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Open data
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Basic information
| Entry | Database: EMDB / ID: EMD-31621 | |||||||||
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| Title | human Pol III elongation complex | |||||||||
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Keywords | RNA Polymerase III / elongation / pre-termination / TRANSCRIPTION / TRANSCRIPTION-RNA-DNA complex | |||||||||
| Function / homology | Function and homology informationsnRNA transcription by RNA polymerase III / RNA Polymerase III Chain Elongation / DNA/RNA hybrid binding / calcitonin gene-related peptide receptor activity / RNA Polymerase III Transcription Termination / regulation of transcription by RNA polymerase III / regulation of transcription by RNA polymerase I / DNA polymerase III complex / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter ...snRNA transcription by RNA polymerase III / RNA Polymerase III Chain Elongation / DNA/RNA hybrid binding / calcitonin gene-related peptide receptor activity / RNA Polymerase III Transcription Termination / regulation of transcription by RNA polymerase III / regulation of transcription by RNA polymerase I / DNA polymerase III complex / 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 / Cytosolic sensors of pathogen-associated DNA / 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 / RNA Polymerase I Transcription Termination / Viral Messenger RNA Synthesis / Signaling by FGFR2 IIIa TM / MicroRNA (miRNA) biogenesis / 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 / 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 / Processing of Capped Intron-Containing Pre-mRNA / PIWI-interacting RNA (piRNA) biogenesis / mRNA Splicing - Minor Pathway / RNA Polymerase I Transcription Initiation / RNA polymerase II transcribes snRNA genes / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / termination of RNA polymerase I transcription / transcription by RNA polymerase III / nucleolar large rRNA transcription by RNA polymerase I / transcription initiation at RNA polymerase I promoter / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / termination of RNA polymerase III transcription / transcription initiation at RNA polymerase III promoter / RNA Polymerase II Transcription Elongation / RNA polymerase I complex / RNA polymerase III complex / Formation of RNA Pol II elongation complex / RNA polymerase II, core complex / transcription elongation by RNA polymerase I / tRNA transcription by RNA polymerase III / transcription by RNA polymerase I / RNA Polymerase II Pre-transcription Events / mRNA Splicing - Major Pathway / positive regulation of interferon-beta production / acrosomal vesicle / Inhibition of DNA recombination at telomere / DNA-templated transcription elongation / TP53 Regulates Transcription of DNA Repair Genes / Transcriptional regulation by small RNAs / RNA Polymerase I Promoter Escape / transcription initiation at RNA polymerase II promoter / protein-DNA complex / transcription elongation by RNA polymerase II / fibrillar center / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / transcription by RNA polymerase II / cell population proliferation / ribonucleoside binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / mRNA Polyadenylation / DNA-directed RNA polymerase / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / DNA-directed RNA polymerase activity / single-stranded DNA binding / 4 iron, 4 sulfur cluster binding / Dengue Virus-Host Interactions / double-stranded DNA binding / defense response to virus / Estrogen-dependent gene expression / nucleic acid binding / nuclear body / protein dimerization activity / protein stabilization / innate immune response / nucleotide binding / centrosome / chromatin binding / magnesium ion binding Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human) | |||||||||
| Method | single particle reconstruction / Resolution: 3.6 Å | |||||||||
Authors | Hou H / Xu Y | |||||||||
| Funding support | China, 1 items
