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- PDB-7a6h: Cryo-EM structure of human apo RNA Polymerase III -

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Entry
Database: PDB / ID: 7a6h
TitleCryo-EM structure of human apo RNA Polymerase III
Components
  • (DNA-directed RNA polymerase III subunit ...Polymerase) x 10
  • (DNA-directed RNA polymerases I and III subunit ...) x 2
  • (DNA-directed RNA polymerases I, II, and III subunit ...RNA polymerase) x 5
KeywordsTRANSCRIPTION / Human RNA polymerase III / Synthesis of short RNAs / apo complex
Function / homology
Function and homology information


snRNA transcription by RNA polymerase III / RNA Polymerase III Chain Elongation / RNA Polymerase III Transcription Termination / DNA/RNA hybrid binding / calcitonin gene-related peptide receptor activity / 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 ...snRNA transcription by RNA polymerase III / RNA Polymerase III Chain Elongation / RNA Polymerase III Transcription Termination / DNA/RNA hybrid binding / calcitonin gene-related peptide receptor activity / 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 / FGFR2 alternative splicing / MicroRNA (miRNA) biogenesis / RNA Polymerase I Transcription Termination / 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 / mRNA Splicing - Minor Pathway / RNA polymerase I activity / 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 / Processing of Capped Intron-Containing Pre-mRNA / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / RNA polymerase II transcribes snRNA genes / 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 / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / 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 / protein dimerization activity / nuclear body / nucleotide binding / innate immune response / intracellular membrane-bounded organelle / centrosome / DNA-templated transcription / chromatin binding / magnesium ion binding / DNA binding / zinc ion binding / nucleoplasm
Similarity search - Function
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 ...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 / 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 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
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / 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 ...IRON/SULFUR CLUSTER / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsGirbig, M. / Misiaszek, A.D. / Vorlaender, M.K. / Mueller, C.W.
CitationJournal: 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, ...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
DepositionAug 25, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 3, 2021Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID

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Structure visualization

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Assembly

Deposited unit
A: DNA-directed RNA polymerase III subunit RPC1
B: DNA-directed RNA polymerase III subunit RPC2
C: DNA-directed RNA polymerases I and III subunit RPAC1
D: DNA-directed RNA polymerase III subunit RPC9
E: DNA-directed RNA polymerases I, II, and III subunit RPABC1
F: DNA-directed RNA polymerases I, II, and III subunit RPABC2
G: DNA-directed RNA polymerase III subunit RPC8
H: DNA-directed RNA polymerases I, II, and III subunit RPABC3
I: DNA-directed RNA polymerase III subunit RPC10
J: DNA-directed RNA polymerases I, II, and III subunit RPABC5
K: DNA-directed RNA polymerases I and III subunit RPAC2
L: DNA-directed RNA polymerases I, II, and III subunit RPABC4
M: DNA-directed RNA polymerase III subunit RPC5
N: DNA-directed RNA polymerase III subunit RPC4
O: DNA-directed RNA polymerase III subunit RPC3
P: DNA-directed RNA polymerase III subunit RPC6
Q: DNA-directed RNA polymerase III subunit RPC7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)709,15526
Polymers708,32217
Non-polymers8349
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area101560 Å2
ΔGint-673 kcal/mol
Surface area209620 Å2
MethodPISA

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Components

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DNA-directed RNA polymerase III subunit ... , 10 types, 10 molecules ABDGIMNOPQ

#1: Protein DNA-directed RNA polymerase III subunit RPC1 / Polymerase / RNA polymerase III subunit C1 / DNA-directed RNA polymerase III largest subunit / DNA-directed RNA ...RNA polymerase III subunit C1 / DNA-directed RNA polymerase III largest subunit / DNA-directed RNA polymerase III subunit A / RNA polymerase III 155 kDa subunit / RPC155 / RNA polymerase III subunit C160


Mass: 155860.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O14802, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase III subunit RPC2 / Polymerase / RNA polymerase III subunit C2 / C128 / DNA-directed RNA polymerase III 127.6 kDa polypeptide / DNA- ...RNA polymerase III subunit C2 / C128 / DNA-directed RNA polymerase III 127.6 kDa polypeptide / DNA-directed RNA polymerase III subunit B


Mass: 127953.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NW08, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase III subunit RPC9 / Polymerase / RNA polymerase III subunit C9 / Calcitonin gene-related peptide-receptor component protein / HsC17


Mass: 16893.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75575
#7: Protein DNA-directed RNA polymerase III subunit RPC8 / Polymerase / RNA polymerase III subunit C8 / DNA-directed RNA polymerase III subunit H / RNA polymerase III ...RNA polymerase III subunit C8 / DNA-directed RNA polymerase III subunit H / RNA polymerase III subunit 22.9 kDa subunit / RPC22.9


Mass: 22938.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y535
#9: Protein DNA-directed RNA polymerase III subunit RPC10 / Polymerase / RNA polymerase III subunit C10 / DNA-directed RNA polymerase III subunit K / RNA polymerase III 12. ...RNA polymerase III subunit C10 / DNA-directed RNA polymerase III subunit K / RNA polymerase III 12.5 kDa subunit / RPC12.5 / RNA polymerase III subunit C11 / hRPC11


Mass: 12354.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y2Y1
#13: Protein DNA-directed RNA polymerase III subunit RPC5 / Polymerase / RNA polymerase III subunit C5 / DNA-directed RNA polymerase III 80 kDa polypeptide


Mass: 80004.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NVU0
#14: Protein DNA-directed RNA polymerase III subunit RPC4 / Polymerase / RNA polymerase III subunit C4 / DNA-directed RNA polymerase III subunit D / Protein BN51 / RNA ...RNA polymerase III subunit C4 / DNA-directed RNA polymerase III subunit D / Protein BN51 / RNA polymerase III 47 kDa subunit / RPC53 homolog


