› 8y6u

Electron Microscopy
3.97Å resolution

Cryo-EM structure of E.coli transcription initiation complex with transcription factor GcvA

Released:
DOI: 10.2210/pdb8y6u/pdb
PDB entry 8y6u coloured by chain, front view.
PDB entry 8y6u coloured by chain, side view.
PDB entry 8y6u coloured by chain, top view.
Source organisms:
Primary publication:
NMR analysis of a loop-bulge structure of UUCGA pentaloop.
Ichijo R, Kawai G
Biochem Biophys Res Commun 691 149327 (2024)
PMID: 38039839
Related structures: EMD-39001

Function and Biology Details

Reaction catalysed: 
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero undecamer (preferred)
PDBe Complex ID:
PDB-CPX-245028 (preferred)
Entry contents:
6 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (8 distinct):
Glycine cleavage system transcriptional activator Chains: H, J
Molecule details ›
Chains: H, J
Length: 305 amino acids
Theoretical weight: 34.45 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0A9F6 (Residues: 1-305; Coverage: 100%)
Gene names: JW2779, b2808, gcvA
Sequence domains:
DNA-directed RNA polymerase subunit alpha Chains: A, B, I
Molecule details ›
Chains: A, B, I
Length: 329 amino acids
Theoretical weight: 36.56 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0A7Z4 (Residues: 1-329; Coverage: 100%)
Gene names: JW3257, b3295, pez, phs, rpoA, sez
Sequence domains:
DNA-directed RNA polymerase subunit beta Chain: C
Molecule details ›
Chain: C
Length: 1342 amino acids
Theoretical weight: 150.8 KDa
Source organism: Escherichia coli K-12
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 K-12
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: 91 amino acids
Theoretical weight: 10.25 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0A800 (Residues: 1-91; Coverage: 100%)
Gene names: JW3624, b3649, rpoZ
Sequence domains: RNA polymerase Rpb6
RNA polymerase sigma factor RpoD Chain: F
Molecule details ›
Chain: F
Length: 613 amino acids
Theoretical weight: 70.35 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q0P6L9 (Residues: 1-613; Coverage: 100%)
Gene name: rpoD
Sequence domains:
Non-template promoter DNA Chain: 1
Molecule details ›
Chain: 1
Length: 92 nucleotides
Theoretical weight: 28.33 KDa
Template promoter DNA Chain: 2
Molecule details ›
Chain: 2
Length: 92 nucleotides
Theoretical weight: 28.58 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.97Å
Relevant EMDB volumes: EMD-39001
Expression system: Escherichia coli BL21(DE3)

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