› 8p8b

Electron Microscopy
2.9Å resolution

Mycoplasma pneumoniae large ribosomal subunit in chloramphenicol-treated cells

Released:
DOI: 10.2210/pdb8p8b/pdb
PDB entry 8p8b coloured by chain, front view.
PDB entry 8p8b coloured by chain, side view.
PDB entry 8p8b coloured by chain, top view.
Source organism: Mycoplasma pneumoniae M129
Primary publication:
Structural insights into context-dependent inhibitory mechanisms of chloramphenicol in cells.
Xue L, Spahn CMT, Schacherl M, Mahamid J
Nat. Struct. Mol. Biol. (2024)
PMID: 39668257
Related structures: EMD-17134

Function and Biology Details

Reaction catalysed: 
Peptidylproline (omega=180) = peptidylproline (omega=0)
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero 38-mer (preferred)
PDBe Complex ID:
PDB-CPX-281604 (preferred)
Entry contents:
31 distinct polypeptide molecules
7 distinct RNA molecules
Macromolecules (38 distinct):
Large ribosomal subunit protein bL34 Chain: 0
Molecule details ›
Chain: 0
Length: 48 amino acids
Theoretical weight: 5.62 KDa
Source organism: Mycoplasma pneumoniae M129
Large ribosomal subunit protein bL35 Chain: 1
Molecule details ›
Chain: 1
Length: 59 amino acids
Theoretical weight: 6.79 KDa
Source organism: Mycoplasma pneumoniae M129
Large ribosomal subunit protein bL36 Chain: 2
Molecule details ›
Chain: 2
Length: 37 amino acids
Theoretical weight: 4.4 KDa
Source organism: Mycoplasma pneumoniae M129
Trigger factor Chain: X
Molecule details ›
Chain: X
Length: 444 amino acids
Theoretical weight: 51.43 KDa
Source organism: Mycoplasma pneumoniae M129
nascent peptide Chain: Z
Molecule details ›
Chain: Z
Length: 36 amino acids
Theoretical weight: 3.13 KDa
Source organism: Mycoplasma pneumoniae M129
Large ribosomal subunit protein uL2 Chain: a
Molecule details ›
Chain: a
Length: 287 amino acids
Theoretical weight: 31.97 KDa
Source organism: Mycoplasma pneumoniae M129
Large ribosomal subunit protein uL3 Chain: b
Molecule details ›
Chain: b
Length: 287 amino acids
Theoretical weight: 31.3 KDa
Source organism: Mycoplasma pneumoniae M129
Large ribosomal subunit protein uL4 Chain: c
Molecule details ›
Chain: c
Length: 212 amino acids
Theoretical weight: 23.63 KDa
Source organism: Mycoplasma pneumoniae M129
Large ribosomal subunit protein uL5 Chain: d
Molecule details ›
Chain: d
Length: 180 amino acids
Theoretical weight: 20.27 KDa
Source organism: Mycoplasma pneumoniae M129
Large ribosomal subunit protein uL6 Chain: e
Molecule details ›
Chain: e
Length: 184 amino acids
Theoretical weight: 20.62 KDa
Source organism: Mycoplasma pneumoniae M129
Large ribosomal subunit protein bL9 Chain: f
Molecule details ›
Chain: f
Length: 149 amino acids
Theoretical weight: 17.19 KDa
Source organism: Mycoplasma pneumoniae M129
Large ribosomal subunit protein uL10 Chain: g
Molecule details ›
Chain: g
Length: 161 amino acids
Theoretical weight: 17.65 KDa
Source organism: Mycoplasma pneumoniae M129
Large ribosomal subunit protein uL11 Chain: h
Molecule details ›
Chain: h
Length: 137 amino acids
Theoretical weight: 14.8 KDa
Source organism: Mycoplasma pneumoniae M129
Large ribosomal subunit protein uL13 Chain: i
Molecule details ›
Chain: i
Length: 146 amino acids
Theoretical weight: 16.82 KDa
Source organism: Mycoplasma pneumoniae M129
Large ribosomal subunit protein uL14 Chain: j
Molecule details ›
Chain: j
Length: 122 amino acids
Theoretical weight: 13.48 KDa
Source organism: Mycoplasma pneumoniae M129
Large ribosomal subunit protein uL15 Chain: k
Molecule details ›
Chain: k
Length: 151 amino acids
Theoretical weight: 16.77 KDa
Source organism: Mycoplasma pneumoniae M129
Large ribosomal subunit protein uL16 Chain: l
Molecule details ›
Chain: l
Length: 139 amino acids
Theoretical weight: 15.65 KDa
Source organism: Mycoplasma pneumoniae M129
Large ribosomal subunit protein bL17 Chain: m
Molecule details ›
Chain: m
Length: 124 amino acids
