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- EMDB-42504: Escherichia coli transcription-translation coupled complex class ... -
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Open data
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Basic information
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Title | Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH bound to ops signal, NusA, mRNA with a 30 nt long spacer, and fMet-tRNA in E-site and P-site of the ribosome | |||||||||
![]() | Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH bound to ops signal, NusA, mRNA with a 30 nt long spacer, and fMet-tRNA in E-site and P-site of the ribosome | |||||||||
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![]() | transcription / translation / coupling / expressome / NusA / RfaH / RNA / RNA polymerase / ribosome | |||||||||
Function / homology | ![]() transcription antitermination factor activity, DNA binding / transcription elongation-coupled chromatin remodeling / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / stringent response / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / transcription antitermination factor activity, RNA binding ...transcription antitermination factor activity, DNA binding / transcription elongation-coupled chromatin remodeling / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / stringent response / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / bacterial-type flagellum-dependent cell motility / nitrate assimilation / translational termination / DnaA-L2 complex / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / mRNA regulatory element binding translation repressor activity / ribosome assembly / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome / transcription elongation factor complex / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / ribosomal large subunit assembly / transcription antitermination / DNA-templated transcription initiation / cell motility / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / ribonucleoside binding / mRNA 5'-UTR binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / large ribosomal subunit / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / response to heat / cytosolic small ribosomal subunit / protein-containing complex assembly / intracellular iron ion homeostasis / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / protein dimerization activity / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / DNA-binding transcription factor activity / response to antibiotic / nucleotide binding / mRNA binding / magnesium ion binding / DNA binding / RNA binding / zinc ion binding / membrane / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
![]() | Molodtsov V / Wang C / Ebright RH | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of RfaH-mediated transcription-translation coupling. Authors: Vadim Molodtsov / Chengyuan Wang / Jing Zhang / Jason T Kaelber / Gregor Blaha / Richard H Ebright / ![]() ![]() ![]() Abstract: The NusG paralog RfaH mediates bacterial transcription-translation coupling in genes that contain a DNA sequence element, termed an ops site, required for pausing RNA polymerase (RNAP) and for ...The NusG paralog RfaH mediates bacterial transcription-translation coupling in genes that contain a DNA sequence element, termed an ops site, required for pausing RNA polymerase (RNAP) and for loading RfaH onto the paused RNAP. Here, we report cryo-electron microscopy structures of transcription-translation complexes (TTCs) containing Escherichia coli RfaH. The results show that RfaH bridges RNAP and the ribosome, with the RfaH N-terminal domain interacting with RNAP and the RfaH C-terminal domain interacting with the ribosome. The results show that the distribution of translational and orientational positions of RNAP relative to the ribosome in RfaH-coupled TTCs is more restricted than in NusG-coupled TTCs because of the more restricted flexibility of the RfaH interdomain linker. The results further suggest that the structural organization of RfaH-coupled TTCs in the 'loading state', in which RNAP and RfaH are located at the ops site during formation of the TTC, is the same as the structural organization of RfaH-coupled TTCs in the 'loaded state', in which RNAP and RfaH are located at positions downstream of the ops site during function of the TTC. The results define the structural organization of RfaH-containing TTCs and set the stage for analysis of functions of RfaH during translation initiation and transcription-translation coupling. | |||||||||
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 410.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 94.6 KB 94.6 KB | Display Display | ![]() |
Images | ![]() | 40.9 KB | ||
Filedesc metadata | ![]() | 31.7 KB | ||
Others | ![]() ![]() | 410.4 MB 411 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8uryMC ![]() 8upoC ![]() 8uprC ![]() 8uqlC ![]() 8uqmC ![]() 8uqpC ![]() 8ur0C ![]() 8urhC ![]() 8uriC ![]() 8urxC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH bound to ops signal, NusA, mRNA with a 30 nt long spacer, and fMet-tRNA in E-site and P-site of the ribosome | ||||||||||||||||||||
Voxel size | X=Y=Z: 1 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: half map 2
File | emd_42504_half_map_1.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
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Density Histograms |
-Half map: half map 1
File | emd_42504_half_map_2.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
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Density Histograms |
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Sample components
+Entire : Escherichia coli transcription-translation coupled complex class ...
