› 8ceu

Electron Microscopy
1.83Å resolution

Retapamulin and Capreomycin bound to the 50S subunit

Released:
DOI: 10.2210/pdb8ceu/pdb
PDB entry 8ceu coloured by chain, front view.
PDB entry 8ceu coloured by chain, side view.
PDB entry 8ceu coloured by chain, top view.
Source organisms:
Primary publication:
Structural conservation of antibiotic interaction with ribosomes.
Paternoga H, Crowe-McAuliffe C, Bock LV, Koller TO, Morici M, Beckert B, Myasnikov AG, Grubmüller H, Nováček J, Wilson DN
Nat Struct Mol Biol (2023)
PMID: 37550453
Related structures: EMD-16613

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 38-mer (preferred)
PDBe Complex ID:
PDB-CPX-222232 (preferred)
Entry contents:
29 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (31 distinct):
Large ribosomal subunit protein bL33 Chain: 0
Molecule details ›
Chain: 0
Length: 55 amino acids
Theoretical weight: 6.39 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0A7N9 (Residues: 1-55; Coverage: 100%)
Gene names: JW3611, b3636, rpmG
Sequence domains: Ribosomal protein L33
Large ribosomal subunit protein bL34 Chain: 1
Molecule details ›
Chain: 1
Length: 46 amino acids
Theoretical weight: 5.4 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0A7P5 (Residues: 1-46; Coverage: 100%)
Gene names: JW3680, b3703, rimA, rpmH, ssaF
Sequence domains: Ribosomal protein L34
Large ribosomal subunit protein bL35 Chain: 2
Molecule details ›
Chain: 2
Length: 65 amino acids
Theoretical weight: 7.31 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0A7Q1 (Residues: 1-65; Coverage: 100%)
Gene names: JW1707, b1717, rpmI
Sequence domains: Ribosomal protein L35
Large ribosomal subunit protein bL36A Chain: 3
Molecule details ›
Chain: 3
Length: 38 amino acids
Theoretical weight: 4.38 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0A7Q6 (Residues: 1-38; Coverage: 100%)
Gene names: JW3261, b3299, rpmJ
Sequence domains: Ribosomal protein L36
Large ribosomal subunit protein uL2 Chain: c
Molecule details ›
Chain: c
Length: 273 amino acids
Theoretical weight: 29.92 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P60422 (Residues: 1-273; Coverage: 100%)
Gene names: JW3279, b3317, rplB
Sequence domains:
Large ribosomal subunit protein uL3 Chain: d
Molecule details ›
Chain: d
Length: 209 amino acids
Theoretical weight: 22.29 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P60438 (Residues: 1-209; Coverage: 100%)
Gene names: JW3282, b3320, rplC
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 Chain: e
Molecule details ›
Chain: e
Length: 201 amino acids
Theoretical weight: 22.12 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P60723 (Residues: 1-201; Coverage: 100%)
Gene names: JW3281, b3319, eryA, rplD
Sequence domains: Ribosomal protein L4/L1 family
Large ribosomal subunit protein uL5 Chain: f
Molecule details ›
Chain: f
Length: 179 amino acids
Theoretical weight: 20.33 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P62399 (Residues: 1-179; Coverage: 100%)
Gene names: JW3270, b3308, rplE
Sequence domains:
Large ribosomal subunit protein uL6 Chain: g
Molecule details ›
Chain: g
Length: 177 amino acids
Theoretical weight: 18.93 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0AG55 (Residues: 1-177; Coverage: 100%)
Gene names: JW3267, b3305, rplF
Sequence domains: Ribosomal protein L6
Large ribosomal subunit protein bL9 Chain: h
Molecule details ›
Chain: h
Length: 149 amino acids
Theoretical weight: 15.79 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0A7R1 (Residues: 1-149; Coverage: 100%)
Gene names: JW4161, b4203, rplI
Sequence domains:
Large ribosomal subunit protein uL13 Chain: i
Molecule details ›
Chain: i
Length: 142 amino acids
Theoretical weight: 16.05 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0AA10 (Residues: 1-142; Coverage: 100%)
Gene names: JW3200, b3231, rplM
Sequence domains: Ribosomal protein L13
Large ribosomal subunit protein uL14 Chain: j
Molecule details ›
Chain: j
Length: 123 amino acids
Theoretical weight: 13.57 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0ADY3 (Residues: 1-123; Coverage: 100%)
Gene names: JW3272, b3310, rplN
Sequence domains: Ribosomal protein L14p/L23e
Large ribosomal subunit protein uL15 Chain: k
Molecule details ›
Chain: k
Length: 144 amino acids
Theoretical weight: 15.01 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P02413 (Residues: 1-144; Coverage: 100%)
Gene names: JW3263, b3301, rplO
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein uL16 Chain: l
Molecule details ›
Chain: l
Length: 136 amino acids
Theoretical weight: 15.33 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0ADY7 (Residues: 1-136; Coverage: 100%)
Gene names: JW3275, b3313, rplP
Sequence domains: Ribosomal protein L16p/L10e
Large ribosomal subunit protein bL17 Chain: m
Molecule details ›
Chain: m
Length: 127 amino acids
Theoretical weight: 14.39 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0AG44 (Residues: 1-127; Coverage: 100%)
Gene names: JW3256, b3294, rplQ
Sequence domains: Ribosomal protein L17
