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Crystal structure of Thermus thermophilus transcription initiation complex containing 2 nt of RNA

X-ray diffraction
2.993Å resolution
PDB entry 4g7o coloured by chain, front view.
PDB entry 4g7o coloured by chain, side view.
PDB entry 4g7o coloured by chain, top view.
Source organism: Thermus thermophilus HB8
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: 141710.32 Å2
Buried surface area: 52500.04 Å2
Dissociation area: 461.19 Å2
Dissociation energy (ΔGdiss): 6.07 kcal/mol
Dissociation entropy (TΔSdiss): 5.6 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-117532
Assembly 2
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Multimeric state: hetero nonamer
Accessible surface area: 142201.2 Å2
Buried surface area: 53016.12 Å2
Dissociation area: 449.61 Å2
Dissociation energy (ΔGdiss): 6.93 kcal/mol
Dissociation entropy (TΔSdiss): 5.61 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-117532

Macromolecules

DNA-directed RNA polymerase subunit alpha
Chains: A, B, K, L
Length: 315 amino acids
Theoretical weight: 35.06 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHR6 (Residues: 1-315; Coverage: 100%)
Gene names: TTHA1664, rpoA
Pfam:
InterPro:
CATH:
DNA-directed RNA polymerase subunit alpha in PDB entry 4g7o, assembly 1, front view.
DNA-directed RNA polymerase subunit alpha in PDB entry 4g7o, assembly 1, side view.
DNA-directed RNA polymerase subunit alpha in PDB entry 4g7o, assembly 1, top view.
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DNA-directed RNA polymerase subunit beta
Chains: C, M
Length: 1119 amino acids
Theoretical weight: 125.44 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q8RQE9 (Residues: 1-1119; Coverage: 100%)
Gene names: TTHA1813, rpoB
Pfam:
InterPro:
CATH:
DNA-directed RNA polymerase subunit beta in PDB entry 4g7o, assembly 1, front view.
DNA-directed RNA polymerase subunit beta in PDB entry 4g7o, assembly 1, side view.
DNA-directed RNA polymerase subunit beta in PDB entry 4g7o, assembly 1, top view.
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DNA-directed RNA polymerase subunit beta'
Chains: D, N
Length: 1524 amino acids
Theoretical weight: 171 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q8RQE8 (Residues: 1-1524; Coverage: 100%)
Gene names: TTHA1812, rpoC
Pfam:
InterPro:
DNA-directed RNA polymerase subunit beta' in PDB entry 4g7o, assembly 1, front view.
DNA-directed RNA polymerase subunit beta' in PDB entry 4g7o, assembly 1, side view.
DNA-directed RNA polymerase subunit beta' in PDB entry 4g7o, assembly 1, top view.
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DNA-directed RNA polymerase subunit omega
Chains: E, O
Length: 99 amino acids
Theoretical weight: 11.53 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q8RQE7 (Residues: 1-99; Coverage: 100%)
Gene names: TTHA1561, rpoZ
Pfam: RNA polymerase Rpb6
InterPro:
CATH: Eukaryotic RPB6 RNA polymerase subunit
DNA-directed RNA polymerase subunit omega in PDB entry 4g7o, assembly 1, front view.
DNA-directed RNA polymerase subunit omega in PDB entry 4g7o, assembly 1, side view.
DNA-directed RNA polymerase subunit omega in PDB entry 4g7o, assembly 1, top view.
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RNA polymerase sigma factor SigA
Chains: F, P
Length: 443 amino acids
Theoretical weight: 50.77 KDa
Source organism: Thermus thermophilus HB8
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q5SKW1 (Residues: 1-423; Coverage: 100%)
Gene names: TTHA0532, sigA
Pfam:
InterPro:
CATH:
RNA polymerase sigma factor SigA in PDB entry 4g7o, assembly 1, front view.
RNA polymerase sigma factor SigA in PDB entry 4g7o, assembly 1, side view.
RNA polymerase sigma factor SigA in PDB entry 4g7o, assembly 1, top view.
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DNA chains G, Q
Name: 5'-D(*CP*CP*T*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*GP*AP*GP*GP*G)-3'
Representative chains: G, Q
Length: 21 nucleotides
Theoretical weight: 6.48 KDa
5'-D(*CP*CP*T*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*GP*AP*GP*GP*G)-3' in PDB entry 4g7o, assembly 1, front view.
5'-D(*CP*CP*T*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*GP*AP*GP*GP*G)-3' in PDB entry 4g7o, assembly 1, side view.
5'-D(*CP*CP*T*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*GP*AP*GP*GP*G)-3' in PDB entry 4g7o, assembly 1, top view.
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DNA chains H, R
Name: 5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*AP*GP*CP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP*GP*CP*AP*GP*G)-3'
Representative chains: H, R
Length: 27 nucleotides
Theoretical weight: 8.42 KDa
5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*AP*GP*CP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP*GP*CP*AP*GP*G)-3' in PDB entry 4g7o, assembly 1, front view.
5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*AP*GP*CP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP*GP*CP*AP*GP*G)-3' in PDB entry 4g7o, assembly 1, side view.
5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*AP*GP*CP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP*GP*CP*AP*GP*G)-3' in PDB entry 4g7o, assembly 1, top view.
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RNA chains I, S
Name: 5'-R(*GP*A)-3'
Representative chains: I, S
Length: 2 nucleotides
Theoretical weight: 629 Da
5'-R(*GP*A)-3' in PDB entry 4g7o, assembly 1, front view.
5'-R(*GP*A)-3' in PDB entry 4g7o, assembly 1, side view.
5'-R(*GP*A)-3' in PDB entry 4g7o, assembly 1, top view.
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