+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11741 | |||||||||
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Title | Cryo-EM structure of human RNA Polymerase III, map G | |||||||||
Map data | Cryo-EM map of human RNA Polymerase III, map G, unsharpened | |||||||||
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 / 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 ...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 / 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 / transcription initiation at RNA polymerase III promoter / 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 / 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 / ribonucleoside binding / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / 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 dimerization activity / protein stabilization / 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 | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Girbig M / Misiaszek AD / Vorlaender MK / Mueller CW | |||||||||
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, ...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 |
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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_11741.map.gz | 73.1 MB | EMDB map data format | |
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Header (meta data) | emd-11741-v30.xml emd-11741.xml | 20.1 KB 20.1 KB | Display Display | EMDB header |
Images | emd_11741.png | 72.2 KB | ||
Masks | emd_11741_msk_1.map | 144.7 MB | Mask map | |
Others | emd_11741_additional_1.map.gz emd_11741_half_map_1.map.gz emd_11741_half_map_2.map.gz | 69.3 MB 134.4 MB 134.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11741 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11741 | HTTPS FTP |
-Related structure data
Related structure data | 7a6hC 7ae1C 7ae3C 7aeaC C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10697 (Title: Cryo-EM structures of human RNA Polymerase III / Data size: 3.3 TB Data #1: LZW-TIFF compressed multiframe micrographs of human RNA Pol III EC [micrographs - multiframe] Data #2: Initially picked particles of human RNA Pol III EC [picked particles - single frame - processed] Data #3: Polished particles of human RNA Pol III EC (final reconstruction) [picked particles - single frame - processed] Data #4: LZW-TIFF compressed multiframe micrographs of human RNA Pol III apo [micrographs - multiframe] Data #5: Initially picked particles of human RNA Pol III apo [picked particles - single frame - processed] Data #6: Polished particles of human RNA Pol III apo (final reconstruction) [picked particles - single frame - processed]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_11741.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM map of human RNA Polymerase III, map G, unsharpened | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_11741_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Cryo-EM map of human RNA Polymerase III, map...
File | emd_11741_additional_1.map | ||||||||||||
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Annotation | Cryo-EM map of human RNA Polymerase III, map G, locally sharpened via LocalDeblur | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_11741_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_11741_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human RNA Polymerase III
Entire | Name: Human RNA Polymerase III |
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Components |
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-Supramolecule #1: Human RNA Polymerase III
Supramolecule | Name: Human RNA Polymerase III / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#20 |
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Source (natural) | Organism: Homo sapiens (human) / Strain: HEK293F |
Molecular weight | Theoretical: 776 kDa/nm |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
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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 |
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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: 2.25 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/Å2 Details: Merged data-set from Micrographs recorded on a Gatan K2 Summit detector and a Gatan K3 detector |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 672400 Details: Particles that yielded final 3D reconstructions of EMDB entries 11673 and 11736 were merged for this 3D reconstruction. |
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CTF correction | Software: (Name: Warp (ver. 1.0.6), RELION (ver. 3.1)) |
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 |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.15.0) / Number images used: 277360 |
Details | Merged data-set from micrographs recorded on a Gatan K2 Summit detector and a Gatan K3 detector. |