› 7vpd

Electron Microscopy
3.77Å resolution

Cryo-EM structure of Streptomyces coelicolor RNAP-promoter open complex with one Zur dimers

Released:
DOI: 10.2210/pdb7vpd/pdb
PDB entry 7vpd coloured by chain, front view.
PDB entry 7vpd coloured by chain, side view.
PDB entry 7vpd coloured by chain, top view.
Source organism: Streptomyces coelicolor A3(2)
Primary publication:
Structural basis of Streptomyces transcription activation by zinc uptake regulator.
Yang X, Wang Y, Liu G, Deng Z, Lin S, Zheng J
OpenAccess logo Nucleic Acids Res (2022)
PMID: 35871291
Related structures: EMD-32063

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 undecamer (preferred)
PDBe Complex ID:
PDB-CPX-105606 (preferred)
Entry contents:
6 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (8 distinct):
DNA-directed RNA polymerase subunit alpha Chains: A, B, S
Molecule details ›
Chains: A, B, S
Length: 340 amino acids
Theoretical weight: 36.73 KDa
Source organism: Streptomyces coelicolor A3(2)
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A6G2M9E1 (Residues: 1-340; Coverage: 100%)
Gene names: GTW64_13255, rpoA
Sequence domains:
DNA-directed RNA polymerase subunit beta Chain: C
Molecule details ›
Chain: C
Length: 1161 amino acids
Theoretical weight: 128.64 KDa
Source organism: Streptomyces coelicolor A3(2)
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9L0L0 (Residues: 1-1161; Coverage: 100%)
Gene names: SCD82.26, SCO4654, rpoB
Sequence domains:
DNA-directed RNA polymerase subunit beta' Chain: D
Molecule details ›
Chain: D
Length: 1307 amino acids
Theoretical weight: 145.91 KDa
Source organism: Streptomyces coelicolor A3(2)
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8CJT1 (Residues: 1-1299; Coverage: 100%)
Gene names: SCD40A.01, SCD82.27, SCO4655, rpoC
Sequence domains:
DNA-directed RNA polymerase subunit omega Chain: E
Molecule details ›
Chain: E
Length: 90 amino acids
Theoretical weight: 9.72 KDa
Source organism: Streptomyces coelicolor A3(2)
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9KXS1 (Residues: 1-90; Coverage: 100%)
Gene names: SC9C5.02c, SCO1478, rpoZ
Sequence domains: RNA polymerase Rpb6
RNA polymerase sigma factor SigA Chain: F
Molecule details ›
Chain: F
Length: 532 amino acids
Theoretical weight: 58.29 KDa
Source organism: Streptomyces coelicolor A3(2)
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A7U9DYK1 (Residues: 52-562; Coverage: 91%)
Gene names: SLI_6088, sigA
Sequence domains:
Metal uptake regulation protein Chains: M, N
Molecule details ›
Chains: M, N
Length: 159 amino acids
Theoretical weight: 16.9 KDa
Source organism: Streptomyces coelicolor A3(2)
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9L2H5 (Residues: 1-139; Coverage: 100%)
Gene names: SCC121.11, SCO2508
Sequence domains: Ferric uptake regulator family
DNA (84-MER) Chain: O
Molecule details ›
Chain: O
Length: 84 nucleotides
Theoretical weight: 25.81 KDa
DNA (84-MER) Chain: P
Molecule details ›
Chain: P
Length: 84 nucleotides
Theoretical weight: 26.02 KDa

Ligands and Environments

2 bound ligands:
Ligand MG 1 x MG
Ligand ZN 8 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.77Å
Relevant EMDB volumes: EMD-32063
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

9 citation in other articles

Identification of the Preferred DNA-Binding Sequence and Transcription Regulatory Network for the Thermophilic Zinc Uptake Regulator TTHA1292.
Barrows et al. (2022)
8 more

1 mention without citation

Structural basis of Streptomyces transcription activation by zinc uptake regulator.
Yang et al. (2022)