[English] 日本語
![](img/lk-miru.gif)
- EMDB-13034: Cryo-EM structure of the cellular negative regulator TFS4 bound t... -
+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-13034 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of the cellular negative regulator TFS4 bound to the archaeal RNA polymerase | |||||||||
![]() | Sharpened map from Autosharpen, Phenix v1.15.2 | |||||||||
![]() |
| |||||||||
![]() | negative regulator / inhibitor / Archaea / Sso TFS4 / trancript cleavage factor / TRANSCRIPTION | |||||||||
Function / homology | ![]() 3 iron, 4 sulfur cluster binding / transcription initiation at RNA polymerase III promoter / RNA polymerase III activity / RNA polymerase II activity / tRNA transcription by RNA polymerase III / RNA polymerase I activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity ...3 iron, 4 sulfur cluster binding / transcription initiation at RNA polymerase III promoter / RNA polymerase III activity / RNA polymerase II activity / tRNA transcription by RNA polymerase III / RNA polymerase I activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / defense response to virus / protein dimerization activity / nucleotide binding / negative regulation of DNA-templated transcription / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.61 Å | |||||||||
![]() | Pilotto S / Fouqueau T | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Structural basis of RNA polymerase inhibition by viral and host factors. Authors: Simona Pilotto / Thomas Fouqueau / Natalya Lukoyanova / Carol Sheppard / Soizick Lucas-Staat / Luis Miguel Díaz-Santín / Dorota Matelska / David Prangishvili / Alan C M Cheung / Finn Werner / ![]() ![]() Abstract: RNA polymerase inhibition plays an important role in the regulation of transcription in response to environmental changes and in the virus-host relationship. Here we present the high-resolution ...RNA polymerase inhibition plays an important role in the regulation of transcription in response to environmental changes and in the virus-host relationship. Here we present the high-resolution structures of two such RNAP-inhibitor complexes that provide the structural bases underlying RNAP inhibition in archaea. The Acidianus two-tailed virus encodes the RIP factor that binds inside the DNA-binding channel of RNAP, inhibiting transcription by occlusion of binding sites for nucleic acid and the transcription initiation factor TFB. Infection with the Sulfolobus Turreted Icosahedral Virus induces the expression of the host factor TFS4, which binds in the RNAP funnel similarly to eukaryotic transcript cleavage factors. However, TFS4 allosterically induces a widening of the DNA-binding channel which disrupts trigger loop and bridge helix motifs. Importantly, the conformational changes induced by TFS4 are closely related to inactivated states of RNAP in other domains of life indicating a deep evolutionary conservation of allosteric RNAP inhibition. | |||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 128.2 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 40.6 KB 40.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11.7 KB | Display | ![]() |
Images | ![]() | 121.8 KB | ||
Filedesc metadata | ![]() | 10.3 KB | ||
Others | ![]() ![]() ![]() | 10 MB 110.4 MB 110.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7oqyMC ![]() 7ok0C ![]() 7oq4C C: citing same article ( M: atomic model generated by this map |
---|---|
Similar structure data |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Sharpened map from Autosharpen, Phenix v1.15.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.085 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Additional map: Sharpened map from postprocess, relion v3.0. The map...
File | emd_13034_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Sharpened map from postprocess, relion v3.0. The map was obtained from Multibody refinement and it corresponds to the smaller body with higher flexibility | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half1 map from 3D refinement, relion v3.0
File | emd_13034_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half1 map from 3D refinement, relion v3.0 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half2 map from 3D refinement, relion v3.0
File | emd_13034_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half2 map from 3D refinement, relion v3.0 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
+Entire : TFS4 bound to the RNA polymerase
+Supramolecule #1: TFS4 bound to the RNA polymerase
+Macromolecule #1: DNA-directed RNA polymerase subunit A'
+Macromolecule #2: DNA-directed RNA polymerase subunit B
+Macromolecule #3: DNA-directed RNA polymerase subunit A''
+Macromolecule #4: DNA-directed RNA polymerase subunit D
+Macromolecule #5: DNA-directed RNA polymerase subunit E
+Macromolecule #6: DNA-directed RNA polymerase, subunit F
+Macromolecule #7: DNA-directed RNA polymerase, subunit G
+Macromolecule #8: DNA-directed RNA polymerase subunit H
+Macromolecule #9: DNA-directed RNA polymerase subunit K
+Macromolecule #10: DNA-directed RNA polymerase subunit L
+Macromolecule #11: DNA-directed RNA polymerase subunit N
+Macromolecule #12: DNA-directed RNA polymerase subunit P
+Macromolecule #13: Conserved protein
+Macromolecule #14: DNA-directed RNA polymerase, subunit M (RpoM-2)
+Macromolecule #15: MAGNESIUM ION
+Macromolecule #16: ZINC ION
+Macromolecule #17: FE3-S4 CLUSTER
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Concentration | 0.4 mg/mL | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 7 Component:
| ||||||||||||||||||
Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR Details: the grid was coated with graphene oxide after to be glow discharged and before applying the sample | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 94 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV | ||||||||||||||||||
Details | the sample was applied twice on the grid before vetrification |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 1760 / Average exposure time: 2.0 sec. / Average electron dose: 45.2 e/Å2 Details: images were collected as movie-stacks of 40 frames in super resolution mode |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |