› 4xls

X-ray diffraction
4.01Å resolution

Crystal structure of T. aquaticus transcription initiation complex with CarD containing upstream fork promoter.

Released:
DOI: 10.2210/pdb4xls/pdb
PDB entry 4xls coloured by chain, front view.
PDB entry 4xls coloured by chain, side view.
PDB entry 4xls coloured by chain, top view.
Source organisms:
Primary publication:
CarD uses a minor groove wedge mechanism to stabilize the RNA polymerase open promoter complex.
Bae B, Chen J, Davis E, Leon K, Darst SA, Campbell EA
Elife 4 (2015)
PMID: 26349034

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

Assemblies composition:
hetero nonamer (preferred)
hetero octamer
PDBe Complex ID:
PDB-CPX-118270 (preferred)
Entry contents:
6 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (8 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/TRCF RNAP-interacting domain-containing protein 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:
DNA (30-MER) Chains: O, R
Molecule details ›
Chains: O, R
Length: 30 nucleotides
Theoretical weight: 9.24 KDa
DNA (5'-D(P*GP*CP*AP*CP*AP*AP*TP*TP*TP*AP*AP*CP*AP*CP*TP*TP*TP*TP*GP*TP*CP*AP*AP*G)-3') Chains: P, S
Molecule details ›
Chains: P, S
Length: 24 nucleotides
Theoretical weight: 7.33 KDa

Ligands and Environments

2 bound ligands:
Ligand ZN 4 x ZN
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P43212
Unit cell:
a: 293.15Å b: 293.15Å c: 539.13Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.234 0.232 0.272
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

7 review citations

Mycobacterium tuberculosis Transcription Machinery: Ready To Respond to Host Attacks.
Flentie et al. (2016)
6 more

3 mentions without citation

From Mfd to TRCF and Back Again-A Perspective on Bacterial Transcription-coupled Nucleotide Excision Repair.
Deaconescu et al. (2017)
2 more