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Yorodumi- PDB-8upr: Escherichia coli transcription-translation coupled complex class ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8upr | ||||||
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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 | ||||||
Components |
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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 / cytosolic DNA-directed RNA polymerase complex / stringent response / 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 / cytosolic DNA-directed RNA polymerase complex / stringent response / 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 / regulation of DNA-templated transcription elongation / cytosolic ribosome assembly / 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 / 5S rRNA binding / response to heat / 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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.3 Å | ||||||
Authors | Molodtsov, V. / Wang, C. / Ebright, R.H. | ||||||
Funding support | United States, 1items
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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, J.T. / Blaha, G. / Ebright, R.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8upr.cif.gz | 5.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8upr.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8upr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8upr_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 8upr_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 8upr_validation.xml.gz | 280.2 KB | Display | |
Data in CIF | 8upr_validation.cif.gz | 500.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/up/8upr ftp://data.pdbj.org/pub/pdb/validation_reports/up/8upr | HTTPS FTP |
-Related structure data
Related structure data | 42454MC 8upoC 8uqlC 8uqmC 8uqpC 8ur0C 8urhC 8uriC 8urxC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 2 types, 2 molecules 0AB
#1: Protein | Mass: 11586.374 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplU, ECMP0215528_3699 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A829CSJ4 |
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#12: Protein | Mass: 18364.217 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rfaH / Production host: Escherichia coli (E. coli) / References: UniProt: C3SK02 |
+50S ribosomal protein ... , 31 types, 31 molecules 12349YZbcefghijklmnopqrstuvwxyz
-DNA chain , 2 types, 2 molecules 56
#6: DNA chain | Mass: 11786.552 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) |
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#7: DNA chain | Mass: 11534.374 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) |
-RNA chain , 5 types, 6 molecules 7ABDad
#8: RNA chain | Mass: 11993.820 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) | ||||||
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#10: RNA chain | Mass: 24496.617 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: GenBank: 1870104878 #17: RNA chain | | Mass: 499690.031 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: GenBank: 1732209707 #40: RNA chain | | Mass: 941635.438 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: GenBank: 937521852 #43: RNA chain | | Mass: 38790.090 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: GenBank: 1273279017 |
-DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules AAACADAEAF
#11: Protein | Mass: 150820.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: rpoB, groN, nitB, rif, ron, stl, stv, tabD, b3987, JW3950 Production host: Escherichia coli (E. coli) / References: UniProt: P0A8V2, DNA-directed RNA polymerase | ||||
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#13: Protein | Mass: 36558.680 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoA, pez, phs, sez, b3295, JW3257 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7Z4, DNA-directed RNA polymerase #14: Protein | | Mass: 155366.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoC, tabB, b3988, JW3951 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A8T7, DNA-directed RNA polymerase #15: Protein | | Mass: 10249.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoZ, b3649, JW3624 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A800, DNA-directed RNA polymerase |
+30S ribosomal protein ... , 21 types, 21 molecules CEFGHIJKLMNOPQRSTUVWX
-Non-polymers , 2 types, 3 molecules
#66: Chemical | ChemComp-MG / |
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#67: Chemical |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: 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 Type: COMPLEX / Entity ID: #1-#64 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Escherichia coli (E. coli) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1250 nm |
Image recording | Electron dose: 28 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 5.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 10509 / Symmetry type: POINT |