› 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
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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
OpenAccess logo 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
DNA-directed RNA polymerase subunit omega Chains: E, K
RNA polymerase sigma factor SigA Chains: F, L
CarD-like/TRCF RNAP-interacting domain-containing protein Chains: M, N
DNA (30-MER) Chains: O, R
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

Ligands and Environments

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

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
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)

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Citations

7 review citations

Diverse and unified mechanisms of transcription initiation in bacteria.
Chen et al. (2021)
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

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