› 1k8a

X-ray diffraction
3Å resolution

Co-crystal structure of Carbomycin A bound to the 50S ribosomal subunit of Haloarcula marismortui

Released:
DOI: 10.2210/pdb1k8a/pdb
PDB entry 1k8a coloured by chain, front view.
PDB entry 1k8a coloured by chain, side view.
PDB entry 1k8a coloured by chain, top view.
Source organism: Haloarcula marismortui
Primary publication:
The structures of four macrolide antibiotics bound to the large ribosomal subunit.
Hansen JL, Ippolito JA, Ban N, Nissen P, Moore PB, Steitz TA
Mol Cell 10 117-28 (2002)
PMID: 12150912

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 30-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-536276 (preferred)
Entry contents:
28 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (30 distinct):
Large ribosomal subunit protein uL2 Chain: C
Molecule details ›
Chain: C
Length: 239 amino acids
Theoretical weight: 25.24 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P20276 (Residues: 2-240; Coverage: 100%)
Gene names: rpl2, rrnAC1608
Sequence domains:
Structure domains:
Large ribosomal subunit protein uL3 Chain: D
Molecule details ›
Chain: D
Length: 337 amino acids
Theoretical weight: 37.27 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P20279 (Residues: 2-338; Coverage: 100%)
Gene names: rpl3, rrnAC1611
Sequence domains: Ribosomal protein L3
Structure domains:
Large ribosomal subunit protein uL4 Chain: E
Molecule details ›
Chain: E
Length: 246 amino acids
Theoretical weight: 26.44 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P12735 (Residues: 1-246; Coverage: 100%)
Gene names: rpl4, rrnAC1610
Sequence domains: Ribosomal protein L4/L1 family
Structure domains: Ribosomal Protein L4; Chain: A;
Large ribosomal subunit protein uL5 Chain: F
Molecule details ›
Chain: F
Length: 176 amino acids
Theoretical weight: 19.42 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P14124 (Residues: 2-177; Coverage: 99%)
Gene names: rpl5, rrnAC1598
Sequence domains:
Structure domains: 50s Ribosomal Protein L5; Chain: A,
Large ribosomal subunit protein uL6 Chain: G
Molecule details ›
Chain: G
Length: 177 amino acids
Theoretical weight: 19.83 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P14135 (Residues: 2-178; Coverage: 99%)
Gene names: rpl6, rrnAC1596
Sequence domains: Ribosomal protein L6
Structure domains: Ribosomal protein L6, alpha-beta domain
Large ribosomal subunit protein eL8 Chain: H
Molecule details ›
Chain: H
Length: 119 amino acids
Theoretical weight: 12.6 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P12743 (Residues: 2-120; Coverage: 99%)
Gene names: rpl7ae, rrnAC0103
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Structure domains: 60s Ribosomal Protein L30; Chain: A;
Large ribosomal subunit protein uL10 Chain: I
Molecule details ›
Chain: I
Length: 348 amino acids
Theoretical weight: 37.21 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P15825 (Residues: 1-348; Coverage: 100%)
Gene names: rpl10, rpl10e, rplP0, rrnAC1417
Sequence domains:
Large ribosomal subunit protein uL16 Chain: J
Molecule details ›
Chain: J
Length: 167 amino acids
Theoretical weight: 18.02 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P60617 (Residues: 4-166; Coverage: 90%)
Gene names: rpl10e, rrnAC2357
Sequence domains: Ribosomal protein L16p/L10e
Structure domains: Ribosomal protein L10e/L16
Large ribosomal subunit protein uL13 Chain: K
Molecule details ›
Chain: K
Length: 145 amino acids
Theoretical weight: 16.25 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P29198 (Residues: 1-145; Coverage: 100%)
Gene names: rpl13, rrnAC0065
Sequence domains: Ribosomal protein L13
Structure domains: Ribosomal protein L13
Large ribosomal subunit protein uL14 Chain: L
Molecule details ›
Chain: L
Length: 132 amino acids
Theoretical weight: 14.22 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P22450 (Residues: 1-132; Coverage: 100%)
Gene names: rpl14, rrnAC1602
Sequence domains: Ribosomal protein L14p/L23e
Structure domains: Ribosomal protein L14
Large ribosomal subunit protein uL15 Chain: M
Molecule details ›
Chain: M
Length: 164 amino acids
Theoretical weight: 17.87 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P12737 (Residues: 2-165; Coverage: 99%)
Gene names: rpl15, rrnAC1590
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Structure domains:
Large ribosomal subunit protein eL15 Chain: N
Molecule details ›
Chain: N
Length: 194 amino acids
Theoretical weight: 22.86 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P60618 (Residues: 2-194; Coverage: 99%)
Gene names: rpl15e, rrnAC2065
Sequence domains: Ribosomal L15
Structure domains: Ribosomal protein l15e
Large ribosomal subunit protein uL18 Chain: O
Molecule details ›
Chain: O
Length: 186 amino acids
Theoretical weight: 20.51 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P14123 (Residues: 2-187; Coverage: 100%)
Gene names: rpl18, rrnAC1593
Sequence domains: Ribosomal large subunit proteins 60S L5, and 50S L18
Structure domains: Nucleotidyltransferase; domain 5
Large ribosomal subunit protein eL18 Chain: P
Molecule details ›
Chain: P
Length: 115 amino acids
Theoretical weight: 12.31 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P12733 (Residues: 2-116; Coverage: 99%)
Gene names: rpl18e, rrnAC0064
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Structure domains: Ribosomal Protein L15; Chain: K; domain 2
Large ribosomal subunit protein eL19 Chain: Q