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Citation | Journal: Nat Commun / Year: 2021Title: Structural insights into RNA polymerase III-mediated transcription termination through trapping poly-deoxythymidine. Authors: Haifeng Hou / Yan Li / Mo Wang / Aijun Liu / Zishuo Yu / Ke Chen / Dan Zhao / Yanhui Xu / ![]() Abstract: Termination of the RNA polymerase III (Pol III)-mediated transcription requires the conversion of an elongation complex (EC) to a pre-termination complex (PTC) on poly-deoxythymidine (dT)-containing ...Termination of the RNA polymerase III (Pol III)-mediated transcription requires the conversion of an elongation complex (EC) to a pre-termination complex (PTC) on poly-deoxythymidine (dT)-containing non-template strand, a mechanism distinct from Pol I and Pol II. Here, our in vitro transcription elongation assay showed that 5-7 dT-containing DNA template led to transcription termination of Pol III, but not Pol I or Pol II. We assembled human Pol III PTC on a 7 dT-containing DNA template and determined the structure at 3.6 Å resolution. The structure reveals that poly-dT are trapped in a narrow exit tunnel formed by RPC2. A hydrophobic gate of the exit tunnel separates the bases of two connected deoxythymidines and may prevent translocation of the non-template strand. The fork loop 2 stabilizes both template and non-template strands around the transcription fork, and may further prevent strand translocation. Our study shows that the Pol III-specific exit tunnel and FL2 allow for efficient translocation of non-poly-dT sequence during transcription elongation but trap poly-dT to promote DNA retention of Pol III, revealing molecular mechanism of poly-dT-dependent transcription termination of Pol III. | |||||||||
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Structure visualization
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| Structure viewer | EM map: SurfView Molmil Jmol/JSmol |
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Downloads & links
-EMDB archive
| Map data | emd_31621.map.gz | 140.9 MB | EMDB map data format | |
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| Header (meta data) | emd-31621-v30.xml emd-31621.xml | 42.8 KB 42.8 KB | Display Display | EMDB header |
| Images | emd_31621.png | 141 KB | ||
| Filedesc metadata | emd-31621.cif.gz | 11.2 KB | ||
| Archive directory | https://data.pdbj.org/pub/emdb/structures/EMD-31621 ftp://data.pdbj.org/pub/emdb/structures/EMD-31621 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 7fjiMC ![]() 7fjjC M: atomic model generated by this map C: citing same article ( |
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| Similar structure data |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_31621.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 1.054 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire : human RNA polymerase III elongation complex
+Supramolecule #1: human RNA polymerase III elongation complex
+Supramolecule #2: human RNA polymerase III elongation
+Supramolecule #3: RNA and DNA
+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 RPC9
+Macromolecule #5: DNA-directed RNA polymerases I, II, and III subunit RPABC1
+Macromolecule #6: DNA-directed RNA polymerases I, II, and III subunit RPABC2
+Macromolecule #7: DNA-directed RNA polymerase III subunit RPC8
+Macromolecule #8: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #9: DNA-directed RNA polymerase III subunit RPC10
+Macromolecule #10: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+Macromolecule #11: DNA-directed RNA polymerases I and III subunit RPAC2
+Macromolecule #12: DNA-directed RNA polymerases I, II, and III subunit RPABC4
+Macromolecule #13: DNA-directed RNA polymerase III subunit RPC5
+Macromolecule #14: DNA-directed RNA polymerase III subunit RPC4
+Macromolecule #15: DNA-directed RNA polymerase III subunit RPC3
+Macromolecule #16: DNA-directed RNA polymerase III subunit RPC6
+Macromolecule #17: DNA-directed RNA polymerase III subunit RPC7
+Macromolecule #18: RNA (5'-R(*CP*CP*GP*GP*GP*UP*GP*CP*UP*G)-3')
+Macromolecule #19: non_template DNA
+Macromolecule #20: template
+Macromolecule #21: ZINC ION
+Macromolecule #22: IRON/SULFUR CLUSTER
-Experimental details
-Structure determination
Processing | single particle reconstruction |
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| Aggregation state | particle |
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Sample preparation
| Buffer | pH: 8 |
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Electron microscopy
| Microscope | FEI TITAN KRIOS |
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| Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 1.38 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 |
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About Yorodumi



Keywords
Homo sapiens (human)
Authors
China, 1 items
Citation
UCSF Chimera




























Z (Sec.)
Y (Row.)
X (Col.)






















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