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

Electron Microscopy
3.13Å resolution
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:
Assembly composition:
hetero decamer (preferred)
Entry contents: 6 distinct polypeptide molecules
2 distinct DNA molecules
1 distinct RNA molecule

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Assemblies

Assembly 1 (preferred)
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Assembly Name: DNA-directed RNA polymerase holoenzyme complex, Sigma70 variant and Antitermination protein Q and RNA and DNA
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Multimeric state: hetero decamer
Accessible surface area: 168012.38 Å2
Buried surface area: 52306.3 Å2
Dissociation area: 2,163.73 Å2
Dissociation energy (ΔGdiss): 18.52 kcal/mol
Dissociation entropy (TΔSdiss): 13.87 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-122182

Macromolecules

DNA-directed RNA polymerase subunit alpha
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
Pfam:
InterPro:
DNA-directed RNA polymerase subunit alpha in PDB entry 7ubm, assembly 1, front view.
DNA-directed RNA polymerase subunit alpha in PDB entry 7ubm, assembly 1, side view.
DNA-directed RNA polymerase subunit alpha in PDB entry 7ubm, assembly 1, top view.
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DNA-directed RNA polymerase subunit beta
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
Pfam:
InterPro:
DNA-directed RNA polymerase subunit beta in PDB entry 7ubm, assembly 1, front view.
DNA-directed RNA polymerase subunit beta in PDB entry 7ubm, assembly 1, side view.
DNA-directed RNA polymerase subunit beta in PDB entry 7ubm, assembly 1, top view.
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DNA-directed RNA polymerase subunit beta'
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
Pfam:
InterPro:
DNA-directed RNA polymerase subunit beta' in PDB entry 7ubm, assembly 1, front view.
DNA-directed RNA polymerase subunit beta' in PDB entry 7ubm, assembly 1, side view.
DNA-directed RNA polymerase subunit beta' in PDB entry 7ubm, assembly 1, top view.
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DNA-directed RNA polymerase subunit omega
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
Pfam: RNA polymerase Rpb6
InterPro:
DNA-directed RNA polymerase subunit omega in PDB entry 7ubm, assembly 1, front view.
DNA-directed RNA polymerase subunit omega in PDB entry 7ubm, assembly 1, side view.
DNA-directed RNA polymerase subunit omega in PDB entry 7ubm, assembly 1, top view.
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RNA polymerase sigma factor RpoD
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
Pfam:
InterPro:
RNA polymerase sigma factor RpoD in PDB entry 7ubm, assembly 1, front view.
RNA polymerase sigma factor RpoD in PDB entry 7ubm, assembly 1, side view.
RNA polymerase sigma factor RpoD in PDB entry 7ubm, assembly 1, top view.
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Antitermination protein Q
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
Pfam: Antitermination protein
InterPro:
Antitermination protein Q in PDB entry 7ubm, assembly 1, front view.
Antitermination protein Q in PDB entry 7ubm, assembly 1, side view.
Antitermination protein Q in PDB entry 7ubm, assembly 1, top view.
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DNA chain 1
Name: DNA (53-MER)
Representative chains: 1
Length: 61 nucleotides
Theoretical weight: 18.93 KDa
DNA (53-MER) in PDB entry 7ubm, assembly 1, front view.
DNA (53-MER) in PDB entry 7ubm, assembly 1, side view.
DNA (53-MER) in PDB entry 7ubm, assembly 1, top view.
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DNA chain 2
Name: DNA (52-MER)
Representative chains: 2
Length: 61 nucleotides
Theoretical weight: 18.6 KDa
DNA (52-MER) in PDB entry 7ubm, assembly 1, front view.
DNA (52-MER) in PDB entry 7ubm, assembly 1, side view.
DNA (52-MER) in PDB entry 7ubm, assembly 1, top view.
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RNA chain R
Name: RNA (5'-R(*UP*GP*GP*GP*AP*GP*AP*GP*GP*UP*A)-3')
Representative chains: R
Length: 11 nucleotides
Theoretical weight: 3.63 KDa
RNA (5'-R(*UP*GP*GP*GP*AP*GP*AP*GP*GP*UP*A)-3') in PDB entry 7ubm, assembly 1, front view.
RNA (5'-R(*UP*GP*GP*GP*AP*GP*AP*GP*GP*UP*A)-3') in PDB entry 7ubm, assembly 1, side view.
RNA (5'-R(*UP*GP*GP*GP*AP*GP*AP*GP*GP*UP*A)-3') in PDB entry 7ubm, assembly 1, top view.
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