› 7o5h

Electron Microscopy
3.1Å resolution

Ribosomal methyltransferase KsgA bound to small ribosomal subunit

Released:
DOI: 10.2210/pdb7o5h/pdb
PDB entry 7o5h coloured by chain, front view.
PDB entry 7o5h coloured by chain, side view.
PDB entry 7o5h coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis of successive adenosine modifications by the conserved ribosomal methyltransferase KsgA.
Stephan NC, Ries AB, Boehringer D, Ban N
OpenAccess logo Nucleic Acids Res 49 6389-6398 (2021)
PMID: 34086932
Related structures: EMD-12736

Function and Biology Details

Reaction catalysed: 
4 S-adenosyl-L-methionine + adenine(1518)/adenine(1519) in 16S rRNA = 4 S-adenosyl-L-homocysteine + N(6)-dimethyladenine(1518)/N(6)-dimethyladenine(1519) in 16S rRNA
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero pentadecamer (preferred)
PDBe Complex ID:
PDB-CPX-135730 (preferred)
Entry contents:
14 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (15 distinct):
Ribosomal RNA small subunit methyltransferase A Chain: V
Molecule details ›
Chain: V
Length: 252 amino acids
Theoretical weight: 27.99 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P06992 (Residues: 17-268; Coverage: 92%)
Gene names: JW0050, b0051, ksgA, rsmA
Sequence domains: Ribosomal RNA adenine dimethylase
Small ribosomal subunit protein uS2 Chain: B
Molecule details ›
Chain: B
Length: 225 amino acids
Theoretical weight: 25.07 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7V0 (Residues: 3-227; Coverage: 93%)
Gene names: JW0164, b0169, rpsB
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein uS4 Chain: D
Molecule details ›
Chain: D
Length: 205 amino acids
Theoretical weight: 23.38 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7V8 (Residues: 2-206; Coverage: 100%)
Gene names: JW3258, b3296, ramA, rpsD
Sequence domains:
Small ribosomal subunit protein uS5 Chain: E
Molecule details ›
Chain: E
Length: 158 amino acids
Theoretical weight: 16.66 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7W1 (Residues: 10-167; Coverage: 95%)
Gene names: JW3265, b3303, rpsE, spc
Sequence domains:
Small ribosomal subunit protein bS6, non-modified isoform Chain: F
Molecule details ›
Chain: F
Length: 106 amino acids
Theoretical weight: 12.33 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P02358 (Residues: 1-106; Coverage: 79%)
Gene names: JW4158, b4200, rpsF
Sequence domains: Ribosomal protein S6
Small ribosomal subunit protein uS8 Chain: H
Molecule details ›
Chain: H
Length: 129 amino acids
Theoretical weight: 14.02 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7W7 (Residues: 2-130; Coverage: 99%)
Gene names: JW3268, b3306, rpsH
Sequence domains: Ribosomal protein S8
Small ribosomal subunit protein uS11 Chain: K
Molecule details ›
Chain: K
Length: 117 amino acids
Theoretical weight: 12.49 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7R9 (Residues: 13-129; Coverage: 91%)
Gene names: JW3259, b3297, rpsK
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS12 Chain: L
Molecule details ›
Chain: L
Length: 123 amino acids
Theoretical weight: 13.64 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7S3 (Residues: 2-124; Coverage: 99%)
Gene names: JW3304, b3342, rpsL, strA
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein uS15 Chain: O
Molecule details ›
Chain: O
Length: 88 amino acids
Theoretical weight: 10.16 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0ADZ4 (Residues: 2-89; Coverage: 99%)
Gene names: JW3134, b3165, rpsO, secC
Sequence domains: Ribosomal protein S15
Small ribosomal subunit protein bS16 Chain: P
Molecule details ›
Chain: P
Length: 82 amino acids
Theoretical weight: 9.21 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7T3 (Residues: 1-82; Coverage: 100%)
Gene names: JW2590, b2609, rpsP
Sequence domains: Ribosomal protein S16
Small ribosomal subunit protein uS17 Chain: Q
Molecule details ›
Chain: Q
Length: 80 amino acids
Theoretical weight: 9.26 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0AG63 (Residues: 4-83; Coverage: 95%)
Gene names: JW3273, b3311, neaA, rpsQ
Sequence domains: Ribosomal protein S17
Small ribosomal subunit protein bS18 Chain: R
Molecule details ›
Chain: R
Length: 55 amino acids
Theoretical weight: 6.47 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7T7 (Residues: 20-74; Coverage: 73%)
Gene names: JW4160, b4202, rpsR
Sequence domains: Ribosomal protein S18
Small ribosomal subunit protein bS20 Chain: T
Molecule details ›
Chain: T
Length: 86 amino acids
Theoretical weight: 9.58 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7U7 (Residues: 2-87; Coverage: 99%)
Gene names: JW0022, b0023, rpsT
Sequence domains: Ribosomal protein S20
Small ribosomal subunit protein bS21 Chain: U
Molecule details ›
Chain: U
Length: 56 amino acids
Theoretical weight: 6.63 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P68679 (Residues: 2-57; Coverage: 79%)
Gene names: JW3037, b3065, rpsU
Sequence domains: Ribosomal protein S21
16S ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 964 nucleotides
Theoretical weight: 312.98 KDa
Sequence domains: Bacterial small subunit ribosomal RNA

Ligands and Environments

1 bound ligand:
Ligand MG 167 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.1Å
Relevant EMDB volumes: EMD-12736
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

7 citation in other articles

Mechanism of mitoribosomal small subunit biogenesis and preinitiation.
Itoh et al. (2022)
6 more

5 mentions without citation

Protein Assistants of Small Ribosomal Subunit Biogenesis in Bacteria.
Maksimova et al. (2022)
4 more