Molecule details ›
Chain: Q
Length: 148 amino acids
Theoretical weight: 16.63 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P14119 (Residues: 2-149; Coverage: 99%)
Gene names: rpl19e, rrnAC1594
Sequence domains: Ribosomal protein L19e
Structure domains:
Large ribosomal subunit protein eL21 Chain: R
Molecule details ›
Chain: R
Length: 95 amino acids
Theoretical weight: 10.44 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P12734 (Residues: 2-96; Coverage: 99%)
Gene names: rpl21e, rrnAC0260
Sequence domains: Ribosomal protein L21e
Structure domains: Ribosomal protein L21
Large ribosomal subunit protein uL22 Chain: S
Molecule details ›
Chain: S
Length: 154 amino acids
Theoretical weight: 16.84 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P10970 (Residues: 2-155; Coverage: 99%)
Gene names: rpl22, rrnAC1606
Sequence domains: Ribosomal protein L22p/L17e
Structure domains: Ribosomal protein L22/L17
Large ribosomal subunit protein uL23 Chain: T
Molecule details ›
Chain: T
Length: 84 amino acids
Theoretical weight: 9.48 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P12732 (Residues: 2-85; Coverage: 99%)
Gene names: rpl23, rrnAC1609
Sequence domains: Ribosomal protein L23
Structure domains: Alpha-Beta Plaits
Large ribosomal subunit protein uL24 Chain: U
Molecule details ›
Chain: U
Length: 119 amino acids
Theoretical weight: 13.54 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P10972 (Residues: 2-120; Coverage: 99%)
Gene names: rpl24, rrnAC1601
Sequence domains:
Structure domains: SH3 type barrels.
Large ribosomal subunit protein eL24 Chain: V
Molecule details ›
Chain: V
Length: 66 amino acids
Theoretical weight: 7.23 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P14116 (Residues: 2-67; Coverage: 99%)
Gene names: rpl24e, rrnAC0104
Sequence domains: Ribosomal protein L24e
Structure domains: Ribosomal protein L24e
Large ribosomal subunit protein uL29 Chain: W
Molecule details ›
Chain: W
Length: 70 amino acids
Theoretical weight: 7.76 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P10971 (Residues: 2-71; Coverage: 99%)
Gene names: rpl29, rrnAC1604
Sequence domains: Ribosomal L29 protein
Structure domains: Helix Hairpins
Large ribosomal subunit protein uL30 Chain: X
Molecule details ›
Chain: X
Length: 154 amino acids
Theoretical weight: 17.06 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P14121 (Residues: 1-154; Coverage: 100%)
Gene names: rpl30, rrnAC1591
Sequence domains: Ribosomal protein L30p/L7e
Structure domains:
Large ribosomal subunit protein eL31 Chain: Y
Molecule details ›
Chain: Y
Length: 91 amino acids
Theoretical weight: 10.25 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P18138 (Residues: 2-92; Coverage: 99%)
Gene names: rpl31e, rrnAC3113
Sequence domains: Ribosomal protein L31e
Structure domains: Ribosomal Protein L31e; Chain: W;
Large ribosomal subunit protein eL32 Chain: Z
Molecule details ›
Chain: Z
Length: 240 amino acids
Theoretical weight: 26.32 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P12736 (Residues: 2-241; Coverage: 100%)
Gene names: rpl32e, rrnAC1595
Sequence domains:
Large ribosomal subunit protein eL43 Chain: 1
Molecule details ›
Chain: 1
Length: 73 amino acids
Theoretical weight: 8.1 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P60619 (Residues: 11-82; Coverage: 78%)
Gene names: rpl37ae, rrnAC1669
Sequence domains: Ribosomal L37ae protein family
Structure domains: N-terminal domain of TfIIb
Large ribosomal subunit protein eL37 Chain: 2
Molecule details ›
Chain: 2
Length: 56 amino acids
Theoretical weight: 6.2 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P32410 (Residues: 2-57; Coverage: 98%)
Gene names: rpl37e, rrnAC0797.1
Sequence domains: Ribosomal protein L37e
Structure domains: N-terminal domain of TfIIb
Large ribosomal subunit protein eL39 Chain: 3
Molecule details ›
Chain: 3
Length: 48 amino acids
Theoretical weight: 5.84 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P22452 (Residues: 2-50; Coverage: 96%)
Gene names: rpl39e, rrnAC3112
Sequence domains: Ribosomal L39 protein
Structure domains: Ribosomal protein L39e
Large ribosomal subunit protein eL42 Chain: 4
Molecule details ›
Chain: 4
Length: 92 amino acids
Theoretical weight: 10.82 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P32411 (Residues: 1-92; Coverage: 100%)
Gene names: rpl44e, rrnAC3514
Sequence domains: Ribosomal protein L44
Structure domains: Nuclear Transport Factor 2; Chain: A,
23S ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 2922 nucleotides
Theoretical weight: 946.03 KDa
Sequence domains: Archaeal large subunit ribosomal RNA
5S ribosomal RNA Chain: B
Molecule details ›
Chain: B
Length: 122 nucleotides
Theoretical weight: 39.32 KDa
Sequence domains: 5S ribosomal RNA

Ligands and Environments

6 bound ligands:
Ligand CAI 1 x CAI
Ligand MG 119 x MG
Ligand NA 83 x NA
Ligand CL 23 x CL
Ligand K 3 x K
Ligand CD 5 x CD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: C2221
Unit cell:
a: 212.902Å b: 300.474Å c: 575.176Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.227 0.227 0.265

Quick links

Citations

80 review citations

Ribosome-targeting antibiotics and mechanisms of bacterial resistance.
Wilson DN. (2014)
79 more

8 mentions without citation

Ribosome-Targeting Antibiotics: Modes of Action, Mechanisms of Resistance, and Implications for Drug Design.
Lin et al. (2018)
7 more