EMD-20464

Single-particle
3.9 Å
EMD-20464
3D View Gallery
Deposition: 13/07/2019
Map released: 25/03/2020
Last modified: 20/03/2024
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Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-20464
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EMICSS annotations (xml)

Escherichia coli RNA polymerase promoter unwinding intermediate (TRPi2) with TraR and rpsT P2 promoter

EMD-20464

Single-particle
3.9 Å
EMD-20464
3D View Gallery
Deposition: 13/07/2019
Map released: 25/03/2020
Last modified: 20/03/2024
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Name: Escherichia coli sigma70-holoenzyme bound to TraR and Wildtype rpsT P2 as TRPi2
Complex [1]
Name: Escherichia coli sigma70-holoenzyme bound to TraR and Wildtype rpsT P2 as TRPi2
Natural source [1]
Organism: Escherichia coli
Complex Portal [1]
ID Name Overlap
CPX-4881 DNA-directed RNA polymerase holoenzyme complex, Sigma70 variant 0.67
Protein [6]
LEVO
Name: Protein TraR
Number of copies: 1
UniProtKB UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [1]

Molecular function:
zinc ion binding
Natural source
Organism: Escherichia coli
Molecular weight
Experimental Theoretical Method
- 8 kDa -
Recombinant Expression
Organism Strain Cell Plasmid
Escherichia coli BL21(DE3) - - -
LEVO
Name: DNA-directed RNA polymerase subunit alpha
EC number: 2.7.7.6
Number of copies: 3
UniProtKB UniProtKB PDBe-KB AlphaFold DB
Domains
Gene Ontology [25]
Biological process:
intracellular iron ion homeostasis DNA-templated transcription initiation DNA-templated transcription regulation of DNA-templated transcription initiation regulation of DNA-templated transcription elongation submerged biofilm formation cellular response to cell envelope stress response to heat bacterial-type flagellum assembly nitrate assimilation regulation of DNA-templated transcription, elongation iron ion homeostasis bacterial-type flagellum-dependent cell motility cell motility regulation of DNA-templated transcription, initiation transcription, DNA-templated transcription antitermination
Molecular function:
DNA-directed 5'-3' RNA polymerase activity protein dimerization activity DNA binding
Cellular location:
transcription elongation factor complex cytosol cytosolic DNA-directed RNA polymerase complex membrane cytoplasm
Natural source
Organism: Escherichia coli
Molecular weight
Experimental Theoretical Method
- 36 kDa -
Recombinant Expression
Organism Strain Cell Plasmid
Escherichia coli BL21(DE3) - - -
LEVO
Name: DNA-directed RNA polymerase subunit beta
EC number: 2.7.7.6
Number of copies: 1
UniProtKB UniProtKB UniProtKB PDBe-KB PDBe-KB AlphaFold DB AlphaFold DB AlphaFold DB
Domains
Gene Ontology [21]
Biological process:
cell motility submerged biofilm formation cellular response to cell envelope stress iron ion homeostasis bacterial-type flagellum assembly nitrate assimilation regulation of DNA-templated transcription, elongation bacterial-type flagellum-dependent cell motility response to heat transcription, DNA-templated response to antibiotic regulation of DNA-templated transcription, initiation transcription antitermination
Molecular function:
ribonucleoside binding DNA-directed 5'-3' RNA polymerase activity DNA binding
Cellular location:
transcription elongation factor complex cytosol cytosolic DNA-directed RNA polymerase complex cytoplasm membrane
Natural source
Organism: Escherichia coli
Molecular weight
Experimental Theoretical Method
- 150 kDa -
Recombinant Expression
Organism Strain Cell Plasmid
Escherichia coli BL21(DE3) - - -
LEVO
Name: DNA-directed RNA polymerase subunit beta'
EC number: 2.7.7.6
Number of copies: 1
UniProtKB UniProtKB UniProtKB PDBe-KB PDBe-KB AlphaFold DB AlphaFold DB
Domains
Gene Ontology [27]
Biological process:
intracellular iron ion homeostasis DNA-templated transcription initiation DNA-templated transcription regulation of DNA-templated transcription elongation regulation of DNA-templated transcription initiation iron ion homeostasis cell motility transcription antitermination response to antibiotic regulation of DNA-templated transcription, elongation submerged biofilm formation nitrate assimilation bacterial-type flagellum-dependent cell motility regulation of DNA-templated transcription, initiation response to heat cellular response to cell envelope stress transcription, DNA-templated bacterial-type flagellum assembly
Molecular function:
zinc ion binding magnesium ion binding DNA binding DNA-directed 5'-3' RNA polymerase activity
Cellular location:
transcription elongation factor complex cytosolic DNA-directed RNA polymerase complex cytosol cytoplasm membrane
Natural source
Organism: Escherichia coli
Molecular weight
Experimental Theoretical Method
- 158 kDa -
Recombinant Expression
Organism Strain Cell Plasmid
Escherichia coli BL21(DE3) - - -
LEVO
Name: DNA-directed RNA polymerase subunit omega
EC number: 2.7.7.6
Number of copies: 1
UniProtKB UniProtKB PDBe-KB AlphaFold DB AlphaFold DB
Domains
Gene Ontology [24]
Biological process:
intracellular iron ion homeostasis DNA-templated transcription initiation regulation of DNA-templated transcription initiation DNA-templated transcription regulation of DNA-templated transcription elongation bacterial-type flagellum assembly regulation of DNA-templated transcription, elongation iron ion homeostasis response to heat nitrate assimilation cell motility bacterial-type flagellum-dependent cell motility submerged biofilm formation cellular response to cell envelope stress transcription, DNA-templated regulation of DNA-templated transcription, initiation protein-containing complex assembly transcription antitermination
Molecular function:
DNA-directed 5'-3' RNA polymerase activity DNA binding
Cellular location:
transcription elongation factor complex RNA polymerase complex cytosol cytosolic DNA-directed RNA polymerase complex
Natural source
Organism: Escherichia coli
Molecular weight
Experimental Theoretical Method
- 10 kDa -
Recombinant Expression
Organism Strain Cell Plasmid
Escherichia coli BL21(DE3) - - -
LEVO
Name: RNA polymerase sigma factor RpoD
Number of copies: 1
UniProtKB UniProtKB PDBe-KB PDBe-KB AlphaFold DB AlphaFold DB
Domains
Gene Ontology [12]
Biological process:
regulation of DNA-templated transcription initiation negative regulation of DNA-templated transcription DNA-templated transcription initiation negative regulation of transcription, DNA-templated regulation of DNA-templated transcription, initiation DNA-templated transcription, initiation response to heat
Molecular function:
sigma factor activity DNA binding
Cellular location:
sigma factor antagonist complex cytosol cytosolic DNA-directed RNA polymerase complex
Natural source
Organism: Escherichia coli
Molecular weight
Experimental Theoretical Method
- 70 kDa -
Recombinant Expression
Organism Strain Cell Plasmid
Escherichia coli BL21(DE3) - - -
DNA [2]
DNA
Name: DNA (85-MER)
Number of copies: 1
Natural source
Organism: Escherichia coli
Molecular weight
Experimental Theoretical Method
- 26 kDa -
DNA
Name: DNA (85-MER)
Number of copies: 1
Details: Template strand of rpsT P2 DNA promoter
Natural source
Organism: Escherichia coli
Molecular weight
Experimental Theoretical Method
- 26 kDa -
Ligand [3]
Name: ZINC ION
HET code: ZN
Number of copies: 3
ChEMBL ChEBI DrugBank
Molecular weight
Experimental Theoretical Method
- 65 Da -
Name: CHAPSO
HET code: 1N7
Number of copies: 4
Molecular weight
Experimental Theoretical Method
- 631 Da -
Name: MAGNESIUM ION
HET code: MG
Number of copies: 1
ChEBI DrugBank
Molecular weight
Experimental Theoretical Method
- 24 Da -