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- EMDB-11851: Atomic structure of the poxvirus initially transcribing complex i... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-11851 | |||||||||
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Title | Atomic structure of the poxvirus initially transcribing complex in conformation 3 | |||||||||
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Function / homology | ![]() viral transcription / RNA polymerase II activity / RNA polymerase I activity / DNA-directed RNA polymerase complex / nucleotidyltransferase activity / virion component / DNA-templated transcription termination / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase ...viral transcription / RNA polymerase II activity / RNA polymerase I activity / DNA-directed RNA polymerase complex / nucleotidyltransferase activity / virion component / DNA-templated transcription termination / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / DNA-binding transcription factor activity / DNA-templated transcription / DNA binding / zinc ion binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.01 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
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 7.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 25.6 KB 25.6 KB | Display Display | ![]() |
Images | ![]() | 65.5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ap9MC ![]() 7amvC ![]() 7aofC ![]() 7aohC ![]() 7aozC ![]() 7ap8C 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 | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.0635 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 : Vaccinia transcription pre-initiation complex
+Supramolecule #1: Vaccinia transcription pre-initiation complex
+Supramolecule #2: DNA-directed RNA polymerase and Protein H4
+Supramolecule #3: RNA
+Supramolecule #4: Synthetic promoter DNA oligomer, template strand
+Macromolecule #1: DNA-directed RNA polymerase 147 kDa polypeptide
+Macromolecule #2: DNA-directed RNA polymerase
+Macromolecule #3: DNA-directed RNA polymerase 35 kDa subunit
+Macromolecule #4: DNA-directed RNA polymerase subunit
+Macromolecule #5: DNA-directed RNA polymerase 19 kDa subunit
+Macromolecule #6: DNA-directed RNA polymerase 18 kDa subunit
+Macromolecule #7: Protein H4
+Macromolecule #8: DNA-directed RNA polymerase 7 kDa subunit
+Macromolecule #10: DNA-directed RNA polymerase 30 kDa polypeptide
+Macromolecule #9: RNA (5'-R(P*AP*UP*AP*AP*A)-3')
+Macromolecule #11: Synthetic promoter DNA oligomer, template strand
+Macromolecule #12: MAGNESIUM ION
+Macromolecule #13: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.15 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: Quantifoil / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE |
Details | monodisperse sample prepared by sucrose gradient centrifugation |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 3 / Average exposure time: 74.99 sec. / Average electron dose: 78.9 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 96165 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |