› 5ipl

X-ray diffraction
3.6Å resolution

SigmaS-transcription initiation complex with 4-nt nascent RNA

Released:
DOI: 10.2210/pdb5ipl/pdb
PDB entry 5ipl coloured by chain, front view.
PDB entry 5ipl coloured by chain, side view.
PDB entry 5ipl coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Structures of E. coli σS-transcription initiation complexes provide new insights into polymerase mechanism.
Liu B, Zuo Y, Steitz TA
Proc Natl Acad Sci U S A 113 4051-6 (2016)
PMID: 27035955

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-118798 (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
Molecule details ›
Chains: A, B
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:
Structure domains:
DNA-directed RNA polymerase subunit beta Chain: C
Molecule details ›
Chain: C
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' Chain: D
Molecule details ›
Chain: D
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 Chain: E
Molecule details ›
Chain: E
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
Structure domains: Eukaryotic RPB6 RNA polymerase subunit
RNA polymerase sigma factor RpoS Chain: F
Molecule details ›
Chain: F
Length: 336 amino acids
Theoretical weight: 38.78 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P13445 (Residues: 1-330; Coverage: 100%)
Gene names: JW5437, appR, b2741, katF, nur, otsX, rpoS, sigS
Sequence domains:
synthetic nontemplate strand DNA (50-MER) Chain: 1
Molecule details ›
Chain: 1
Length: 50 nucleotides
Theoretical weight: 15.33 KDa
synthetic template strand DNA (50-MER) Chain: 2
Molecule details ›
Chain: 2
Length: 50 nucleotides
Theoretical weight: 15.55 KDa
nascent RNA 4-mer Chain: 3
Molecule details ›
Chain: 3
Length: 4 nucleotides
Theoretical weight: 1.44 KDa

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P212121
Unit cell:
a: 131.71Å b: 152.671Å c: 226.698Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.249 0.247 0.293
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

4 review citations

The essential activities of the bacterial sigma factor.
Davis et al. (2017)
3 more

17 mentions without citation

The Mechanisms of Substrate Selection, Catalysis, and Translocation by the Elongating RNA Polymerase.
Belogurov et al. (2019)
16 more