+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30779 | |||||||||
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Title | Structure of Human RNA Polymerase III elongation complex | |||||||||
Map data | Insert Funnel conformation (RPC10 inserts in Funnel) | |||||||||
Sample |
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Keywords | RNA Polymerase III / transcription | |||||||||
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 / regulation of transcription by RNA polymerase III / RPAP3/R2TP/prefoldin-like complex / 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 / regulation of transcription by RNA polymerase III / RPAP3/R2TP/prefoldin-like complex / 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 / positive regulation of innate immune response / nucleobase-containing compound metabolic process / Abortive elongation of HIV-1 transcript in the absence of Tat / 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 / PIWI-interacting RNA (piRNA) biogenesis / termination of RNA polymerase III transcription / 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 / RNA polymerase III activity / transcription initiation at RNA polymerase III promoter / mRNA Splicing - Minor Pathway / RNA Polymerase I Transcription Initiation / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / transcription by RNA polymerase I / Processing of Capped Intron-Containing Pre-mRNA / transcription by RNA polymerase III / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / RNA polymerase II transcribes snRNA genes / neuropeptide signaling pathway / Tat-mediated elongation of the HIV-1 transcript / transcription elongation by RNA polymerase I / tRNA transcription by RNA polymerase III / Formation of HIV-1 elongation complex containing HIV-1 Tat / RNA polymerase I activity / RNA polymerase I complex / RNA polymerase III complex / 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) / Formation of TC-NER Pre-Incision Complex / fibrillar center / ribonucleoside binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / 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 / cell population proliferation / nucleic acid binding / protein dimerization activity / nuclear body / protein stabilization / intracellular membrane-bounded organelle / innate immune response / nucleotide binding / centrosome / DNA-templated transcription / chromatin binding / magnesium ion binding / DNA binding / zinc ion binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Li L / Yu Z | |||||||||
Citation | Journal: Cell Res / Year: 2021 Title: Structure of human RNA polymerase III elongation complex. Authors: Liang Li / Zishuo Yu / Dan Zhao / Yulei Ren / Haifeng Hou / Yanhui Xu / Abstract: RNA polymerase III (Pol III) transcribes essential structured small RNAs, such as tRNAs, 5S rRNA and U6 snRNA. The transcriptional activity of Pol III is tightly controlled and its dysregulation is ...RNA polymerase III (Pol III) transcribes essential structured small RNAs, such as tRNAs, 5S rRNA and U6 snRNA. The transcriptional activity of Pol III is tightly controlled and its dysregulation is associated with human diseases, such as cancer. Human Pol III has two isoforms with difference only in one of its subunits RPC7 (α and β). Despite structural studies of yeast Pol III, structure of human Pol III remains unsolved. Here, we determined the structures of 17-subunit human Pol IIIα complex in the backtracked and post-translocation states, respectively. Human Pol III contains a generally conserved catalytic core, similar to that of yeast counterpart, and structurally unique RPC3-RPC6-RPC7 heterotrimer and RPC10. The N-ribbon of TFIIS-like RPC10 docks on the RPC4-RPC5 heterodimer and the C-ribbon inserts into the funnel of Pol III in the backtracked state but is more flexible in the post-translocation state. RPC7 threads through the heterotrimer and bridges the stalk and Pol III core module. The winged helix 1 domain of RPC6 and the N-terminal region of RPC7α stabilize each other and may prevent Maf1-mediated repression of Pol III activity. The C-terminal FeS cluster of RPC6 coordinates a network of interactions that mediate core-heterotrimer contacts and stabilize Pol III. Our structural analysis sheds new light on the molecular mechanism of human Pol IIIα-specific transcriptional regulation and provides explanations for upregulated Pol III activity in RPC7α-dominant cancer cells. | |||||||||
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_30779.map.gz | 62.5 MB | EMDB map data format | |
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Header (meta data) | emd-30779-v30.xml emd-30779.xml | 42.9 KB 42.9 KB | Display Display | EMDB header |
Images | emd_30779.png | 72.7 KB | ||
Filedesc metadata | emd-30779.cif.gz | 10.5 KB | ||
Others | emd_30779_additional_1.map.gz emd_30779_additional_2.map.gz | 97.9 MB 118.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30779 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30779 | HTTPS FTP |
-Validation report
Summary document | emd_30779_validation.pdf.gz | 551.6 KB | Display | EMDB validaton report |
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Full document | emd_30779_full_validation.pdf.gz | 551.2 KB | Display | |
Data in XML | emd_30779_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | emd_30779_validation.cif.gz | 7.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30779 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30779 | HTTPS FTP |
-Related structure data
Related structure data | 7dn3MC 7du2C C: citing same article (ref.) M: atomic model generated by this map |
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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_30779.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Insert Funnel conformation (RPC10 inserts in Funnel) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Masked RPC6 WH domain
File | emd_30779_additional_1.map | ||||||||||||
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Annotation | Masked RPC6 WH domain | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: the best resolved map of hPol3 in backtracked state
File | emd_30779_additional_2.map | ||||||||||||
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Annotation | the best resolved map of hPol3 in backtracked state | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Structure of Human RNA Polymerase III elongation complex
+Supramolecule #1: Structure of Human RNA Polymerase III elongation complex
+Supramolecule #2: RNA Polymerase III elongation
+Supramolecule #3: DNA
+Supramolecule #4: RNA
+Macromolecule #1: DNA-directed RNA polymerase III subunit RPC1
+Macromolecule #2: DNA-directed RNA polymerase III subunit RPC2
+Macromolecule #3: DNA-directed RNA polymerases I and III subunit RPAC1
+Macromolecule #4: DNA-directed RNA polymerase III subunit RPC8
+Macromolecule #5: DNA-directed RNA polymerase III subunit RPC10
+Macromolecule #6: DNA-directed RNA polymerases I and III subunit RPAC2
+Macromolecule #7: DNA-directed RNA polymerases I, II, and III subunit RPABC4
+Macromolecule #8: DNA-directed RNA polymerase III subunit RPC6
+Macromolecule #9: DNA-directed RNA polymerases I, II, and III subunit RPABC1
+Macromolecule #10: DNA-directed RNA polymerases I, II, and III subunit RPABC2
+Macromolecule #11: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #12: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+Macromolecule #13: DNA-directed RNA polymerase III subunit RPC3
+Macromolecule #14: DNA-directed RNA polymerase III subunit RPC7
+Macromolecule #15: DNA-directed RNA polymerase III subunit RPC9
+Macromolecule #16: DNA-directed RNA polymerase III subunit RPC5
+Macromolecule #17: DNA-directed RNA polymerase III subunit RPC4
+Macromolecule #18: DNA (5'-D(P*TP*CP*GP*TP*CP*TP*GP*AP*TP*CP*TP*CP*GP*GP*AP*A)-3')
+Macromolecule #19: DNA (5'-D(P*TP*TP*CP*CP*GP*AP*GP*AP*TP*CP*AP*GP*AP*CP*GP*AP*GP*AP...
+Macromolecule #20: RNA (5'-R(P*CP*CP*CP*GP*AP*U)-3')
+Macromolecule #21: MAGNESIUM ION
+Macromolecule #22: ZINC ION
+Macromolecule #23: IRON/SULFUR CLUSTER
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 98293 |
Initial angle assignment | Type: OTHER |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |