› 1yi2

X-ray diffraction
2.65Å resolution

Crystal Structure Of Erythromycin Bound To The G2099A Mutant 50S Ribosomal Subunit Of Haloarcula Marismortui

Released:
DOI: 10.2210/pdb1yi2/pdb
PDB 1yi2 coloured by chain and viewed from the front.
PDB 1yi2 coloured by chain and viewed from the side.
PDB 1yi2 coloured by chain and viewed from the top.
Source organism: Haloarcula marismortui
Primary publication:
Structures of MLSBK antibiotics bound to mutated large ribosomal subunits provide a structural explanation for resistance.
Tu D, Blaha G, Moore PB, Steitz TA
Cell 121 257-70 (2005)
PMID: 15851032

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 31-mer (preferred)
Entry contents:
29 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (31 distinct):
50S ribosomal protein L2 Chain: A
Molecule details ›
Chain: A
Length: 240 amino acids
Theoretical weight: 25.35 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P20276 (Residues: 1-240; Coverage: 100%)
Gene names: rpl2, rrnAC1608
Structure domains:
50S ribosomal protein L3 Chain: B
Molecule details ›
Chain: B
Length: 338 amino acids
Theoretical weight: 37.4 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P20279 (Residues: 1-338; Coverage: 100%)
Gene names: rpl3, rrnAC1611
Structure domains:
50S ribosomal protein L4 Chain: C
Molecule details ›
Chain: C
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
Structure domains: Ribosomal Protein L4; Chain: A;
50S ribosomal protein L5 Chain: D
Molecule details ›
Chain: D
Length: 177 amino acids
Theoretical weight: 19.55 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P14124 (Residues: 1-177; Coverage: 100%)
Gene names: rpl5, rrnAC1598
Structure domains: 50s Ribosomal Protein L5; Chain: A,
50S ribosomal protein L6 Chain: E
Molecule details ›
Chain: E
Length: 178 amino acids
Theoretical weight: 19.96 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P14135 (Residues: 1-178; Coverage: 100%)
Gene names: rpl6, rrnAC1596
Structure domains: Ribosomal protein L6, alpha-beta domain
50S ribosomal protein L7Ae Chain: F
Molecule details ›
Chain: F
Length: 120 amino acids
Theoretical weight: 12.79 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P12743 (Residues: 1-120; Coverage: 100%)
Gene names: rpl7ae, rrnAC0103
Structure domains: 60s Ribosomal Protein L30; Chain: A;
50S ribosomal protein L10 Chain: G
Molecule details ›
Chain: G
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
50S ribosomal protein L10e Chain: H
Molecule details ›
Chain: H
Length: 177 amino acids
Theoretical weight: 19.94 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P60617 (Residues: 1-177; Coverage: 100%)
Gene names: rpl10e, rrnAC2357
Structure domains: Ribosomal protein L10e/L16
50S ribosomal protein L11 Chain: I
Molecule details ›
Chain: I
Length: 162 amino acids
Theoretical weight: 17.1 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P14122 (Residues: 1-162; Coverage: 100%)
Gene names: rpl11, rrnAC1414
Structure domains: Ribosomal protein L11, C-terminal domain
50S ribosomal protein L13 Chain: J
Molecule details ›
Chain: J
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
Structure domains: Ribosomal protein L13
50S ribosomal protein L14 Chain: K
Molecule details ›
Chain: K
Length: 132 amino acids
Theoretical weight: 14.19 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P22450 (Residues: 1-132; Coverage: 100%)
Gene names: rpl14, rrnAC1602
Structure domains: Ribosomal protein L14
50S ribosomal protein L15 Chain: L
Molecule details ›
Chain: L
Length: 165 amino acids
Theoretical weight: 18.01 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P12737 (Residues: 1-165; Coverage: 100%)
Gene names: rpl15, rrnAC1590
Structure domains:
50S ribosomal protein L15e Chain: M
Molecule details ›
Chain: M
Length: 195 amino acids
Theoretical weight: 22.28 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P60618 (Residues: 1-195; Coverage: 100%)
Gene names: rpl15e, rrnAC2065
Structure domains: Ribosomal protein l15e
50S ribosomal protein L18 Chain: N
Molecule details ›
Chain: N
Length: 187 amino acids
Theoretical weight: 20.64 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P14123 (Residues: 1-187; Coverage: 100%)
Gene names: rpl18, rrnAC1593
Structure domains: Nucleotidyltransferase; domain 5
50S ribosomal protein L18e Chain: O
Molecule details ›
Chain: O
Length: 116 amino acids
Theoretical weight: 12.44 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P12733 (Residues: 1-116; Coverage: 100%)
Gene names: rpl18e, rrnAC0064
Structure domains: Ribosomal Protein L15; Chain: K; domain 2