Large ribosomal subunit protein uL18 Chain: n
Molecule details ›
Chain: n
Length: 117 amino acids
Theoretical weight: 12.79 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0C018 (Residues: 1-117; Coverage: 100%)
Gene names: JW3266, b3304, rplR
Sequence domains: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
Large ribosomal subunit protein bL19 Chain: o
Molecule details ›
Chain: o
Length: 115 amino acids
Theoretical weight: 13.16 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0A7K6 (Residues: 1-115; Coverage: 100%)
Gene names: JW2587, b2606, rplS
Sequence domains: Ribosomal protein L19
Large ribosomal subunit protein bL20 Chain: p
Molecule details ›
Chain: p
Length: 118 amino acids
Theoretical weight: 13.53 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0A7L3 (Residues: 1-118; Coverage: 100%)
Gene names: JW1706, b1716, pdzA, rplT
Sequence domains: Ribosomal protein L20
Large ribosomal subunit protein bL21 Chain: q
Molecule details ›
Chain: q
Length: 103 amino acids
Theoretical weight: 11.59 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0AG48 (Residues: 1-103; Coverage: 100%)
Gene names: JW3153, b3186, rplU
Sequence domains: Ribosomal prokaryotic L21 protein
Large ribosomal subunit protein uL22 Chain: r
Molecule details ›
Chain: r
Length: 110 amino acids
Theoretical weight: 12.25 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P61175 (Residues: 1-110; Coverage: 100%)
Gene names: JW3277, b3315, eryB, rplV
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein uL23 Chain: s
Molecule details ›
Chain: s
Length: 100 amino acids
Theoretical weight: 11.22 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0ADZ0 (Residues: 1-100; Coverage: 100%)
Gene names: JW3280, b3318, rplW
Sequence domains: Ribosomal protein L23
Large ribosomal subunit protein uL24 Chain: t
Molecule details ›
Chain: t
Length: 104 amino acids
Theoretical weight: 11.34 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P60624 (Residues: 1-104; Coverage: 100%)
Gene names: JW3271, b3309, rplX
Sequence domains:
Large ribosomal subunit protein bL25 Chain: u
Molecule details ›
Chain: u
Length: 94 amino acids
Theoretical weight: 10.71 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P68919 (Residues: 1-94; Coverage: 100%)
Gene names: JW2173, b2185, rplY
Sequence domains: Ribosomal L25p family
Large ribosomal subunit protein bL27 Chain: v
Molecule details ›
Chain: v
Length: 85 amino acids
Theoretical weight: 9.15 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0A7L8 (Residues: 1-85; Coverage: 100%)
Gene names: JW3152, b3185, rpmA
Sequence domains: Ribosomal L27 protein
Large ribosomal subunit protein bL28 Chain: w
Molecule details ›
Chain: w
Length: 78 amino acids
Theoretical weight: 9.03 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0A7M2 (Residues: 1-78; Coverage: 100%)
Gene names: JW3612, b3637, rpmB
Sequence domains: Ribosomal L28 family
Large ribosomal subunit protein uL29 Chain: x
Molecule details ›
Chain: x
Length: 63 amino acids
Theoretical weight: 7.29 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0A7M6 (Residues: 1-63; Coverage: 100%)
Gene names: JW3274, b3312, rpmC
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein uL30 Chain: y
Molecule details ›
Chain: y
Length: 59 amino acids
Theoretical weight: 6.55 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0AG51 (Residues: 1-59; Coverage: 100%)
Gene names: JW3264, b3302, rpmD
Sequence domains: Ribosomal protein L30p/L7e
Large ribosomal subunit protein bL32 Chain: z
Molecule details ›
Chain: z
Length: 57 amino acids
Theoretical weight: 6.46 KDa
Source organism: Escherichia coli BW25113
UniProt:
  • Canonical: P0A7N4 (Residues: 1-57; Coverage: 100%)
Gene names: JW1075, b1089, rpmF
Sequence domains: Ribosomal L32p protein family
Capreomycin IA Chains: C, D, E, F, G, H, I, V
Molecule details ›
Chains: C, D, E, F, G, H, I, V
Length: 6 amino acids
Theoretical weight: 687 Da
Source organism: Streptomyces californicus
Expression system: Not provided
23S ribosomal RNA Chain: a
Molecule details ›
Chain: a
Length: 2904 nucleotides
Theoretical weight: 941.81 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chain: b
Molecule details ›
Chain: b
Length: 120 nucleotides
Theoretical weight: 38.79 KDa
Sequence domains: 5S ribosomal RNA

Ligands and Environments

4 bound ligands:
Ligand ZN 1 x ZN
Ligand G34 1 x G34
Ligand MG 220 x MG
Ligand K 81 x K
17 modified residues:
Ligand 1MG 1 x 1MG
Ligand PSU 9 x PSU
Ligand 5MU 2 x 5MU
Ligand 6MZ 2 x 6MZ
Ligand 2MG 2 x 2MG
Ligand 3TD 1 x 3TD
Ligand 5MC 1 x 5MC
Ligand G7M 1 x G7M
Ligand OMG 1 x OMG
Ligand H2U 1 x H2U
Ligand OMC 1 x OMC
Ligand 2MA 1 x 2MA
Ligand OMU 1 x OMU
Ligand 4D4 1 x 4D4
Ligand KBE 8 x KBE
Ligand DPP 16 x DPP
Ligand MYN 8 x MYN

Experiments and Validation Details

Entry percentile scores
Resolution: 1.83Å
Relevant EMDB volumes: EMD-16613
Expression system: Not provided

Quick links

Citations

1 mention without citation

Structural conservation of antibiotic interaction with ribosomes.
Paternoga et al. (2023)