› 6wqq

Electron Microscopy
3.1Å resolution

Structure of the 50S subunit of the ribosome from Methicillin Resistant Staphylococcus aureus in complex with the antibiotic, radezolid

Released:
DOI: 10.2210/pdb6wqq/pdb
PDB entry 6wqq coloured by chain, front view.
PDB entry 6wqq coloured by chain, side view.
PDB entry 6wqq coloured by chain, top view.
Source organism: Staphylococcus aureus
Primary publication:
Characterization of the Core Ribosomal Binding Region for the Oxazolidone Family of Antibiotics Using Cryo-EM.
Wright A, Deane-Alder K, Marschall E, Bamert R, Venugopal H, Lithgow T, Lupton DW, Belousoff MJ
ACS Pharmacol Transl Sci 3 425-432 (2020)
PMID: 32566908
Related structures: EMD-21873

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 27-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-140923 (preferred)
Entry contents:
25 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (27 distinct):
Large ribosomal subunit protein bL19 Chain: A
Molecule details ›
Chain: A
Length: 116 amino acids
Theoretical weight: 13.39 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: Q2FZ42 (Residues: 1-116; Coverage: 100%)
Gene names: SAOUHSC_01211, rplS
Sequence domains: Ribosomal protein L19
Large ribosomal subunit protein uL2 Chain: B
Molecule details ›
Chain: B
Length: 277 amino acids
Theoretical weight: 30.22 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: P60430 (Residues: 1-277; Coverage: 100%)
Gene names: SAOUHSC_02509, rplB
Sequence domains:
Large ribosomal subunit protein bL20 Chain: C
Molecule details ›
Chain: C
Length: 118 amino acids
Theoretical weight: 13.72 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: Q2FXQ1 (Residues: 1-118; Coverage: 100%)
Gene names: SAOUHSC_01784, rplT
Sequence domains: Ribosomal protein L20
Large ribosomal subunit protein bL21 Chain: D
Molecule details ›
Chain: D
Length: 105 amino acids
Theoretical weight: 11.7 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: Q2FXS8 (Residues: 1-102; Coverage: 100%)
Gene names: SAOUHSC_01757, rplU
Sequence domains: Ribosomal prokaryotic L21 protein
Large ribosomal subunit protein uL22 Chain: E
Molecule details ›
Chain: E
Length: 117 amino acids
Theoretical weight: 12.87 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: Q2FW11 (Residues: 1-117; Coverage: 100%)
Gene names: SAOUHSC_02507, rplV
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein uL23 Chain: F
Molecule details ›
Chain: F
Length: 91 amino acids
Theoretical weight: 10.63 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: Q2FW08 (Residues: 1-91; Coverage: 100%)
Gene names: SAOUHSC_02510, rplW
Sequence domains: Ribosomal protein L23
Large ribosomal subunit protein uL24 Chain: G
Molecule details ›
Chain: G
Length: 105 amino acids
Theoretical weight: 11.59 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: Q2FW17 (Residues: 1-105; Coverage: 100%)
Gene names: SAOUHSC_02501, rplX
Sequence domains:
Large ribosomal subunit protein bL25 Chain: H
Molecule details ›
Chain: H
Length: 107 amino acids
Theoretical weight: 12.06 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: Q2G0S0 (Residues: 1-99; Coverage: 46%)
Gene names: SAOUHSC_00474, ctc, rplY
Sequence domains: Ribosomal L25p family
Large ribosomal subunit protein bL28 Chain: J
Molecule details ›
Chain: J
Length: 62 amino acids
Theoretical weight: 6.97 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: Q2FZ60 (Residues: 1-61; Coverage: 98%)
Gene names: SAOUHSC_01191, rpmB
Sequence domains: Ribosomal L28 family
Large ribosomal subunit protein uL29 Chain: K
Molecule details ›
Chain: K
Length: 72 amino acids
Theoretical weight: 8.49 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: Q2FW14 (Residues: 2-69; Coverage: 99%)
Gene names: SAOUHSC_02504, rpmC
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein uL3 Chain: L
Molecule details ›
Chain: L
Length: 217 amino acids
Theoretical weight: 23.46 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: Q2FW06 (Residues: 1-217; Coverage: 99%)
Gene names: SAOUHSC_02512, rplC
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL30 Chain: M
Molecule details ›
Chain: M
Length: 58 amino acids
Theoretical weight: 6.43 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: P0A0G2 (Residues: 2-59; Coverage: 98%)
Gene names: SAOUHSC_02493, rpmD
Sequence domains: Ribosomal protein L30p/L7e
Large ribosomal subunit protein bL32 Chain: N
Molecule details ›
Chain: N
Length: 57 amino acids
