› 6j9e

Electron Microscopy
3.41Å resolution

Cryo-EM structure of Xanthomonos oryzae transcription elongation complex with NusA and the bacteriophage protein P7

Released:
DOI: 10.2210/pdb6j9e/pdb
PDB entry 6j9e coloured by chain, front view.
PDB entry 6j9e coloured by chain, side view.
PDB entry 6j9e coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis for transcription antitermination at bacterial intrinsic terminator.
You L, Shi J, Shen L, Li L, Fang C, Yu C, Cheng W, Feng Y, Zhang Y
Nat Commun 10 3048 (2019)
PMID: 31296855
Related structures: EMD-9785

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 decamer (preferred)
PDBe Complex ID:
PDB-CPX-102287 (preferred)
Entry contents:
6 distinct polypeptide molecules
2 distinct DNA molecules
1 distinct RNA molecule
Macromolecules (9 distinct):
DNA-directed RNA polymerase subunit alpha Chains: A, B
Molecule details ›
Chains: A, B
Length: 346 amino acids
Theoretical weight: 38.03 KDa
Source organism: Xanthomonas oryzae pv. oryzae PXO99A
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: B2SQT4 (Residues: 1-332; Coverage: 100%)
Gene names: PXO_04496, rpoA
Sequence domains:
DNA-directed RNA polymerase subunit beta Chain: C
Molecule details ›
Chain: C
Length: 1383 amino acids
Theoretical weight: 154.47 KDa
Source organism: Xanthomonas oryzae pv. oryzae PXO99A
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: B2SQQ1 (Residues: 1-1383; Coverage: 100%)
Gene names: PXO_04530, rpoB
Sequence domains:
DNA-directed RNA polymerase subunit beta' Chain: D
Molecule details ›
Chain: D
Length: 1405 amino acids
Theoretical weight: 155.44 KDa
Source organism: Xanthomonas oryzae pv. oryzae PXO99A
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: B2SQQ2 (Residues: 1-1405; Coverage: 100%)
Gene names: PXO_04529, rpoC
Sequence domains:
DNA-directed RNA polymerase subunit omega Chain: E
Molecule details ›
Chain: E
Length: 99 amino acids
Theoretical weight: 11.11 KDa
Source organism: Xanthomonas oryzae pv. oryzae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q5H3R9 (Residues: 1-99; Coverage: 100%)
Gene names: XOO1148, rpoZ
Sequence domains: RNA polymerase Rpb6
RNA polymerase inhibitor p7 Chain: J
Molecule details ›
Chain: J
Length: 77 amino acids
Theoretical weight: 8.52 KDa
Source organism: Xipdecavirus Xp10
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8LTJ5 (Residues: 1-73; Coverage: 100%)
Sequence domains: Xanthomonas phage Xp10 Transcription regulator P7
Transcription termination/antitermination protein NusA Chain: F
Molecule details ›
Chain: F
Length: 507 amino acids
Theoretical weight: 55.46 KDa
Source organism: Xanthomonas oryzae pv. oryzae PXO99A
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A0K0GMR0 (Residues: 1-495; Coverage: 100%)
Gene names: PXO_01302, nusA
Sequence domains:
DNA (29-MER) Chain: G
Molecule details ›
Chain: G
Length: 29 nucleotides
Theoretical weight: 8.81 KDa
DNA (29-MER) Chain: H
Molecule details ›
Chain: H
Length: 29 nucleotides
Theoretical weight: 8.84 KDa
RNA (5'-R(*GP*CP*AP*UP*UP*CP*AP*AP*AP*GP*CP*GP*GP*AP*GP*AP*GP*GP*UP*A)-3') Chain: I
Molecule details ›
Chain: I
Length: 20 nucleotides
Theoretical weight: 6.51 KDa

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
Resolution: 3.41Å
Relevant EMDB volumes: EMD-9785
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

Archaeal transcription.
Wenck et al. (2020)
1 more

2 mentions without citation

Biological and Genomic Characterization of a Novel Jumbo Bacteriophage, vB_VhaM_pir03 with Broad Host Lytic Activity against Vibrio harveyi.
Misol et al. (2020)
1 more