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- PDB-7amv: Atomic structure of the poxvirus transcription pre-initiation com... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7amv | ||||||
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Title | Atomic structure of the poxvirus transcription pre-initiation complex in the initially melted state | ||||||
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![]() | TRANSCRIPTION / Vaccinia / Virus / RNA polymerase / DNA-dependent / pre-initiation complex / PIC / initially melted / poxvirus / poxviridae | ||||||
Function / homology | ![]() virion component => GO:0044423 / hydrolase activity, acting on glycosyl bonds / viral transcription / RNA polymerase I activity / metabolic process / DNA-directed RNA polymerase complex / RNA polymerase II activity / nucleotidyltransferase activity / virion component / DNA-templated transcription termination ...virion component => GO:0044423 / hydrolase activity, acting on glycosyl bonds / viral transcription / RNA polymerase I activity / metabolic process / DNA-directed RNA polymerase complex / RNA polymerase II activity / nucleotidyltransferase activity / virion component / DNA-templated transcription termination / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / membrane => GO:0016020 / DNA-binding transcription factor activity / DNA-templated transcription / positive regulation of DNA-templated transcription / DNA binding / zinc ion binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||
![]() | Grimm, C. / Bartuli, J. / Fischer, U. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of the complete poxvirus transcription initiation process. Authors: Clemens Grimm / Julia Bartuli / Bettina Boettcher / Aladar A Szalay / Utz Fischer / ![]() Abstract: Poxviruses express their genes in the cytoplasm of infected cells using a virus-encoded multi-subunit polymerase (vRNAP) and unique transcription factors. We present cryo-EM structures that uncover ...Poxviruses express their genes in the cytoplasm of infected cells using a virus-encoded multi-subunit polymerase (vRNAP) and unique transcription factors. We present cryo-EM structures that uncover the complete transcription initiation phase of the poxvirus vaccinia. In the pre-initiation complex, the heterodimeric early transcription factor VETFs/l adopts an arc-like shape spanning the polymerase cleft and anchoring upstream and downstream promoter elements. VETFI emerges as a TBP-like protein that inserts asymmetrically into the DNA major groove, triggers DNA melting, ensures promoter recognition and enforces transcription directionality. The helicase VETFs fosters promoter melting and the phospho-peptide domain (PPD) of vRNAP subunit Rpo30 enables transcription initiation. An unprecedented upstream promoter scrunching mechanism assisted by the helicase NPH-I probably fosters promoter escape and transition into elongation. Our structures shed light on unique mechanisms of poxviral gene expression and aid the understanding of thus far unexplained universal principles in transcription. | ||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1009.1 KB | Display | ![]() |
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PDB format | ![]() | 827.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 848.3 KB | Display | ![]() |
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Full document | ![]() | 869.4 KB | Display | |
Data in XML | ![]() | 121 KB | Display | |
Data in CIF | ![]() | 190.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 11824MC ![]() 7aofC ![]() 7aohC ![]() 7aozC ![]() 7ap8C ![]() 7ap9C 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 ... , 7 types, 7 molecules ACEFGJS
#1: Protein | Mass: 146995.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#3: Protein | Mass: 35430.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#4: Protein | Mass: 21365.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#5: Protein | Mass: 19020.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#6: Protein | Mass: 17917.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#8: Protein | Mass: 7299.715 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#11: Protein | Mass: 29834.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Protein , 4 types, 4 molecules BIKW
#2: Protein | Mass: 133526.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#7: Protein | Mass: 93667.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#9: Protein | Mass: 82398.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#13: Protein | Mass: 73923.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Synthetic promoter DNA oligomer, ... , 2 types, 2 molecules NT
#10: DNA chain | Mass: 18417.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#12: DNA chain | Mass: 18547.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Non-polymers , 2 types, 5 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/ZN.gif)
#14: Chemical | ChemComp-MG / |
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#15: Chemical | ChemComp-ZN / |
-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 |
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Sample preparation
Component | Name: Vaccinia transcription pre-initiation complex / Type: COMPLEX / Entity ID: #1-#13 / Source: NATURAL |
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Molecular weight | Value: 0.67 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 0.15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: monodisperse sample prepared by sucrose gradient centrifugation |
Specimen support | Grid material: COPPER / Grid type: Quantifoil |
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 |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 74.99 sec. / Electron dose: 78.9 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 3 |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 181788 / Symmetry type: POINT |