+Open data
-Basic information
Entry | Database: PDB / ID: 7ozp | ||||||||||||||||||
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Title | RNA Polymerase II dimer (Class 3) | ||||||||||||||||||
Components |
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Keywords | TRANSCRIPTION / Polymerase / Dimer / Complex | ||||||||||||||||||
Function / homology | Function and homology information : / B-WICH complex positively regulates rRNA expression / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase I Transcription Termination / 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 / Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex ...: / B-WICH complex positively regulates rRNA expression / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase I Transcription Termination / 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 / Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Transcriptional regulation by small RNAs / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Elongation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / mRNA Splicing - Major Pathway / organelle membrane / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / RNA polymerase III activity / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / RNA polymerase II activity / transcription elongation by RNA polymerase I / transcription-coupled nucleotide-excision repair / tRNA transcription by RNA polymerase III / RNA polymerase I activity / RNA polymerase I complex / RNA polymerase III complex / positive regulation of translational initiation / RNA polymerase II, core complex / translation initiation factor binding / transcription initiation at RNA polymerase II promoter / P-body / fibrillar center / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / single-stranded DNA binding / transcription by RNA polymerase II / nucleic acid binding / single-stranded RNA binding / protein dimerization activity / nuclear speck / nucleotide binding / DNA-templated transcription / nucleolus / DNA binding / zinc ion binding / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||||||||||||||
Biological species | Sus scrofa domesticus (domestic pig) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||||||||||||||
Authors | Aibara, S. / Dienemann, C. / Cramer, P. | ||||||||||||||||||
Funding support | Germany, 5items
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Citation | Journal: Nucleic Acids Res / Year: 2021 Title: Structure of an inactive RNA polymerase II dimer. Authors: Shintaro Aibara / Christian Dienemann / Patrick Cramer / Abstract: Eukaryotic gene transcription is carried out by three RNA polymerases: Pol I, Pol II and Pol III. Although it has long been known that Pol I can form homodimers, it is unclear whether and how the two ...Eukaryotic gene transcription is carried out by three RNA polymerases: Pol I, Pol II and Pol III. Although it has long been known that Pol I can form homodimers, it is unclear whether and how the two other RNA polymerases dimerize. Here we present the cryo-electron microscopy (cryo-EM) structure of a mammalian Pol II dimer at 3.5 Å resolution. The structure differs from the Pol I dimer and reveals that one Pol II copy uses its RPB4-RPB7 stalk to penetrate the active centre cleft of the other copy, and vice versa, giving rise to a molecular handshake. The polymerase clamp domain is displaced and mobile, and the RPB7 oligonucleotide-binding fold mimics the DNA-RNA hybrid that occupies the cleft during active transcription. The Pol II dimer is incompatible with nucleic acid binding as required for transcription and may represent an inactive storage form of the polymerase. | ||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7ozp.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7ozp.ent.gz | 982.8 KB | Display | PDB format |
PDBx/mmJSON format | 7ozp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ozp_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 7ozp_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7ozp_validation.xml.gz | 177.3 KB | Display | |
Data in CIF | 7ozp_validation.cif.gz | 268.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oz/7ozp ftp://data.pdbj.org/pub/pdb/validation_reports/oz/7ozp | HTTPS FTP |
-Related structure data
Related structure data | 13131MC 7oznC 7ozoC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-DNA-directed RNA polymerase ... , 7 types, 14 molecules AMBNCOEQFRGSIU
#1: Protein | Mass: 217450.078 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / References: DNA-directed RNA polymerase #2: Protein | Mass: 134041.422 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) References: UniProt: A0A0B8RVL1, DNA-directed RNA polymerase #3: Protein | Mass: 31439.074 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / References: UniProt: A0A481DF93 #5: Protein | Mass: 24644.318 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / References: UniProt: I3LSI7 #6: Protein | Mass: 14477.001 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / References: UniProt: F1SKN8 #7: Protein | Mass: 19314.283 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / References: UniProt: I3LJZ9 #9: Protein | Mass: 14541.221 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / References: UniProt: P60899 |
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-RNA polymerase II subunit ... , 2 types, 4 molecules DPLX
#4: Protein | Mass: 16331.255 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / References: UniProt: A0A287ADR4 #12: Protein | Mass: 7018.244 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / References: UniProt: I3LN51 |
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-DNA-directed RNA polymerases I, II, and III subunit ... , 2 types, 4 molecules HTJV
#8: Protein | Mass: 17162.273 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / References: UniProt: A0A4X1ULF2 #10: Protein | Mass: 7655.123 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / References: UniProt: A0A7K6NXI9 |
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-Protein / Non-polymers , 2 types, 12 molecules KW
#11: Protein | Mass: 13310.284 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa domesticus (domestic pig) / References: UniProt: A0A4X1UK25 #13: Chemical | ChemComp-ZN / |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: RNA Polymerase II dimer / Type: COMPLEX / Entity ID: #1-#12 / Source: NATURAL |
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Molecular weight | Value: 1.1 MDa / Experimental value: NO |
Source (natural) | Organism: Sus scrofa domesticus (domestic pig) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 42 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 41379 / Symmetry type: POINT |