› 7ubm

Electron Microscopy
3.13Å resolution

Transcription antitermination complex: "pre-engaged" Qlambda-loading complex

Released:
DOI: 10.2210/pdb7ubm/pdb
PDB entry 7ubm coloured by chain, front view.
PDB entry 7ubm coloured by chain, side view.
PDB entry 7ubm coloured by chain, top view.
Source organisms:
Primary publication:
In transcription antitermination by Qλ, NusA induces refolding of Qλ to form a nozzle that extends the RNA polymerase RNA-exit channel.
Yin Z, Bird JG, Kaelber JT, Nickels BE, Ebright RH
Proc Natl Acad Sci U S A 119 e2205278119 (2022)
PMID: 35951650
Related structures: EMD-26438

Function and Biology Details

Reaction catalysed: 
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero decamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-122182 (preferred)
Entry contents:
6 distinct polypeptide molecules
2 distinct DNA molecules
1 distinct RNA molecule
Macromolecules (9 distinct):
DNA-directed RNA polymerase subunit alpha Chains: A, B
Molecule details ›
Chains: A, B
Length: 329 amino acids
Theoretical weight: 36.56 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A7Z4 (Residues: 1-329; Coverage: 100%)
Gene names: JW3257, b3295, pez, phs, rpoA, sez
Sequence domains:
DNA-directed RNA polymerase subunit beta Chain: C
Molecule details ›
Chain: C
Length: 1342 amino acids
Theoretical weight: 150.82 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A8V2 (Residues: 1-1342; Coverage: 100%)
Gene names: JW3950, b3987, groN, nitB, rif, ron, rpoB, stl, stv, tabD
Sequence domains:
DNA-directed RNA polymerase subunit beta' Chain: D
Molecule details ›
Chain: D
Length: 1430 amino acids
Theoretical weight: 158.31 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A8T7 (Residues: 1-1407; Coverage: 100%)
Gene names: JW3951, b3988, rpoC, tabB
Sequence domains:
DNA-directed RNA polymerase subunit omega Chain: E
Molecule details ›
Chain: E
Length: 91 amino acids
Theoretical weight: 10.25 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A800 (Residues: 1-91; Coverage: 100%)
Gene names: JW3624, b3649, rpoZ
Sequence domains: RNA polymerase Rpb6
RNA polymerase sigma factor RpoD Chain: F
Molecule details ›
Chain: F
Length: 627 amino acids
Theoretical weight: 71.91 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P00579 (Residues: 1-613; Coverage: 100%)
Gene names: JW3039, alt, b3067, rpoD
Sequence domains:
Antitermination protein Q Chain: Q
Molecule details ›
Chain: Q
Length: 207 amino acids
Theoretical weight: 22.51 KDa
Source organism: Escherichia phage Lambda
Expression system: Escherichia coli
UniProt:
  • Canonical: P03047 (Residues: 1-207; Coverage: 100%)
Gene name: Q
Sequence domains: Antitermination protein
DNA (53-MER) Chain: 1
Molecule details ›
Chain: 1
Length: 61 nucleotides
Theoretical weight: 18.93 KDa
DNA (52-MER) Chain: 2
Molecule details ›
Chain: 2
Length: 61 nucleotides
Theoretical weight: 18.6 KDa
RNA (5'-R(*UP*GP*GP*GP*AP*GP*AP*GP*GP*UP*A)-3') Chain: R
Molecule details ›
Chain: R
Length: 11 nucleotides
Theoretical weight: 3.63 KDa

Ligands and Environments

2 bound ligands:
Ligand ZN 3 x ZN
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.13Å
Relevant EMDB volumes: EMD-26438
Expression system: Escherichia coli

Quick links

Citations

2 citation in other articles

An ensemble of interconverting conformations of the elemental paused transcription complex creates regulatory options.
Kang et al. (2023)
1 more