+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20233 | |||||||||
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Title | Q21 transcription antitermination complex: loading complex | |||||||||
Map data | Q21 transcription antitermination complex: loading complex | |||||||||
Sample |
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Keywords | RNA polymerase / DNA Binding / transcription / Q-dependent antitermination / Q antiterminator factor / GENE REGULATION | |||||||||
Function / homology | Function and homology information negative regulation of termination of DNA-templated transcription / sigma factor antagonist complex / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / sigma factor activity / bacterial-type flagellum assembly ...negative regulation of termination of DNA-templated transcription / sigma factor antagonist complex / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / sigma factor activity / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / nitrate assimilation / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription initiation / cell motility / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / response to heat / protein-containing complex assembly / intracellular iron ion homeostasis / protein dimerization activity / response to antibiotic / negative regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) / Phage 21 (virus) / Escherichia coli (strain K12) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Yin Z / Ebright RH | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2019 Title: Structural basis of Q-dependent antitermination. Authors: Zhou Yin / Jason T Kaelber / Richard H Ebright / Abstract: Lambdoid bacteriophage Q protein mediates the switch from middle to late bacteriophage gene expression by enabling RNA polymerase (RNAP) to read through transcription terminators preceding ...Lambdoid bacteriophage Q protein mediates the switch from middle to late bacteriophage gene expression by enabling RNA polymerase (RNAP) to read through transcription terminators preceding bacteriophage late genes. Q loads onto RNAP engaged in promoter-proximal pausing at a Q binding element (QBE) and adjacent sigma-dependent pause element (SDPE) to yield a Q-loading complex, and Q subsequently translocates with RNAP as a pausing-deficient, termination-deficient Q-loaded complex. Here, we report high-resolution structures of 4 states on the pathway of antitermination by Q from bacteriophage 21 (Q21): Q21, the Q21-QBE complex, the Q21-loading complex, and the Q21-loaded complex. The results show that Q21 forms a torus, a "nozzle," that narrows and extends the RNAP RNA-exit channel, extruding topologically linked single-stranded RNA and preventing the formation of pause and terminator hairpins. | |||||||||
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_20233.map.gz | 39.2 MB | EMDB map data format | |
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Header (meta data) | emd-20233-v30.xml emd-20233.xml | 29.5 KB 29.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_20233_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_20233.png | 58.6 KB | ||
Filedesc metadata | emd-20233.cif.gz | 9.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20233 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20233 | HTTPS FTP |
-Validation report
Summary document | emd_20233_validation.pdf.gz | 462.5 KB | Display | EMDB validaton report |
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Full document | emd_20233_full_validation.pdf.gz | 462.1 KB | Display | |
Data in XML | emd_20233_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | emd_20233_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20233 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20233 | HTTPS FTP |
-Related structure data
Related structure data | 6p18MC 6p19C 6p1aC 6p1bC 6p1cC M: atomic model generated by this map C: citing same article (ref.) |
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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_20233.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Q21 transcription antitermination complex: loading complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.066 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : Q21-loading complex
+Supramolecule #1: Q21-loading complex
+Macromolecule #1: DNA (67-MER) fragment carrying phage-21 pR' promoter and pause el...
+Macromolecule #2: DNA (67-MER) fragment carrying phage-21 pR' promoter and pause el...
+Macromolecule #3: DNA-directed RNA polymerase subunit alpha
+Macromolecule #4: DNA-directed RNA polymerase subunit beta
+Macromolecule #5: DNA-directed RNA polymerase subunit beta'
+Macromolecule #6: DNA-directed RNA polymerase subunit omega
+Macromolecule #7: RNA polymerase sigma factor RpoD
+Macromolecule #8: Q protein
+Macromolecule #9: RNA (5'-R(P*UP*GP*GP*GP*AP*GP*AP*GP*GP*UP*A)-3')
+Macromolecule #10: ZINC ION
+Macromolecule #11: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 9 mg/mL | ||||||||||||
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Buffer | pH: 7.8 Component:
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Grid | Model: UltrAuFoil / Material: GOLD / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 300 sec. / Pretreatment - Atmosphere: AIR | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-30 / Number grids imaged: 1 / Number real images: 3010 / Average electron dose: 1.4 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 47608 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 22500 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT / Overall B value: 50 / Target criteria: 0.143 | ||||||||||||||||||||
Output model | PDB-6p18: |