› 5d4c

X-ray diffraction
3.28Å resolution

Crystal structure of Thermus thermophilus product complex for transcription initiation with ATP and CTP

Released:
DOI: 10.2210/pdb5d4c/pdb
PDB entry 5d4c coloured by chain, front view.
PDB entry 5d4c coloured by chain, side view.
PDB entry 5d4c coloured by chain, top view.
Source organisms:
Primary publication:
The mechanism of RNA 5′ capping with NAD+, NADH and desphospho-CoA.
Bird JG, Zhang Y, Tian Y, Panova N, Barvík I, Greene L, Liu M, Buckley B, Krásný L, Lee JK, Kaplan CD, Ebright RH, Nickels BE
Nature 535 444-7 (2016)
PMID: 27383794

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

Assembly composition:
hetero octamer (preferred)
PDBe Complex ID:
PDB-CPX-118532 (preferred)
Entry contents:
5 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (7 distinct):
DNA-directed RNA polymerase subunit alpha Chains: A, B, K, L
Molecule details ›
Chains: A, B, K, L
Length: 315 amino acids
Theoretical weight: 35.06 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SHR6 (Residues: 1-315; Coverage: 100%)
Gene names: TTHA1664, rpoA
Sequence domains:
Structure domains:
DNA-directed RNA polymerase subunit beta Chains: C, M
Molecule details ›
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
Sequence domains:
DNA-directed RNA polymerase subunit beta' Chains: D, N
Molecule details ›
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
Sequence domains:
DNA-directed RNA polymerase subunit omega Chains: E, O
Molecule details ›
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
Sequence domains: RNA polymerase Rpb6
Structure domains: Eukaryotic RPB6 RNA polymerase subunit
RNA polymerase sigma factor SigA Chains: F, P
Molecule details ›
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
Sequence domains:
DNA (5'-D(*CP*CP*T*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*AP*GP*AP*G)-3') Chains: G, R
Molecule details ›
Chains: G, R
Length: 19 nucleotides
Theoretical weight: 5.85 KDa
DNA (27-MER) Chains: H, S
Molecule details ›
Chains: H, S
Length: 27 nucleotides
Theoretical weight: 8.42 KDa

Ligands and Environments

5 bound ligands:
Ligand MG 11 x MG
Ligand ZN 4 x ZN
Ligand C 2 x C
Ligand CTP 2 x CTP
Ligand ATP 2 x ATP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P21
Unit cell:
a: 185.96Å b: 103.64Å c: 297.42Å
α: 90° β: 98.3° γ: 90°
R-values:
R R work R free
0.214 0.212 0.257
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

27 review citations

NAD+ metabolism: pathophysiologic mechanisms and therapeutic potential.
Xie et al. (2020)
26 more

1 mention without citation

The mechanism of RNA 5′ capping with NAD+, NADH and desphospho-CoA.
Bird et al. (2016)