+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7997 | |||||||||
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Title | RNA Pol II(G) | |||||||||
Map data | RNA Pol II(G) | |||||||||
Sample |
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Function / homology | Function and homology information maintenance of ER location / RNA polymerase II, holoenzyme / LRR domain binding / microfibril binding / RNA Polymerase III Chain Elongation / RNA Polymerase III Transcription Termination / regulation of transcription by RNA polymerase I / RPAP3/R2TP/prefoldin-like complex / Cytosolic sensors of pathogen-associated DNA / RNA Polymerase III Transcription Initiation From Type 1 Promoter ...maintenance of ER location / RNA polymerase II, holoenzyme / LRR domain binding / microfibril binding / RNA Polymerase III Chain Elongation / RNA Polymerase III Transcription Termination / regulation of transcription by RNA polymerase I / RPAP3/R2TP/prefoldin-like 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 / Abortive elongation of HIV-1 transcript in the absence of Tat / MicroRNA (miRNA) biogenesis / FGFR2 alternative splicing / 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 / PIWI-interacting RNA (piRNA) biogenesis / 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 / mRNA Splicing - Minor Pathway / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / RNA Polymerase I Transcription Initiation / transcription by RNA polymerase I / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / nuclear-transcribed mRNA catabolic process / transcription by RNA polymerase III / Processing of Capped Intron-Containing Pre-mRNA / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / RNA polymerase II transcribes snRNA genes / RNA polymerase II activity / transcription elongation by RNA polymerase I / Tat-mediated elongation of the HIV-1 transcript / tRNA transcription by RNA polymerase III / Formation of HIV-1 elongation complex containing HIV-1 Tat / RNA polymerase I complex / RNA polymerase III complex / positive regulation of translational initiation / Formation of HIV elongation complex in the absence of HIV Tat / transcription-coupled nucleotide-excision repair / RNA polymerase II, core complex / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / Inhibition of DNA recombination at telomere / translation initiation factor binding / RNA Polymerase II Pre-transcription Events / mRNA Splicing - Major Pathway / positive regulation of RNA splicing / RNA Polymerase I Promoter Escape / promoter-specific chromatin binding / Transcriptional regulation by small RNAs / transcription initiation at RNA polymerase II promoter / protein-DNA complex / TP53 Regulates Transcription of DNA Repair Genes / DNA-templated transcription termination / kinase binding / P-body / 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 / ribonucleoside binding / fibrillar center / 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 / chromosome / nuclear envelope / single-stranded DNA binding / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / Estrogen-dependent gene expression / nucleic acid binding / transcription by RNA polymerase II / single-stranded RNA binding / protein dimerization activity / protein stabilization / intracellular signal transduction / nuclear speck / hydrolase activity / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / chromatin binding / nucleotide binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Human (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Yu X / Jishage M / Shi Y / Ganesan S / Sali A / Chait BT / Asturias F / Roeder RG | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2018 Title: Architecture of Pol II(G) and molecular mechanism of transcription regulation by Gdown1. Authors: Miki Jishage / Xiaodi Yu / Yi Shi / Sai J Ganesan / Wei-Yi Chen / Andrej Sali / Brian T Chait / Francisco J Asturias / Robert G Roeder / Abstract: Tight binding of Gdown1 represses RNA polymerase II (Pol II) function in a manner that is reversed by Mediator, but the structural basis of these processes is unclear. Although Gdown1 is ...Tight binding of Gdown1 represses RNA polymerase II (Pol II) function in a manner that is reversed by Mediator, but the structural basis of these processes is unclear. Although Gdown1 is intrinsically disordered, its Pol II interacting domains were localized and shown to occlude transcription factor IIF (TFIIF) and transcription factor IIB (TFIIB) binding by perfect positioning on their Pol II interaction sites. Robust binding of Gdown1 to Pol II is established by cooperative interactions of a strong Pol II binding region and two weaker binding modulatory regions, thus providing a mechanism both for tight Pol II binding and transcription inhibition and for its reversal. In support of a physiological function for Gdown1 in transcription repression, Gdown1 co-localizes with Pol II in transcriptionally silent nuclei of early Drosophila embryos but re-localizes to the cytoplasm during zygotic genome activation. Our study reveals a self-inactivation through Gdown1 binding as a unique mode of repression in Pol II function. | |||||||||
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_7997.map.gz | 5.2 MB | EMDB map data format | |
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Header (meta data) | emd-7997-v30.xml emd-7997.xml | 23.9 KB 23.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_7997_fsc.xml | 7.9 KB | Display | FSC data file |
Images | emd_7997.png | 68.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7997 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7997 | HTTPS FTP |
-Validation report
Summary document | emd_7997_validation.pdf.gz | 387.7 KB | Display | EMDB validaton report |
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Full document | emd_7997_full_validation.pdf.gz | 387.2 KB | Display | |
Data in XML | emd_7997_validation.xml.gz | 10.2 KB | Display | |
Data in CIF | emd_7997_validation.cif.gz | 13.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7997 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7997 | HTTPS FTP |
-Related structure data
Related structure data | 6drdMC 7998C 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_7997.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | RNA Pol II(G) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.31 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 : hPolII_Gdown1
+Supramolecule #1: hPolII_Gdown1
+Macromolecule #1: DNA-directed RNA polymerase II subunit RPB1
+Macromolecule #2: DNA-directed RNA polymerase II subunit RPB2
+Macromolecule #3: DNA-directed RNA polymerase II subunit RPB3
+Macromolecule #4: DNA-directed RNA polymerase II subunit RPB4
+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 II subunit RPB7
+Macromolecule #8: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #9: DNA-directed RNA polymerase II subunit RPB9
+Macromolecule #10: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+Macromolecule #11: DNA-directed RNA polymerase II subunit RPB11-a
+Macromolecule #12: DNA-directed RNA polymerases I, II, and III subunit RPABC4
+Macromolecule #13: DNA-directed RNA polymerase II subunit GRINL1A
+Macromolecule #14: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Pretreatment - Type: PLASMA CLEANING / Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |