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Yorodumi- EMDB-42473: Escherichia coli transcription-translation coupled complex class ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-42473 | |||||||||
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Title | Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH in loaded state, mRNA with a 24 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome | |||||||||
Map data | Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH in loaded state, mRNA with a 24 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome | |||||||||
Sample |
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Keywords | transcription / translation / RfaH / gene expression / regulation / ops / ribosome / coupling | |||||||||
Function / homology | Function and homology information transcription antitermination factor activity, DNA binding / negative regulation of cytoplasmic translational initiation / 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, DNA binding / negative regulation of cytoplasmic translational initiation / 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 / misfolded RNA binding / Group I intron splicing / RNA folding / bacterial-type flagellum-dependent cell motility / positive regulation of ribosome biogenesis / nitrate assimilation / translational termination / DnaA-L2 complex / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / translational initiation / ribosome assembly / mRNA regulatory element binding translation repressor activity / 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 / transcription antitermination / DNA-templated transcription initiation / cell motility / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / ribosomal large subunit assembly / ribonucleoside binding / mRNA 5'-UTR binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / large ribosomal subunit / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / response to heat / 5S rRNA binding / large ribosomal subunit rRNA binding / protein-containing complex assembly / cytosolic small ribosomal subunit / intracellular iron ion homeostasis / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / protein dimerization activity / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic / mRNA binding / magnesium ion binding / DNA binding / RNA binding / zinc ion binding / membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Molodtsov V / Wang C / Ebright RH | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2024 Title: Escherichia coli transcription-translation coupled complex class A (TTC-A) containing RfaH bound to ops signal, mRNA with a 21 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome Authors: Molodtsov V / Wang C / Zhang J / Kaelber JT / Blaha G / Ebright RH | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_42473.map.gz | 591.2 MB | EMDB map data format | |
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Header (meta data) | emd-42473-v30.xml emd-42473.xml | 93 KB 93 KB | Display Display | EMDB header |
Images | emd_42473.png | 40.3 KB | ||
Filedesc metadata | emd-42473.cif.gz | 19.6 KB | ||
Others | emd_42473_half_map_1.map.gz emd_42473_half_map_2.map.gz | 591.8 MB 591.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-42473 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-42473 | HTTPS FTP |
-Validation report
Summary document | emd_42473_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_42473_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_42473_validation.xml.gz | 20.3 KB | Display | |
Data in CIF | emd_42473_validation.cif.gz | 24.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42473 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42473 | HTTPS FTP |
-Related structure data
Related structure data | 8uqlMC 8upoC 8uprC 8uqmC 8uqpC 8ur0C 8urhC 8uriC 8urxC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_42473.map.gz / Format: CCP4 / Size: 729 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH in loaded state, mRNA with a 24 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.7983 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_42473_half_map_1.map | ||||||||||||
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Annotation | half-map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half-map 1
File | emd_42473_half_map_2.map | ||||||||||||
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Annotation | half-map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Escherichia coli transcription-translation coupled complex class ...
+Supramolecule #1: Escherichia coli transcription-translation coupled complex class ...
+Macromolecule #1: Ribosomal protein L21
+Macromolecule #2: 50S ribosomal protein L22
+Macromolecule #3: 50S ribosomal protein L23
+Macromolecule #4: 50S ribosomal protein L24
+Macromolecule #5: 50S ribosomal protein L25
+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: 30S ribosomal protein S18
+Macromolecule #18: 30S ribosomal protein S20
+Macromolecule #19: 30S ribosomal protein S21
+Macromolecule #20: 30S ribosomal protein S2
+Macromolecule #21: 30S ribosomal protein S1
+Macromolecule #22: 30S ribosomal protein S3
+Macromolecule #23: 30S ribosomal protein S4
+Macromolecule #24: 30S ribosomal protein S5
+Macromolecule #25: 30S ribosomal protein S6
+Macromolecule #26: 30S ribosomal protein S7
+Macromolecule #27: 30S ribosomal protein S8
+Macromolecule #28: 30S ribosomal protein S9
+Macromolecule #29: 30S ribosomal protein S10
+Macromolecule #30: 30S ribosomal protein S11
+Macromolecule #31: 30S ribosomal protein S12
+Macromolecule #32: 30S ribosomal protein S14
+Macromolecule #33: 30S ribosomal protein S15
+Macromolecule #34: 30S ribosomal protein S16
+Macromolecule #35: 30S ribosomal protein S17
+Macromolecule #36: 30S ribosomal protein S19
+Macromolecule #37: 30S ribosomal protein S13
+Macromolecule #38: 50S ribosomal protein L11
+Macromolecule #39: 50S ribosomal protein L7/L12
+Macromolecule #41: 50S ribosomal protein L27
+Macromolecule #42: 50S ribosomal protein L28
+Macromolecule #44: 50S ribosomal protein L29
+Macromolecule #45: 50S ribosomal protein L30
+Macromolecule #46: 50S ribosomal protein L31
+Macromolecule #47: 50S ribosomal protein L2
+Macromolecule #48: 50S ribosomal protein L32
+Macromolecule #49: 50S ribosomal protein L3
+Macromolecule #50: 50S ribosomal protein L33
+Macromolecule #51: 50S ribosomal protein L4
+Macromolecule #52: 50S ribosomal protein L34
+Macromolecule #53: 50S ribosomal protein L5
+Macromolecule #54: 50S ribosomal protein L35
+Macromolecule #55: 50S ribosomal protein L6
+Macromolecule #56: 50S ribosomal protein L36
+Macromolecule #57: 50S ribosomal protein L9
+Macromolecule #58: 50S ribosomal protein L13
+Macromolecule #59: 50S ribosomal protein L14
+Macromolecule #60: 50S ribosomal protein L15
+Macromolecule #61: 50S ribosomal protein L16
+Macromolecule #62: 50S ribosomal protein L17
+Macromolecule #63: 50S ribosomal protein L18
+Macromolecule #64: 50S ribosomal protein L19
+Macromolecule #65: 50S ribosomal protein L20
+Macromolecule #6: NT DNA
+Macromolecule #7: T DNA
+Macromolecule #8: mRNA with 24 nt long spacer
+Macromolecule #10: E-site and P-site fMet-tRNA
+Macromolecule #17: 16S rRNA
+Macromolecule #40: 23S rRNA
+Macromolecule #43: 5S rRNA
+Macromolecule #66: MAGNESIUM ION
+Macromolecule #67: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 28.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.25 µm |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 35602 |
Initial angle assignment | Type: COMMON LINE |
Final angle assignment | Type: COMMON LINE |