Mass: 44471.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P05423
#15: Protein DNA-directed RNA polymerase III subunit RPC3 / Polymerase / RNA polymerase III subunit C3 / DNA-directed RNA polymerase III subunit C / RNA polymerase III 62 ...RNA polymerase III subunit C3 / DNA-directed RNA polymerase III subunit C / RNA polymerase III 62 kDa subunit / RPC62


Mass: 60692.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BUI4
#16: Protein DNA-directed RNA polymerase III subunit RPC6 / Polymerase / RNA polymerase III subunit C6 / DNA-directed RNA polymerase III subunit F / RNA polymerase III 39 ...RNA polymerase III subunit C6 / DNA-directed RNA polymerase III subunit F / RNA polymerase III 39 kDa subunit / RPC39


Mass: 35726.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9H1D9
#17: Protein DNA-directed RNA polymerase III subunit RPC7 / Polymerase / RNA polymerase III subunit C7 / DNA-directed RNA polymerase III subunit G / RNA polymerase III 32 ...RNA polymerase III subunit C7 / DNA-directed RNA polymerase III subunit G / RNA polymerase III 32 kDa apha subunit / RPC32-alpha / RNA polymerase III 32 kDa subunit / RPC32


Mass: 25953.510 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O15318

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DNA-directed RNA polymerases I and III subunit ... , 2 types, 2 molecules CK

#3: Protein DNA-directed RNA polymerases I and III subunit RPAC1 / RNA polymerases I and III subunit AC1 / AC40 / DNA-directed RNA polymerases I and III 40 kDa ...RNA polymerases I and III subunit AC1 / AC40 / DNA-directed RNA polymerases I and III 40 kDa polypeptide / RPA40 / RPA39 / RPC40


Mass: 39301.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O15160
#11: Protein DNA-directed RNA polymerases I and III subunit RPAC2 / RNA polymerases I and III subunit AC2 / AC19 / DNA-directed RNA polymerase I subunit D / RNA ...RNA polymerases I and III subunit AC2 / AC19 / DNA-directed RNA polymerase I subunit D / RNA polymerase I 16 kDa subunit / RPA16 / RPC16 / hRPA19


Mass: 15259.222 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P0DPB6

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DNA-directed RNA polymerases I, II, and III subunit ... , 5 types, 5 molecules EFHJL

#5: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerase / RNA polymerases I / II / and III subunit ABC1 / DNA-directed RNA polymerase II 23 kDa polypeptide / ...RNA polymerases I / II / and III subunit ABC1 / DNA-directed RNA polymerase II 23 kDa polypeptide / DNA-directed RNA polymerase II subunit E / RPB5 homolog / XAP4


Mass: 24584.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P19388
#6: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC2 / RNA polymerase / RNA polymerases I / II / and III subunit ABC2 / DNA-directed RNA polymerase II subunit F / DNA- ...RNA polymerases I / II / and III subunit ABC2 / DNA-directed RNA polymerase II subunit F / DNA-directed RNA polymerases I / and III 14.4 kDa polypeptide / RPABC14.4 / RPB14.4 / RPB6 homolog / RPC15


Mass: 14491.026 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61218
#8: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerase / RNA polymerases I / II / and III subunit ABC3 / DNA-directed RNA polymerase II subunit H / DNA- ...RNA polymerases I / II / and III subunit ABC3 / DNA-directed RNA polymerase II subunit H / DNA-directed RNA polymerases I / and III 17.1 kDa polypeptide / RPB17 / RPB8 homolog / hRPB8


Mass: 17162.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P52434
#10: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC5 / RNA polymerase / RNA polymerases I / II / and III subunit ABC5 / DNA-directed RNA polymerase III subunit L / RNA ...RNA polymerases I / II / and III subunit ABC5 / DNA-directed RNA polymerase III subunit L / RNA polymerase II 7.6 kDa subunit / RPB7.6 / RPB10 homolog


Mass: 7655.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62875
#12: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase / RNA polymerases I / II / and III subunit ABC4 / ABC10-alpha / DNA-directed RNA polymerase II ...RNA polymerases I / II / and III subunit ABC4 / ABC10-alpha / DNA-directed RNA polymerase II subunit K / RNA polymerase II 7.0 kDa subunit / RPB7.0 / RPB10alpha


Mass: 7018.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P53803

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Non-polymers , 3 types, 9 molecules

#18: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#19: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#20: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-EM structure of human apo RNA Polymerase III / Type: COMPLEX / Entity ID: #1-#17 / Source: NATURAL
Molecular weightValue: 0.776 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human) / Strain: HEK293F
Buffer solutionpH: 7.5
Buffer component
IDConc.NameBuffer-ID
115 mMHEPES1
2150 mMammonium sulfate1
35 mMmagnesium chloride1
410 mMDTT1
54 mMCHAPSOCHAPS detergent1
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: Wait time 10 s Blot force 4 Blot time 4 s

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 105000 X / Nominal defocus max: 2250 nm / Nominal defocus min: 750 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 38.11 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: UCSF ChimeraX / Version: 0.92/v8 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: Windows / Type: package
EM software
IDNameVersionCategoryDetails
1Warp1.0.6particle selection
2SerialEMimage acquisitionImage acquisition
4Warp1.0.6CTF correction
5RELION3.1CTF correction
8Coot0.8.9.1model fitting
10RELION3.1initial Euler assignment
11RELION3.1final Euler assignment
12RELION3.1classification
13RELION3.13D reconstruction
14PHENIX1.13model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 304683
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 111289 / Symmetry type: POINT

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