50S ribosomal protein L19e Chain: P
Molecule details ›
Chain: P
Length: 149 amino acids
Theoretical weight: 16.8 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P14119 (Residues: 1-149; Coverage: 100%)
Gene names: rpl19e, rrnAC1594
Structure domains:
50S ribosomal protein L21e Chain: Q
Molecule details ›
Chain: Q
Length: 96 amino acids
Theoretical weight: 10.57 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P12734 (Residues: 1-96; Coverage: 100%)
Gene names: rpl21e, rrnAC0260
Structure domains: Ribosomal protein L21
50S ribosomal protein L22 Chain: R
Molecule details ›
Chain: R
Length: 155 amino acids
Theoretical weight: 16.97 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P10970 (Residues: 1-155; Coverage: 100%)
Gene names: rpl22, rrnAC1606
Structure domains: Ribosomal protein L22/L17
50S ribosomal protein L23 Chain: S
Molecule details ›
Chain: S
Length: 85 amino acids
Theoretical weight: 9.61 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P12732 (Residues: 1-85; Coverage: 100%)
Gene names: rpl23, rrnAC1609
Structure domains: Alpha-Beta Plaits
50S ribosomal protein L24 Chain: T
Molecule details ›
Chain: T
Length: 120 amino acids
Theoretical weight: 13.67 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P10972 (Residues: 1-120; Coverage: 100%)
Gene names: rpl24, rrnAC1601
Structure domains: SH3 type barrels.
50S ribosomal protein L24e Chain: U
Molecule details ›
Chain: U
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
Structure domains: Ribosomal protein L24e
50S ribosomal protein L29 Chain: V
Molecule details ›
Chain: V
Length: 71 amino acids
Theoretical weight: 7.89 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P10971 (Residues: 1-71; Coverage: 100%)
Gene names: rpl29, rrnAC1604
Structure domains: Helix Hairpins
50S ribosomal protein L30 Chain: W
Molecule details ›
Chain: W
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
Structure domains:
50S ribosomal protein L31e Chain: X
Molecule details ›
Chain: X
Length: 92 amino acids
Theoretical weight: 10.38 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P18138 (Residues: 1-92; Coverage: 100%)
Gene names: rpl31e, rrnAC3113
Structure domains: Ribosomal Protein L31e; Chain: W;
50S ribosomal protein L32e Chain: Y
Molecule details ›
Chain: Y
Length: 241 amino acids
Theoretical weight: 26.46 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P12736 (Residues: 1-241; Coverage: 100%)
Gene names: rpl32e, rrnAC1595
50S ribosomal protein L37Ae Chain: Z
Molecule details ›
Chain: Z
Length: 83 amino acids
Theoretical weight: 9.41 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P60619 (Residues: 10-92; Coverage: 90%)
Gene names: rpl37ae, rrnAC1669
Structure domains: N-terminal domain of TfIIb
50S ribosomal protein L37e Chain: 1
Molecule details ›
Chain: 1
Length: 57 amino acids
Theoretical weight: 6.33 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P32410 (Residues: 1-57; Coverage: 100%)
Gene names: rpl37e, rrnAC0797.1
Structure domains: N-terminal domain of TfIIb
50S ribosomal protein L39e Chain: 2
Molecule details ›
Chain: 2
Length: 50 amino acids
Theoretical weight: 6.13 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P22452 (Residues: 1-50; Coverage: 100%)
Gene names: rpl39e, rrnAC3112
Structure domains: Ribosomal protein L39e
50S ribosomal protein L44e Chain: 3
Molecule details ›
Chain: 3
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
Structure domains: Nuclear Transport Factor 2; Chain: A,
23S ribosomal RNA Chain: 0
Molecule details ›
Chain: 0
Length: 2922 nucleotides
Theoretical weight: 946.14 KDa
Sequence domains: Archaeal large subunit ribosomal RNA
5S ribosomal RNA Chain: 9
Molecule details ›
Chain: 9
Length: 122 nucleotides
Theoretical weight: 39.3 KDa
Sequence domains: 5S ribosomal RNA

Ligands and Environments

6 bound ligands:
Ligand ERY 1 x ERY
Ligand MG 116 x MG
Ligand K 2 x K
Ligand NA 86 x NA
Ligand CL 22 x CL
Ligand CD 5 x CD
5 modified residues:
Ligand 1MA 1 x 1MA
Ligand OMU 1 x OMU
Ligand OMG 1 x OMG
Ligand UR3 1 x UR3
Ligand PSU 1 x PSU

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: C2221
Unit cell:
a: 212.435Å b: 299.989Å c: 574.176Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.176 0.176 0.214

Quick links

Citations

63 review citations

Antibiotics: Conventional Therapy and Natural Compounds with Antibacterial Activity-A Pharmaco-Toxicological Screening.
Pancu et al. (2021)
62 more

4 mentions without citation

The key function of a conserved and modified rRNA residue in the ribosomal response to the nascent peptide.
Vázquez-Laslop et al. (2010)
3 more