL LSNYEVFQLL TDLKEQRKES GKNKHSSGQQ NLNTITYETL KYISKTPCRH QSPEIVREFL TALKSHKLTK AEKLQLLNH RPVTAVEIQL MVEESEERLT EEQIEALLHT VTSILPAEPE AEQKKNTNSN VAMDEEDPA

UniProtKB: DNA-directed RNA polymerase III subunit RPC9

Macromolecule #5: DNA-directed RNA polymerases I, II, and III subunit RPABC1

• Macromolecule: Name: 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: Homo sapiens (human)
• Molecular weight: Theoretical: 24.584223 KDa

Sequence

String:

MDDEEETYRL WKIRKTIMQL CHDRGYLVTQ DELDQTLEEF KAQSGDKPSE GRPRRTDLTV LVAHNDDPTD QMFVFFPEEP KVGIKTIKV YCQRMQEENI TRALIVVQQG MTPSAKQSLV DMAPKYILEQ FLQQELLINI TEHELVPEHV VMTKEEVTEL L ARYKLREN QLPRIQAGDP VARYFGIKRG QVVKIIRPSE TAGRYITYRL VQ

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

Macromolecule #6: DNA-directed RNA polymerases I, II, and III subunit RPABC2

• Macromolecule: Name: 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: Homo sapiens (human)
• Molecular weight: Theoretical: 14.491026 KDa

Sequence

String:

MSDNEDNFDG DDFDDVEEDE GLDDLENAEE EGQENVEILP SGERPQANQK RITTPYMTKY ERARVLGTRA LQIAMCAPVM VELEGETDP LLIAMKELKA RKIPIIIRRY LPDGSYEDWG VDELIITD

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

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

• Macromolecule: Name: DNA-directed RNA polymerase III subunit RPC8 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 22.938846 KDa

Sequence

String:

MFVLVEMVDT VRIPPWQFER KLNDSIAEEL NKKLANKVVY NVGLCICLFD ITKLEDAYVF PGDGASHTKV HFRCVVFHPF LDEILIGKI KGCSPEGVHV SLGFFDDILI PPESLQQPAK FDEAEQVWVW EYETEEGAHD LYMDTGEEIR FRVVDESFVD T SPTGPSSA DATTSSEELP KKEAPYTLVG SISEPGLGLL SWWTSN

UniProtKB: DNA-directed RNA polymerase III subunit RPC8

Macromolecule #8: DNA-directed RNA polymerases I, II, and III subunit RPABC3

• Macromolecule: Name: 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: Homo sapiens (human)
• Molecular weight: Theoretical: 17.162273 KDa

Sequence

String:

MAGILFEDIF DVKDIDPEGK KFDRVSRLHC ESESFKMDLI LDVNIQIYPV DLGDKFRLVI ASTLYEDGTL DDGEYNPTDD RPSRADQFE YVMYGKVYRI EGDETSTEAA TRLSAYVSYG GLLMRLQGDA NNLHGFEVDS RVYLLMKKLA F

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

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

• Macromolecule: Name: DNA-directed RNA polymerase III subunit RPC10 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 12.354104 KDa

Sequence

String:

MLLFCPGCGN GLIVEEGQRC HRFSCNTCPY VHNITRKVTN RKYPKLKEVD DVLGGAAAWE NVDSTAESCP KCEHPRAYFM QLQTRSADE PMTTFYKCCN AQCGHRWRD

UniProtKB: DNA-directed RNA polymerase III subunit RPC10

Macromolecule #10: DNA-directed RNA polymerases I, II, and III subunit RPABC5

• Macromolecule: Name: 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: Homo sapiens (human)
• Molecular weight: Theoretical: 7.655123 KDa

Sequence

String:

MIIPVRCFTC GKIVGNKWEA YLGLLQAEYT EGDALDALGL KRYCCRRMLL AHVDLIEKLL NYAPLEK

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

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

• Macromolecule: Name: DNA-directed RNA polymerases I and III subunit RPAC2 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 15.259222 KDa

Sequence

String:

MEEDQELERK ISGLKTSMAE GERKTALEMV QAAGTDRHCV TFVLHEEDHT LGNSLRYMIM KNPEVEFCGY TTTHPSESKI NLRIQTRGT LPAVEPFQRG LNELMNVCQH VLDKFEASIK DYKDQKASRN ESTF

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

Macromolecule #12: DNA-directed RNA polymerases I, II, and III subunit RPABC4

• Macromolecule: Name: 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: Homo sapiens (human)
• Molecular weight: Theoretical: 7.018244 KDa

Sequence

String:

MDTQKDVQPP KQQPMIYICG ECHTENEIKS RDPIRCRECG YRIMYKKRTK RLVVFDAR

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

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

• Macromolecule: Name: DNA-directed RNA polymerase III subunit RPC5 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 80.004031 KDa

