› 7bgd

Electron Microscopy
3.2Å resolution

Staphylococcus aureus 30S ribosomal subunit in presence of spermidine (body only)

Released:
DOI: 10.2210/pdb7bgd/pdb
PDB entry 7bgd coloured by chain, front view.
PDB entry 7bgd coloured by chain, side view.
PDB entry 7bgd coloured by chain, top view.
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
Primary publication:
Stabilization of Ribosomal RNA of the Small Subunit by Spermidine in Staphylococcus aureus
Belinite M, Khusainov I, Soufari H, Marzi S, Romby P, Yusupov M, Hashem Y
Front Mol Biosci 8 1022- (2021)
Related structures: EMD-12178

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetradecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-140927 (preferred)
Entry contents:
12 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (14 distinct):
Small ribosomal subunit protein uS2 Chain: b
Molecule details ›
Chain: b
Length: 255 amino acids
Theoretical weight: 29.14 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FZ25 (Residues: 1-255; Coverage: 100%)
Gene names: SAOUHSC_01232, rpsB
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein uS4 Chain: d
Molecule details ›
Chain: d
Length: 200 amino acids
Theoretical weight: 23.05 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FXK6 (Residues: 1-200; Coverage: 100%)
Gene names: SAOUHSC_01829, rpsD
Sequence domains:
Small ribosomal subunit protein uS5 Chain: e
Molecule details ›
Chain: e
Length: 166 amino acids
Theoretical weight: 17.77 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW23 (Residues: 1-166; Coverage: 100%)
Gene names: SAOUHSC_02494, rpsE
Sequence domains:
Small ribosomal subunit protein bS6 Chain: f
Molecule details ›
Chain: f
Length: 98 amino acids
Theoretical weight: 11.61 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2G113 (Residues: 1-98; Coverage: 100%)
Gene names: SAOUHSC_00348, rpsF
Sequence domains: Ribosomal protein S6
Small ribosomal subunit protein uS8 Chain: h
Molecule details ›
Chain: h
Length: 132 amino acids
Theoretical weight: 14.85 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW20 (Residues: 1-132; Coverage: 100%)
Gene names: SAOUHSC_02498, rpsH
Sequence domains: Ribosomal protein S8
Small ribosomal subunit protein uS11 Chain: k
Molecule details ›
Chain: k
Length: 129 amino acids
Theoretical weight: 13.91 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW31 (Residues: 1-129; Coverage: 100%)
Gene names: SAOUHSC_02486, rpsK
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS12 Chain: l
Molecule details ›
Chain: l
Length: 137 amino acids
Theoretical weight: 15.32 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: P0A0H0 (Residues: 1-137; Coverage: 100%)
Gene names: SAOUHSC_00527, rpsL
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein uS15 Chain: o
Molecule details ›
Chain: o
Length: 89 amino acids
Theoretical weight: 10.63 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2G2Q1 (Residues: 1-89; Coverage: 100%)
Gene names: SAOUHSC_01250, rpsO
Sequence domains: Ribosomal protein S15
Small ribosomal subunit protein bS16 Chain: p
Molecule details ›
Chain: p
Length: 91 amino acids
Theoretical weight: 10.25 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FZ45 (Residues: 1-91; Coverage: 100%)
Gene names: SAOUHSC_01208, rpsP
Sequence domains: Ribosomal protein S16
Small ribosomal subunit protein uS17 Chain: q
Molecule details ›
Chain: q
Length: 87 amino acids
Theoretical weight: 10.2 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW15 (Residues: 1-87; Coverage: 100%)
Gene names: SAOUHSC_02503, rpsQ
Sequence domains: Ribosomal protein S17
Small ribosomal subunit protein bS18 Chain: r
Molecule details ›
Chain: r
Length: 80 amino acids
Theoretical weight: 9.33 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2G111 (Residues: 1-80; Coverage: 100%)
Gene names: SAOUHSC_00350, rpsR
Sequence domains: Ribosomal protein S18
Small ribosomal subunit protein bS20 Chain: t
Molecule details ›
Chain: t
Length: 83 amino acids
Theoretical weight: 9.04 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FXY6 (Residues: 1-83; Coverage: 100%)
Gene names: SAOUHSC_01689, rpsT
Sequence domains: Ribosomal protein S20
Messenger RNA Chain: A
Molecule details ›
Chain: A
Length: 32 nucleotides
Theoretical weight: 10.39 KDa
16S ribosomal RNA Chain: a
Molecule details ›
Chain: a
Length: 1556 nucleotides
Theoretical weight: 503.22 KDa
Sequence domains: Bacterial small subunit ribosomal RNA

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.2Å
Relevant EMDB volumes: EMD-12178

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