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E. coli Transcription Initiation Complex - 17-bp spacer and 4-nt RNA

X-ray diffraction
5.5Å resolution
PDB entry 4yln coloured by chain, front view.
PDB entry 4yln coloured by chain, side view.
PDB entry 4yln coloured by chain, top view.
Source organism: Escherichia coli
Assembly composition:
hetero nonamer (preferred)
Entry contents: 5 distinct polypeptide molecules
2 distinct DNA molecules
1 distinct RNA molecule

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero nonamer
Accessible surface area: 178843.0 Å2
Buried surface area: 56785.78 Å2
Dissociation area: 2,860.16 Å2
Dissociation energy (ΔGdiss): 6.4 kcal/mol
Dissociation entropy (TΔSdiss): 16.15 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-108534
Assembly 2
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Multimeric state: hetero nonamer
Accessible surface area: 179719.26 Å2
Buried surface area: 57519.55 Å2
Dissociation area: 2,811.89 Å2
Dissociation energy (ΔGdiss): 2.04 kcal/mol
Dissociation entropy (TΔSdiss): 16.15 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-108534
Assembly 3
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Multimeric state: hetero nonamer
Accessible surface area: 180217.81 Å2
Buried surface area: 57873.37 Å2
Dissociation area: 2,867.07 Å2
Dissociation energy (ΔGdiss): 4.23 kcal/mol
Dissociation entropy (TΔSdiss): 16.16 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-108534

Macromolecules

DNA-directed RNA polymerase subunit alpha
Chains: A, B, G, H, M, N
Length: 242 amino acids
Theoretical weight: 26.9 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A7ZSI4 (Residues: 1-235; Coverage: 71%)
Gene names: EcE24377A_3778, rpoA
Pfam:
InterPro:
DNA-directed RNA polymerase subunit alpha in PDB entry 4yln, assembly 1, front view.
DNA-directed RNA polymerase subunit alpha in PDB entry 4yln, assembly 1, side view.
DNA-directed RNA polymerase subunit alpha in PDB entry 4yln, assembly 1, top view.
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DNA-directed RNA polymerase subunit beta
Chains: C, I, O
Length: 1342 amino acids
Theoretical weight: 150.82 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A7ZUK1 (Residues: 1-1342; Coverage: 100%)
Gene names: EcE24377A_4528, rpoB
Pfam:
InterPro:
DNA-directed RNA polymerase subunit beta in PDB entry 4yln, assembly 1, front view.
DNA-directed RNA polymerase subunit beta in PDB entry 4yln, assembly 1, side view.
DNA-directed RNA polymerase subunit beta in PDB entry 4yln, assembly 1, top view.
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DNA-directed RNA polymerase subunit beta'
Chains: D, J, P
Length: 1407 amino acids
Theoretical weight: 155.37 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A7ZUK2 (Residues: 1-1407; Coverage: 100%)
Gene names: EcE24377A_4529, rpoC
Pfam:
InterPro:
DNA-directed RNA polymerase subunit beta' in PDB entry 4yln, assembly 1, front view.
DNA-directed RNA polymerase subunit beta' in PDB entry 4yln, assembly 1, side view.
DNA-directed RNA polymerase subunit beta' in PDB entry 4yln, assembly 1, top view.
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DNA-directed RNA polymerase subunit omega
Chains: E, K, Q
Length: 90 amino acids
Theoretical weight: 10.12 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A7ZTK1 (Residues: 2-91; Coverage: 99%)
Gene names: EcE24377A_4152, rpoZ
Pfam: RNA polymerase Rpb6
InterPro:
DNA-directed RNA polymerase subunit omega in PDB entry 4yln, assembly 1, front view.
DNA-directed RNA polymerase subunit omega in PDB entry 4yln, assembly 1, side view.
DNA-directed RNA polymerase subunit omega in PDB entry 4yln, assembly 1, top view.
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RNA polymerase sigma factor RpoD
Chains: F, L, R
Length: 628 amino acids
Theoretical weight: 72.21 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P00579 (Residues: 1-613; Coverage: 100%)
Gene names: JW3039, alt, b3067, rpoD
Pfam:
InterPro:
RNA polymerase sigma factor RpoD in PDB entry 4yln, assembly 1, front view.
RNA polymerase sigma factor RpoD in PDB entry 4yln, assembly 1, side view.
RNA polymerase sigma factor RpoD in PDB entry 4yln, assembly 1, top view.
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DNA chains 1, 4, 7
Name: NT strand DNA (49-MER)
Representative chains: 1, 4, 7
Length: 49 nucleotides
Theoretical weight: 15.02 KDa
NT strand DNA (49-MER) in PDB entry 4yln, assembly 1, front view.
NT strand DNA (49-MER) in PDB entry 4yln, assembly 1, side view.
NT strand DNA (49-MER) in PDB entry 4yln, assembly 1, top view.
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DNA chains 2, 5, 8
Name: T strand DNA (49-MER)
Representative chains: 2, 5, 8
Length: 49 nucleotides
Theoretical weight: 15.23 KDa
T strand DNA (49-MER) in PDB entry 4yln, assembly 1, front view.
T strand DNA (49-MER) in PDB entry 4yln, assembly 1, side view.
T strand DNA (49-MER) in PDB entry 4yln, assembly 1, top view.
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RNA chains 3, 6, 9
Name: RNA (5'-D(*(GTP))-R(P*AP*GP*U)-3')
Representative chains: 3, 6, 9
Length: 4 nucleotides
Theoretical weight: 1.44 KDa
RNA (5'-D(*(GTP))-R(P*AP*GP*U)-3') in PDB entry 4yln, assembly 1, front view.
RNA (5'-D(*(GTP))-R(P*AP*GP*U)-3') in PDB entry 4yln, assembly 1, side view.
RNA (5'-D(*(GTP))-R(P*AP*GP*U)-3') in PDB entry 4yln, assembly 1, top view.
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