Theoretical weight: 6.47 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: Q2FZF1 (Residues: 1-58; Coverage: 98%)
Gene names: SAOUHSC_01078, rpmF
Sequence domains: Ribosomal L32p protein family
Large ribosomal subunit protein bL33B Chain: O
Molecule details ›
Chain: O
Length: 49 amino acids
Theoretical weight: 5.89 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: Q2FY22 (Residues: 1-49; Coverage: 100%)
Gene names: SAOUHSC_01651, rpmG2
Sequence domains: Ribosomal protein L33
Large ribosomal subunit protein bL34 Chain: P
Molecule details ›
Chain: P
Length: 50 amino acids
Theoretical weight: 6.06 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: Q2FUQ0 (Residues: 1-45; Coverage: 100%)
Gene names: SAOUHSC_03055, rpmH
Sequence domains: Ribosomal protein L34
Large ribosomal subunit protein bL35 Chain: Q
Molecule details ›
Chain: Q
Length: 65 amino acids
Theoretical weight: 7.59 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: Q2FXQ0 (Residues: 1-65; Coverage: 99%)
Gene names: SAOUHSC_01785, rpmI
Sequence domains: Ribosomal protein L35
Large ribosomal subunit protein bL36 Chain: R
Molecule details ›
Chain: R
Length: 37 amino acids
Theoretical weight: 4.32 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: Q2FW29 (Residues: 1-37; Coverage: 100%)
Gene names: SAOUHSC_02488, rpmJ
Sequence domains: Ribosomal protein L36
Large ribosomal subunit protein uL4 Chain: S
Molecule details ›
Chain: S
Length: 207 amino acids
Theoretical weight: 22.52 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: Q2FW07 (Residues: 1-207; Coverage: 100%)
Gene names: SAOUHSC_02511, rplD
Sequence domains: Ribosomal protein L4/L1 family
Large ribosomal subunit protein uL13 Chain: V
Molecule details ›
Chain: V
Length: 145 amino acids
Theoretical weight: 16.36 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: Q2FW38 (Residues: 1-145; Coverage: 100%)
Gene names: SAOUHSC_02478, rplM
Sequence domains: Ribosomal protein L13
Large ribosomal subunit protein uL14 Chain: W
Molecule details ›
Chain: W
Length: 122 amino acids
Theoretical weight: 13.16 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: Q2FW16 (Residues: 1-122; Coverage: 100%)
Gene names: SAOUHSC_02502, rplN
Sequence domains: Ribosomal protein L14p/L23e
Large ribosomal subunit protein uL15 Chain: X
Molecule details ›
Chain: X
Length: 146 amino acids
Theoretical weight: 15.63 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: P0A0F8 (Residues: 1-146; Coverage: 100%)
Gene names: SAOUHSC_02492, rplO
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein uL16 Chain: Y
Molecule details ›
Chain: Y
Length: 144 amino acids
Theoretical weight: 16.27 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: Q2FW13 (Residues: 1-144; Coverage: 100%)
Gene names: SAOUHSC_02505, rplP
Sequence domains: Ribosomal protein L16p/L10e
Large ribosomal subunit protein bL17 Chain: Z
Molecule details ›
Chain: Z
Length: 122 amino acids
Theoretical weight: 13.77 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: Q2FW33 (Residues: 1-122; Coverage: 100%)
Gene names: SAOUHSC_02484, rplQ
Sequence domains: Ribosomal protein L17
Large ribosomal subunit protein uL18 Chain: a
Molecule details ›
Chain: a
Length: 119 amino acids
Theoretical weight: 13.12 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: Q2FW22 (Residues: 1-119; Coverage: 100%)
Gene names: SAOUHSC_02495, rplR
Sequence domains: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
Large ribosomal subunit protein bL27 Chain: I
Molecule details ›
Chain: I
Length: 85 amino acids
Theoretical weight: 9.2 KDa
Source organism: Staphylococcus aureus
UniProt:
  • Canonical: Q2FXT0 (Residues: 10-94; Coverage: 90%)
Gene names: SAOUHSC_01755, rpmA
Sequence domains: Ribosomal L27 protein
23S ribosomal RNA Chain: 1
Molecule details ›
Chain: 1
Length: 2923 nucleotides
Theoretical weight: 946.68 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chain: 2
Molecule details ›
Chain: 2
Length: 115 nucleotides
Theoretical weight: 36.96 KDa
Sequence domains: 5S ribosomal RNA

Ligands and Environments

1 bound ligand:
Ligand RD8 1 x RD8
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.1Å
Relevant EMDB volumes: EMD-21873

Quick links

Citations

2 review citations

Strategies to Improve the Potency of Oxazolidinones towards Bacterial Biofilms.
Ndukwe et al. (2022)
1 more

4 mentions without citation

A Comprehensive Overview of the Antibiotics Approved in the Last Two Decades: Retrospects and Prospects.
Shi et al. (2023)
3 more