Sequence

String:

MANEEDDPVV QEIDVYLAKS LAEKLYLFQY PVRPASMTYD DIPHLSAKIK PKQQKVELEM AIDTLNPNYC RSKGEQIALN VDGACADET STYSSKLMDK QTFCSSQTTS NTSRYAAALY RQGELHLTPL HGILQLRPSF SYLDKADAKH REREAANEAG D SSQDEAED DVKQITVRFS RPESEQARQR RVQSYEFLQK KHAEEPWVHL HYYGLRDSRS EHERQYLLCP GSSGVENTEL VK SPSEYLM MLMPPSQEEE KDKPVAPSNV LSMAQLRTLP LADQIKILMK NVKVMPFANL MSLLGPSIDS VAVLRGIQKV AML VQGNWV VKSDILYPKD SSSPHSGVPA EVLCRGRDFV MWKFTQSRWV VRKEVATVTK LCAEDVKDFL EHMAVVRINK GWEF ILPYD GEFIKKHPDV VQRQHMLWTG IQAKLEKVYN LVKETMPKKP DAQSGPAGLV CGDQRIQVAK TKAQQNHALL ERELQ RRKE QLRVPAVPPG VRIKEEPVSE EGEEDEEQEA EEEPMDTSPS GLHSKLANGL PLGRAAGTDS FNGHPPQGCA STPVAR ELK AFVEATFQRQ FVLTLSELKR LFNLHLASLP PGHTLFSGIS DRMLQDTVLA AGCKQILVPF PPQTAASPDE QKVFALW ES GDMSDQHRQV LLEIFSKNYR VRRNMIQSRL TQECGEDLSK QEVDKVLKDC CVSYGGMWYL KGTVQS

UniProtKB: DNA-directed RNA polymerase III subunit RPC5

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

• Macromolecule: Name: DNA-directed RNA polymerase III subunit RPC4 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 44.471875 KDa

Sequence

String:

MSEGNAAGEP STPGGPRPLL TGARGLIGRR PAPPLTPGRL PSIRSRDLTL GGVKKKTFTP NIISRKIKEE PKEEVTVKKE KRERDRDRQ REGHGRGRGR PEVIQSHSIF EQGPAEMMKK KGNWDKTVDV SDMGPSHIIN IKKEKRETDE ETKQILRMLE K DDFLDDPG LRNDTRNMPV QLPLAHSGWL FKEENDEPDV KPWLAGPKEE DMEVDIPAVK VKEEPRDEEE EAKMKAPPKA AR KTPGLPK DVSVAELLRE LSLTKEEELL FLQLPDTLPG QPPTQDIKPI KTEVQGEDGQ VVLIKQEKDR EAKLAENACT LAD LTEGQV GKLLIRKSGR VQLLLGKVTL DVTMGTACSF LQELVSVGLG DSRTGEMTVL GHVKHKLVCS PDFESLLDHK HR

UniProtKB: DNA-directed RNA polymerase III subunit RPC4

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

• Macromolecule: Name: DNA-directed RNA polymerase III subunit RPC3 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 60.692555 KDa

Sequence

String:

MTQAEIKLCS LLLQEHFGEI VEKIGVHLIR TGSQPLRVIA HDTGTSLDQV KKALCVLVQH NLVSYQVHKR GVVEYEAQCS RVLRMLRYP RYIYTTKTLY SDTGELIVEE LLLNGKLTMS AVVKKVADRL TETMEDGKTM DYAEVSNTFV RLADTHFVQR C PSVPTTEN SDPGPPPPAP TLVINEKDMY LVPKLSLIGK GKRRRSSDED AAGEPKAKRP KYTTDNKEPI PDDGIYWQAN LD RFHQHFR DQAIVSAVAN RMDQTSSEIV RTMLRMSEIT TSSSAPFTQP LSSNEIFRSL PVGYNISKQV LDQYLTLLAD DPL EFVGKS GDSGGGMYVI NLHKALASLA TATLESVVQE RFGSRCARIF RLVLQKKHIE QKQVEDFAMI PAKEAKDMLY KMLS ENFMS LQEIPKTPDH APSRTFYLYT VNILSAARML LHRCYKSIAN LIERRQFETK ENKRLLEKSQ RVEAIIASMQ ATGAE EAQL QEIEEMITAP ERQQLETLKR NVNKLDASEI QVDETIFLLE SYIECTMKRQ

UniProtKB: DNA-directed RNA polymerase III subunit RPC3

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

• Macromolecule: Name: DNA-directed RNA polymerase III subunit RPC6 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 35.726914 KDa

Sequence

String:

