› 4ylp

X-ray diffraction
5.5Å resolution

E. coli Transcription Initiation Complex - 16-bp spacer and 5-nt RNA

Released:
DOI: 10.2210/pdb4ylp/pdb
PDB entry 4ylp coloured by chain, front view.
PDB entry 4ylp coloured by chain, side view.
PDB entry 4ylp coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Crystal structures of the E. coli transcription initiation complexes with a complete bubble.
Zuo Y, Steitz TA
Mol Cell 58 534-40 (2015)
PMID: 25866247

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 nonamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118324 (preferred)
Entry contents:
5 distinct polypeptide molecules
2 distinct DNA molecules
1 distinct RNA molecule
Macromolecules (8 distinct):
DNA-directed RNA polymerase subunit alpha Chains: A, B, G, H, M, N
Molecule details ›
Chains: A, B, G, H, M, N
Length: 242 amino acids
Theoretical weight: 26.9 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0A7Z4 (Residues: 1-235; Coverage: 71%)
Gene names: JW3257, b3295, pez, phs, rpoA, sez
Sequence domains:
DNA-directed RNA polymerase subunit beta Chains: C, I, O
Molecule details ›
Chains: C, I, O
Length: 1342 amino acids
Theoretical weight: 150.82 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0A8V2 (Residues: 1-1342; Coverage: 100%)
Gene names: JW3950, b3987, groN, nitB, rif, ron, rpoB, stl, stv, tabD
Sequence domains:
DNA-directed RNA polymerase subunit beta' Chains: D, J, P
Molecule details ›
Chains: D, J, P
Length: 1407 amino acids
Theoretical weight: 155.37 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0A8T7 (Residues: 1-1407; Coverage: 100%)
Gene names: JW3951, b3988, rpoC, tabB
Sequence domains:
DNA-directed RNA polymerase subunit omega Chains: E, K, Q
Molecule details ›
Chains: E, K, Q
Length: 90 amino acids
Theoretical weight: 10.12 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0A800 (Residues: 2-91; Coverage: 99%)
Gene names: JW3624, b3649, rpoZ
Sequence domains: RNA polymerase Rpb6
RNA polymerase sigma factor RpoD Chains: F, L, R
Molecule details ›
Chains: F, L, R
Length: 628 amino acids
Theoretical weight: 72.21 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P00579 (Residues: 1-613; Coverage: 100%)
Gene names: JW3039, alt, b3067, rpoD
Sequence domains:
NT strand DNA (49-MER) Chains: 1, 4, 7
Molecule details ›
Chains: 1, 4, 7
Length: 49 nucleotides
Theoretical weight: 15.02 KDa
T strand DNA (49-MER) Chains: 2, 5, 8
Molecule details ›
Chains: 2, 5, 8
Length: 49 nucleotides
Theoretical weight: 15.23 KDa
RNA (5'-R(*(GTP))-R(P*AP*GP*UP*C)-3') Chains: 3, 6, 9
Molecule details ›
Chains: 3, 6, 9
Length: 5 nucleotides
Theoretical weight: 1.75 KDa

Ligands and Environments

2 bound ligands:
Ligand ZN 6 x ZN
Ligand MG 3 x MG
1 modified residue:
Ligand GTP 3 x GTP

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P21
Unit cell:
a: 237.674Å b: 204.988Å c: 248.838Å
α: 90° β: 116.86° γ: 90°
R-values:
R R work R free
0.235 0.231 0.313
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

28 review citations

Organization and regulation of gene transcription.
Cramer P. (2019)
27 more

9 mentions without citation

Crystal structures of the E. coli transcription initiation complexes with a complete bubble.
Zuo et al. (2015)
8 more