+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11904 | ||||||||||||
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Title | Apo Human RNA Polymerase III | ||||||||||||
Map data | |||||||||||||
Sample |
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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 / transcription by RNA polymerase II / nucleic acid binding / protein stabilization / protein dimerization activity / nucleotide binding / innate immune response / intracellular membrane-bounded organelle / centrosome / DNA-templated transcription / chromatin binding / magnesium ion binding / DNA binding / zinc ion binding / nucleoplasm / membrane / nucleus Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) / Human (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | ||||||||||||
Authors | Ramsay EP / Abascal-Palacios G / Daiss JL / King H / Gouge J / Pilsl M / Beuron F / Morris E / Gunkel P / Engel C / Vannini A | ||||||||||||
Funding support | United Kingdom, Germany, 3 items
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Citation | Journal: Nat Commun / Year: 2020 Title: Structure of human RNA polymerase III. Authors: Ewan Phillip Ramsay / Guillermo Abascal-Palacios / Julia L Daiß / Helen King / Jerome Gouge / Michael Pilsl / Fabienne Beuron / Edward Morris / Philip Gunkel / Christoph Engel / Alessandro Vannini / Abstract: In eukaryotes, RNA Polymerase (Pol) III is specialized for the transcription of tRNAs and other short, untranslated RNAs. Pol III is a determinant of cellular growth and lifespan across eukaryotes. ...In eukaryotes, RNA Polymerase (Pol) III is specialized for the transcription of tRNAs and other short, untranslated RNAs. Pol III is a determinant of cellular growth and lifespan across eukaryotes. Upregulation of Pol III transcription is observed in cancer and causative Pol III mutations have been described in neurodevelopmental disorders and hypersensitivity to viral infection. Here, we report a cryo-EM reconstruction at 4.0 Å of human Pol III, allowing mapping and rationalization of reported genetic mutations. Mutations causing neurodevelopmental defects cluster in hotspots affecting Pol III stability and/or biogenesis, whereas mutations affecting viral sensing are located in proximity to DNA binding regions, suggesting an impairment of Pol III cytosolic viral DNA-sensing. Integrating x-ray crystallography and SAXS, we also describe the structure of the higher eukaryote specific RPC5 C-terminal extension. Surprisingly, experiments in living cells highlight a role for this module in the assembly and stability of human Pol III. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11904.map.gz | 103 MB | EMDB map data format | |
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Header (meta data) | emd-11904-v30.xml emd-11904.xml | 31.8 KB 31.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11904_fsc.xml | 12.8 KB | Display | FSC data file |
Images | emd_11904.png | 60.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11904 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11904 | HTTPS FTP |
-Related structure data
Related structure data | 7astMC 7asuC 7asvC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_11904.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.065 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : Human RNA Polymerase III
+Supramolecule #1: Human RNA Polymerase III
+Macromolecule #1: DNA-directed RNA polymerase III subunit RPC1
+Macromolecule #2: DNA-directed RNA polymerase III subunit RPC10
+Macromolecule #3: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+Macromolecule #4: DNA-directed RNA polymerases I, II, and III subunit RPABC4
+Macromolecule #5: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #6: DNA-directed RNA polymerases I, II, and III subunit RPABC2
+Macromolecule #7: DNA-directed RNA polymerases I, II, and III subunit RPABC1
+Macromolecule #8: DNA-directed RNA polymerases I and III subunit RPAC2
+Macromolecule #9: DNA-directed RNA polymerases I and III subunit RPAC1
+Macromolecule #10: DNA-directed RNA polymerase III subunit RPC9
+Macromolecule #11: DNA-directed RNA polymerase III subunit RPC8
+Macromolecule #12: DNA-directed RNA polymerase III subunit RPC5
+Macromolecule #13: DNA-directed RNA polymerase III subunit RPC4
+Macromolecule #14: DNA-directed RNA polymerase III subunit RPC2
+Macromolecule #15: DNA-directed RNA polymerase III subunit RPC6
+Macromolecule #16: DNA-directed RNA polymerase III subunit RPC3
+Macromolecule #17: DNA-directed RNA polymerase III subunit RPC7-beta
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.06 mg/mL | ||||||||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV | ||||||||||||||||||
Details | The sample was monodisperse with well-defined complex particles. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average exposure time: 70.0 sec. / Average electron dose: 40.8 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |