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Open data
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Basic information
Entry | Database: PDB / ID: 6drd | ||||||
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Title | RNA Pol II(G) | ||||||
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![]() | TRANSFERASE / RNA Pol II(G) / Gdown1 / transcription repression / molecular mechanism | ||||||
Function / homology | ![]() 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 / translation initiation factor binding / RNA Polymerase II Pre-transcription Events / Inhibition of DNA recombination at telomere / mRNA Splicing - Major Pathway / positive regulation of RNA splicing / promoter-specific chromatin binding / transcription initiation at RNA polymerase II promoter / protein-DNA complex / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase I Promoter Escape / DNA-templated transcription termination / Transcriptional regulation by small RNAs / 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 / kinase binding / 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 / nuclear envelope / chromosome / single-stranded DNA binding / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / Estrogen-dependent gene expression / transcription by RNA polymerase II / nucleic acid binding / single-stranded RNA binding / protein dimerization activity / protein stabilization / hydrolase activity / intracellular signal transduction / nuclear speck / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / nucleotide binding / neuronal cell body Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||
![]() | Yu, X. / Jishage, M. / Shi, Y. / Ganesan, S. / Sali, A. / Chait, B.T. / Asturias, F. / Roeder, R.G. | ||||||
Funding support | ![]()
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![]() | ![]() 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
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 620.4 KB | Display | ![]() |
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PDB format | ![]() | 497.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7997MC ![]() 7998C M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-DNA-directed RNA polymerase II subunit ... , 8 types, 8 molecules ABCDGIKM
#1: Protein | Mass: 217450.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: P24928, DNA-directed RNA polymerase, RNA-directed RNA polymerase |
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#2: Protein | Mass: 134071.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#3: Protein | Mass: 31478.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#4: Protein | Mass: 16331.255 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#7: Protein | Mass: 19314.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#9: Protein | Mass: 14541.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#11: Protein | Mass: 13310.284 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#13: Protein | Mass: 5756.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-DNA-directed RNA polymerases I, II, and III subunit ... , 5 types, 5 molecules EFHJL
#5: Protein | Mass: 24659.291 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#6: Protein | Mass: 14491.026 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#8: Protein | Mass: 17162.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#10: Protein | Mass: 7655.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#12: Protein | Mass: 7018.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Non-polymers , 1 types, 5 molecules ![](data/chem/img/ZN.gif)
#14: Chemical | ChemComp-ZN / |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: CELL / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: hPolII_Gdown1 / Type: COMPLEX / Entity ID: #1-#13 / Source: NATURAL |
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Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Cs: 2.7 mm / C2 aperture diameter: 100 µm |
Image recording | Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: dev_2666: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 141619 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||
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