Theoretical weight: 14.27 KDa
Source organism: Mycoplasma pneumoniae M129
Large ribosomal subunit protein uL18 Chain: n
Molecule details ›
Chain: n
Length: 116 amino acids
Theoretical weight: 13.07 KDa
Source organism: Mycoplasma pneumoniae M129
Large ribosomal subunit protein bL19 Chain: o
Molecule details ›
Chain: o
Length: 119 amino acids
Theoretical weight: 13.87 KDa
Source organism: Mycoplasma pneumoniae M129
Large ribosomal subunit protein bL20 Chain: p
Molecule details ›
Chain: p
Length: 127 amino acids
Theoretical weight: 14.74 KDa
Source organism: Mycoplasma pneumoniae M129
Large ribosomal subunit protein bL21 Chain: q
Molecule details ›
Chain: q
Length: 100 amino acids
Theoretical weight: 11.66 KDa
Source organism: Mycoplasma pneumoniae M129
Large ribosomal subunit protein uL22 Chain: r
Molecule details ›
Chain: r
Length: 159 amino acids
Theoretical weight: 17.36 KDa
Source organism: Mycoplasma pneumoniae M129
Large ribosomal subunit protein uL23 Chain: s
Molecule details ›
Chain: s
Length: 237 amino acids
Theoretical weight: 25.89 KDa
Source organism: Mycoplasma pneumoniae M129
Large ribosomal subunit protein uL24 Chain: t
Molecule details ›
Chain: t
Length: 111 amino acids
Theoretical weight: 12.46 KDa
Source organism: Mycoplasma pneumoniae M129
Large ribosomal subunit protein bL27 Chain: u
Molecule details ›
Chain: u
Length: 104 amino acids
Theoretical weight: 11.53 KDa
Source organism: Mycoplasma pneumoniae M129
Large ribosomal subunit protein bL28 Chain: v
Molecule details ›
Chain: v
Length: 65 amino acids
Theoretical weight: 7.55 KDa
Source organism: Mycoplasma pneumoniae M129
Large ribosomal subunit protein uL29 Chain: w
Molecule details ›
Chain: w
Length: 111 amino acids
Theoretical weight: 13 KDa
Source organism: Mycoplasma pneumoniae M129
Large ribosomal subunit protein bL31 Chain: x
Molecule details ›
Chain: x
Length: 97 amino acids
Theoretical weight: 10.98 KDa
Source organism: Mycoplasma pneumoniae M129
Large ribosomal subunit protein bL32 Chain: y
Molecule details ›
Chain: y
Length: 57 amino acids
Theoretical weight: 6.64 KDa
Source organism: Mycoplasma pneumoniae M129
Large ribosomal subunit protein bL33A Chain: z
Molecule details ›
Chain: z
Length: 53 amino acids
Theoretical weight: 6.3 KDa
Source organism: Mycoplasma pneumoniae M129
23S ribosomal RNA Chain: 3
Molecule details ›
Chain: 3
Length: 2907 nucleotides
Theoretical weight: 940.95 KDa
Source organism: Mycoplasma pneumoniae M129
5S ribosomal RNA Chain: 4
Molecule details ›
Chain: 4
Length: 108 nucleotides
Theoretical weight: 34.8 KDa
Source organism: Mycoplasma pneumoniae M129
16S ribosomal RNA Chain: 5
Molecule details ›
Chain: 5
Length: 1520 nucleotides
Theoretical weight: 491.33 KDa
Source organism: Mycoplasma pneumoniae M129
tRNA-Ala (E-site) Chain: 6
Molecule details ›
Chain: 6
Length: 76 nucleotides
Theoretical weight: 24.44 KDa
Source organism: Mycoplasma pneumoniae M129
tRNA-Asp (P-site) Chain: 7
Molecule details ›
Chain: 7
Length: 75 nucleotides
Theoretical weight: 24.14 KDa
Source organism: Mycoplasma pneumoniae M129
tRNA-Lys (A-site) Chain: 8
Molecule details ›
Chain: 8
Length: 76 nucleotides
Theoretical weight: 24.4 KDa
Source organism: Mycoplasma pneumoniae M129
Messenger RNA Chain: Y
Molecule details ›
Chain: Y
Length: 9 nucleotides
Theoretical weight: 2.89 KDa
Source organism: Mycoplasma pneumoniae M129

Ligands and Environments

9 bound ligands:
Ligand ZN 4 x ZN
Ligand CLM 1 x CLM
Ligand K 1 x K
Ligand MG 229 x MG
Ligand PUT 7 x PUT
Ligand SPM 4 x SPM
Ligand SPD 16 x SPD
Ligand N2P 3 x N2P
Ligand LYS 1 x LYS
7 modified residues:
Ligand 1MG 1 x 1MG
Ligand OMG 1 x OMG
Ligand 2MA 1 x 2MA
Ligand 7MG 1 x 7MG
Ligand 5MC 1 x 5MC
Ligand B8T 1 x B8T
Ligand MA6 2 x MA6

Experiments and Validation Details

Entry percentile scores
Resolution: 2.9Å
Relevant EMDB volumes: EMD-17134

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