PDBe 4xlr

X-ray diffraction
4.3Å resolution

Crystal structure of T.aquaticus transcription initiation complex with CarD containing bubble promoter and RNA

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero decamer (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, G, H
Molecule details ›
Chains: A, B, G, H
Length: 314 amino acids
Theoretical weight: 34.83 KDa
Source organism: Thermus aquaticus
UniProt:
  • Canonical: Q9KWU8 (Residues: 1-314; Coverage: 100%)
Gene name: rpoA
Sequence domains:
DNA-directed RNA polymerase subunit beta Chains: C, I
Molecule details ›
Chains: C, I
Length: 1119 amino acids
Theoretical weight: 124.93 KDa
Source organism: Thermus aquaticus
UniProt:
  • Canonical: Q9KWU7 (Residues: 1-1119; Coverage: 100%)
Gene name: rpoB
Sequence domains:
DNA-directed RNA polymerase subunit beta' Chains: D, J
Molecule details ›
Chains: D, J
Length: 1524 amino acids
Theoretical weight: 171.19 KDa
Source organism: Thermus aquaticus
UniProt:
  • Canonical: Q9KWU6 (Residues: 1-1524; Coverage: 100%)
Gene name: rpoC
Sequence domains:
DNA-directed RNA polymerase subunit omega Chains: E, K
Molecule details ›
Chains: E, K
Length: 99 amino acids
Theoretical weight: 11.64 KDa
Source organism: Thermus aquaticus
UniProt:
  • Canonical: Q9EVV4 (Residues: 1-99; Coverage: 100%)
Gene name: rpoZ
Sequence domains: RNA polymerase Rpb6
RNA polymerase sigma factor SigA Chains: F, L
Molecule details ›
Chains: F, L
Length: 347 amino acids
Theoretical weight: 39.86 KDa
Source organism: Thermus aquaticus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9EZJ8 (Residues: 92-438; Coverage: 79%)
Gene name: sigA
Sequence domains:
CarD-like transcriptional regulator Chains: M, N
Molecule details ›
Chains: M, N
Length: 164 amino acids
Theoretical weight: 18.32 KDa
Source organism: Thermus thermophilus JL-18
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: H9ZP94 (Residues: 1-164; Coverage: 100%)
Gene name: TtJL18_0238
Sequence domains: CarD-like/TRCF domain
DNA (48-MER) Chains: O, R
Molecule details ›
Chains: O, R
Length: 48 nucleotides
Theoretical weight: 14.88 KDa
DNA (48-MER) Chains: P, S
Molecule details ›
Chains: P, S
Length: 48 nucleotides
Theoretical weight: 14.83 KDa
RNA (5'-R(P*UP*CP*GP*A)-3') Chains: Q, T
Molecule details ›
Chains: Q, T
Length: 4 nucleotides
Theoretical weight: 1.24 KDa

Ligands and Environments

2 bound ligands:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P43212
Unit cell:
a: 289.84Å b: 289.84Å c: 536.34Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.277 0.275 0.31
Expression system: Escherichia coli BL21(DE3)