› 6utz

X-ray diffraction
3.8Å resolution

E. coli sigma-S transcription initiation complex with a 6-nt RNA ("Fresh" crystal soaked with CTP and UTP for 30 minutes)

Released:
DOI: 10.2210/pdb6utz/pdb
PDB entry 6utz coloured by chain, front view.
PDB entry 6utz coloured by chain, side view.
PDB entry 6utz coloured by chain, top view.
Source organisms:
Primary publication:
Structural Insights into Transcription Initiation from De Novo RNA Synthesis to Transitioning into Elongation.
Zuo Y, De S, Feng Y, Steitz TA
iScience 23 101445 (2020)
PMID: 32829286

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-199455 (preferred)
Entry contents:
5 distinct polypeptide molecules
2 distinct DNA molecules
1 distinct RNA molecule
Macromolecules (8 distinct):
DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein; DNA-directed RNA polymerase subunit alpha Chains: AAA, BBB
Molecule details ›
Chains: AAA, BBB
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%)
  • Canonical: A0A377D9Q8 (Residues: 1-235; Coverage: 91%)
Gene names: JW3257, NCTC9962_06804, b3295, pez, phs, rpoA, rpoA_1, sez
Sequence domains:
DNA-directed RNA polymerase subunit beta Chain: CCC
Molecule details ›
Chain: CCC
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: DDD
Molecule details ›
Chain: DDD
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: EEE
Molecule details ›
Chain: EEE
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 RpoS Chain: FFF
Molecule details ›
Chain: FFF
Length: 336 amino acids
Theoretical weight: 38.78 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P13445 (Residues: 1-328; Coverage: 99%)
Gene names: JW5437, appR, b2741, katF, nur, otsX, rpoS, sigS
Sequence domains:
Synthetic DNA 50-MER (promoter non-template strand) Chain: 111
Molecule details ›
Chain: 111
Length: 50 nucleotides
Theoretical weight: 15.31 KDa
Synthetic DNA 50-MER (promoter template strand) Chain: 222
Molecule details ›
Chain: 222
Length: 50 nucleotides
Theoretical weight: 15.56 KDa
RNA 6-mer Chain: 333
Molecule details ›
Chain: 333
Length: 6 nucleotides
Theoretical weight: 2.05 KDa

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: P212121
Unit cell:
a: 132.933Å b: 155.987Å c: 233.576Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.277 0.274 0.343
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

The Context-Dependent Influence of Promoter Sequence Motifs on Transcription Initiation Kinetics and Regulation.
Jensen et al. (2021)
2 other articles

1 mention without citation

Structural Insights into Transcription Initiation from De Novo RNA Synthesis to Transitioning into Elongation.
Zuo et al. (2020)