+Supramolecule #1: Escherichia coli transcription-translation coupled complex class ...
+Macromolecule #1: 50S ribosomal protein L21
+Macromolecule #2: 50S ribosomal protein L22
+Macromolecule #3: 50S ribosomal protein L23
+Macromolecule #4: 50S ribosomal protein L24
+Macromolecule #5: Large ribosomal subunit protein bL25
+Macromolecule #9: 50S ribosomal protein L10
+Macromolecule #11: DNA-directed RNA polymerase subunit beta
+Macromolecule #12: Transcription antitermination protein RfaH
+Macromolecule #13: DNA-directed RNA polymerase subunit alpha
+Macromolecule #14: DNA-directed RNA polymerase subunit beta'
+Macromolecule #15: DNA-directed RNA polymerase subunit omega
+Macromolecule #16: Transcription termination/antitermination protein NusA
+Macromolecule #17: 30S ribosomal protein S18
+Macromolecule #19: 30S ribosomal protein S20
+Macromolecule #20: 30S ribosomal protein S21
+Macromolecule #21: 30S ribosomal protein S2
+Macromolecule #22: Small ribosomal subunit protein bS1
+Macromolecule #23: 30S ribosomal protein S3
+Macromolecule #24: 30S ribosomal protein S4
+Macromolecule #25: 30S ribosomal protein S5
+Macromolecule #26: 30S ribosomal protein S6
+Macromolecule #27: 30S ribosomal protein S7
+Macromolecule #28: 30S ribosomal protein S8
+Macromolecule #29: 30S ribosomal protein S9
+Macromolecule #30: Small ribosomal subunit protein uS10
+Macromolecule #31: 30S ribosomal protein S11
+Macromolecule #32: 30S ribosomal protein S12
+Macromolecule #33: 30S ribosomal protein S14
+Macromolecule #34: 30S ribosomal protein S15
+Macromolecule #35: 30S ribosomal protein S16
+Macromolecule #36: 30S ribosomal protein S17
+Macromolecule #37: 30S ribosomal protein S19
+Macromolecule #38: 30S ribosomal protein S13
+Macromolecule #39: 50S ribosomal protein L11
+Macromolecule #40: 50S ribosomal protein L7/L12
+Macromolecule #42: Large ribosomal subunit protein bL27
+Macromolecule #43: 50S ribosomal protein L28
+Macromolecule #45: Large ribosomal subunit protein uL29
+Macromolecule #46: 50S ribosomal protein L30
+Macromolecule #47: Large ribosomal subunit protein bL31
+Macromolecule #48: 50S ribosomal protein L2
+Macromolecule #49: 50S ribosomal protein L32
+Macromolecule #50: 50S ribosomal protein L3
+Macromolecule #51: 50S ribosomal protein L33
+Macromolecule #52: 50S ribosomal protein L4
+Macromolecule #53: 50S ribosomal protein L34
+Macromolecule #54: 50S ribosomal protein L5
+Macromolecule #55: Large ribosomal subunit protein bL35
+Macromolecule #56: 50S ribosomal protein L6
+Macromolecule #57: 50S ribosomal protein L36
+Macromolecule #58: 50S ribosomal protein L9
+Macromolecule #59: Large ribosomal subunit protein uL13
+Macromolecule #60: 50S ribosomal protein L14
+Macromolecule #61: 50S ribosomal protein L15
+Macromolecule #62: 50S ribosomal protein L16
+Macromolecule #63: 50S ribosomal protein L17
+Macromolecule #64: 50S ribosomal protein L18
+Macromolecule #65: Large ribosomal subunit protein bL19
+Macromolecule #66: 50S ribosomal protein L20
+Macromolecule #6: NT DNA ops
+Macromolecule #7: T DNA
+Macromolecule #8: mRNA with 30 nt long spacer
+Macromolecule #10: E-site and P-site fMet-tRNA
+Macromolecule #18: 16S rRNA
+Macromolecule #41: 23S rRNA
+Macromolecule #44: 5S rRNA
+Macromolecule #67: MAGNESIUM ION
+Macromolecule #68: 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
Buffer | pH: 7.6 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 45.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 12096 |
Initial angle assignment | Type: COMMON LINE |
Final angle assignment | Type: COMMON LINE |