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Yorodumi- EMDB-12960: Cryo-EM structure of the Sulfolobus acidocaldarius RNA polymerase... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12960 | |||||||||
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Title | Cryo-EM structure of the Sulfolobus acidocaldarius RNA polymerase at 2.88 A | |||||||||
Map data | sharpened map obtained from Autosharpen (Phenix v.1.15), box size 332 pixels | |||||||||
Sample |
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Function / homology | Function and homology information 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 / protein dimerization activity / nucleotide binding / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770) (acidophilic) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Pilotto S / Fouqueau T / Lukoyanova N / Sheppard C / Lucas-Staat S / Diaz-Santin LM / Matelska D / Prangishvili D / Cheung ACM / Werner F | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Nat Commun / Year: 2021 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12960.map.gz | 125.8 MB | EMDB map data format | |
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Header (meta data) | emd-12960-v30.xml emd-12960.xml | 37.1 KB 37.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12960_fsc.xml | 11.7 KB | Display | FSC data file |
Images | emd_12960.png | 104.4 KB | ||
Others | emd_12960_half_map_1.map.gz emd_12960_half_map_2.map.gz | 110.2 MB 110.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12960 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12960 | HTTPS FTP |
-Related structure data
Related structure data | 7ok0MC 7oq4C 7oqyC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_12960.map.gz / Format: CCP4 / Size: 139.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | sharpened map obtained from Autosharpen (Phenix v.1.15), box size 332 pixels | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.085 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: half1 map obtained from Refine3D (Relion v.3.0), box size 332 pixels
File | emd_12960_half_map_1.map | ||||||||||||
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Annotation | half1 map obtained from Refine3D (Relion v.3.0), box size 332 pixels | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half2 map obtained from Refine3D (Relion v.3.0), box size 332 pixels
File | emd_12960_half_map_2.map | ||||||||||||
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Annotation | half2 map obtained from Refine3D (Relion v.3.0), box size 332 pixels | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : apo-RNA polymerase
+Supramolecule #1: apo-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: MAGNESIUM ION
+Macromolecule #15: ZINC ION
+Macromolecule #16: FE3-S4 CLUSTER
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.06 mg/mL | |||||||||||||||
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Buffer | pH: 7 Component:
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Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR Details: The grid was coated with graphene oxide prior to use | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 94 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV | |||||||||||||||
Details | The sample was crosslinked with bis(sulfosuccinimidyl)suberate (BS3) |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 1676 / Average electron dose: 44.46 e/Å2 Details: Images were collected in movie-mode for a total of 40 frames in super-resolution mode and with a tilt of 30 degrees |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.3 µm / Nominal magnification: 81000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 57.7772 / Target criteria: CC |
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Output model | PDB-7ok0: |