MAEVKVKVQP PDADPVEIEN RIIELCHQFP HGITDQVIQN EMPHIEAQQR AVAINRLLSM GQLDLLRSNT GLLYRIKDSQ NAGKMKGSD NQEKLVYQII EDAGNKGIWS RDIRYKSNLP LTEINKILKN LESKKLIKAV KSVAASKKKV YMLYNLQPDR S VTGGAWYS DQDFESEFVE VLNQQCFKFL QSKAETARES KQNPMIQRNS SFASSHEVWK YICELGISKV ELSMEDIETI LN TLIYDGK VEMTIIAAKE GTVGSVDGHM KLYRAVNPII PPTGLVRAPC GLCPVFDDCH EGGEISPSNC IYMTEWLEF

UniProtKB: DNA-directed RNA polymerase III subunit RPC6

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

• Macromolecule: Name: DNA-directed RNA polymerase III subunit RPC7 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 25.95351 KDa

Sequence

String:

MAGNKGRGRA AYTFNIEAVG FSKGEKLPDV VLKPPPLFPD TDYKPVPLKT GEGEEYMLAL KQELRETMKR MPYFIETPEE RQDIERYSK RYMKVYKEEW IPDWRRLPRE MMPRNKCKKA GPKPKKAKDA GKGTPLTNTE DVLKKMEELE KRGDGEKSDE E NEEKEGSK EKSKEGDDDD DDDAAEQEEY DEEEQEEEND YINSYFEDGD DFGADSDDNM DEATY

UniProtKB: DNA-directed RNA polymerase III subunit RPC7

Macromolecule #18: RNA

• Macromolecule: Name: RNA / type: rna / ID: 18 / Number of copies: 1
• Source (natural): Organism: synthetic construct (others)
• Molecular weight: Theoretical: 6.084713 KDa

Sequence

String:

UAUGCAUAAC GCCACAGAG

Macromolecule #19: Non-template DNA

• Macromolecule: Name: Non-template DNA / type: dna / ID: 19 / Number of copies: 1 / Classification: DNA
• Source (natural): Organism: synthetic construct (others)
• Molecular weight: Theoretical: 14.102053 KDa

Sequence

String:

(DC)(DG)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DT) (DG)(DC)(DC)(DA)(DT)(DG)(DT)(DT)(DA)(DA) (DC)(DG)(DG)(DA)(DC)(DT)(DA)(DG)(DT) (DC)(DC)(DA)(DG)(DC)(DT)(DC)(DC)(DA)(DC) (DT) (DT)(DA)(DA)(DA)(DA)(DC)

Macromolecule #20: Template-DNA

• Macromolecule: Name: Template-DNA / type: dna / ID: 20 / Number of copies: 1 / Classification: DNA
• Source (natural): Organism: synthetic construct (others)
• Molecular weight: Theoretical: 14.254121 KDa

Sequence

String:

(DG)(DT)(DT)(DT)(DT)(DA)(DA)(DG)(DT)(DG) (DG)(DA)(DG)(DC)(DT)(DG)(DG)(DA)(DT)(DG) (DC)(DT)(DC)(DT)(DG)(DT)(DG)(DG)(DC) (DT)(DC)(DA)(DT)(DG)(DG)(DC)(DA)(DA)(DC) (DG) (DA)(DC)(DC)(DA)(DC)(DG)

Macromolecule #21: ZINC ION

• Macromolecule: Name: ZINC ION / type: ligand / ID: 21 / Number of copies: 7 / Formula: ZN
• Molecular weight: Theoretical: 65.409 Da

Macromolecule #22: IRON/SULFUR CLUSTER

• Macromolecule: Name: IRON/SULFUR CLUSTER / type: ligand / ID: 22 / Number of copies: 1 / Formula: SF4
• Molecular weight: Theoretical: 351.64 Da

Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER / Iron–sulfur cluster

Macromolecule #23: MAGNESIUM ION

• Macromolecule: Name: MAGNESIUM ION / type: ligand / ID: 23 / Number of copies: 1 / Formula: MG
• Molecular weight: Theoretical: 24.305 Da

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: particle

Sample preparation

• Concentration: 2 mg/mL

Buffer

pH: 7.5
Component:

Concentration	Name
15.0 mM	HEPES
150.0 mM	ammonium sulfate
5.0 mM	magnesium chloride
10.0 mM	DTT
4.0 mM	CHAPSOCHAPS detergent

• Grid: Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER
• Vitrification: Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Wait time 10 s Blot force 4 Blot time 4 s.

Electron microscopy

• Microscope: FEI TITAN KRIOS
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 130000
• Sample stage: Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
• Image recording: Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.4 e/Ų
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• Particle selection: Number selected: 367717
• Startup model: Type of model: INSILICO MODEL / Details: Initial model was generated in cryoSPARC
• Initial angle assignment: Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
• Final angle assignment: Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
• Final reconstruction: Applied symmetry - Point group: C₁ (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 166071