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Yorodumi- EMDB-9786: Cryo-EM structure of Xanthomonos oryzae transcription elongation ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9786 | |||||||||
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Title | Cryo-EM structure of Xanthomonos oryzae transcription elongation complex with the bacteriophage protein P7 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | RNA polymerase / transcription termination / anti-termination / RNAP clamp / phage / transcription initiation / P7 / Xanthomonos oryzae / Xp10 / transcription | |||||||||
Function / homology | Function and homology information DNA-directed RNA polymerase complex / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Xanthomonas oryzae (bacteria) / Xanthomonas oryzae pv. oryzae PXO99A (bacteria) / Xanthomonas oryzae pv. oryzae MAFF 311018 (bacteria) / Xanthomonas oryzae pv. oryzae (bacteria) / Xanthomonas virus Xp10 / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.95 Å | |||||||||
Authors | You LL / Zhang Y | |||||||||
Funding support | China, 1 items
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Citation | Journal: Nat Commun / Year: 2019 Title: Structural basis for transcription antitermination at bacterial intrinsic terminator. Authors: Linlin You / Jing Shi / Liqiang Shen / Lingting Li / Chengli Fang / Chengzhi Yu / Wenbo Cheng / Yu Feng / Yu Zhang / Abstract: Bacteriophages typically hijack the host bacterial transcriptional machinery to regulate their own gene expression and that of the host bacteria. The structural basis for bacteriophage protein- ...Bacteriophages typically hijack the host bacterial transcriptional machinery to regulate their own gene expression and that of the host bacteria. The structural basis for bacteriophage protein-mediated transcription regulation-in particular transcription antitermination-is largely unknown. Here we report the 3.4 Å and 4.0 Å cryo-EM structures of two bacterial transcription elongation complexes (P7-NusA-TEC and P7-TEC) comprising the bacteriophage protein P7, a master host-transcription regulator encoded by bacteriophage Xp10 of the rice pathogen Xanthomonas oryzae pv. Oryzae (Xoo) and discuss the mechanisms by which P7 modulates the host bacterial RNAP. The structures together with biochemical evidence demonstrate that P7 prevents transcription termination by plugging up the RNAP RNA-exit channel and impeding RNA-hairpin formation at the intrinsic terminator. Moreover, P7 inhibits transcription initiation by restraining RNAP-clamp motions. Our study reveals the structural basis for transcription antitermination by phage proteins and provides insights into bacterial transcription regulation. | |||||||||
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_9786.map.gz | 8 MB | EMDB map data format | |
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Header (meta data) | emd-9786-v30.xml emd-9786.xml | 31.8 KB 31.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_9786_fsc.xml | 10.7 KB | Display | FSC data file |
Images | emd_9786.png | 175.6 KB | ||
Filedesc metadata | emd-9786.cif.gz | 9.3 KB | ||
Others | emd_9786_half_map_1.map.gz emd_9786_half_map_2.map.gz | 80.8 MB 80.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9786 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9786 | HTTPS FTP |
-Validation report
Summary document | emd_9786_validation.pdf.gz | 796.8 KB | Display | EMDB validaton report |
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Full document | emd_9786_full_validation.pdf.gz | 796.3 KB | Display | |
Data in XML | emd_9786_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | emd_9786_validation.cif.gz | 23.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9786 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9786 | HTTPS FTP |
-Related structure data
Related structure data | 6j9fMC 9785C 6j9eC 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_9786.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.014 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: #2
File | emd_9786_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_9786_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Xoo transcription elongation complex with P7(P7-TEC)
+Supramolecule #1: Xoo transcription elongation complex with P7(P7-TEC)
+Macromolecule #1: DNA-directed RNA polymerase subunit alpha
+Macromolecule #2: DNA-directed RNA polymerase subunit beta
+Macromolecule #3: DNA-directed RNA polymerase subunit beta'
+Macromolecule #4: DNA-directed RNA polymerase subunit omega
+Macromolecule #8: 45L
+Macromolecule #5: DNA (29-MER)
+Macromolecule #6: DNA (29-MER)
+Macromolecule #7: RNA (5'-R(P*AP*GP*CP*GP*GP*AP*GP*AP*GP*GP*UP*A)-3')
+Macromolecule #9: MAGNESIUM ION
+Macromolecule #10: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 9.5 mg/mL | |||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: C-flat-1.2/1.3 4C / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 120 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: OTHER | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 8 seconds before plunging. | |||||||||||||||
Details | This sample was monodisperse |
-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 / Number grids imaged: 1 / Number real images: 2271 / Average exposure time: 8.0 sec. / Average electron dose: 1.675 e/Å2 |
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: 2.6 µm / Nominal defocus min: 2.0 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing #1
+Image processing #2
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT | ||||||
Output model | PDB-6j9f: |