› 3g71

X-ray diffraction
2.85Å resolution

Co-crystal structure of Bruceantin bound to the large ribosomal subunit

Released:
DOI: 10.2210/pdb3g71/pdb
PDB entry 3g71 coloured by chain, front view.
PDB entry 3g71 coloured by chain, side view.
PDB entry 3g71 coloured by chain, top view.
Source organism: Haloarcula marismortui
Primary publication:
U2504 determines the species specificity of the A-site cleft antibiotics: the structures of tiamulin, homoharringtonine, and bruceantin bound to the ribosome.
Gürel G, Blaha G, Moore PB, Steitz TA
J Mol Biol 389 146-56 (2009)
PMID: 19362093

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 31-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-145590 (preferred)
Entry contents:
29 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (31 distinct):
Large ribosomal subunit protein uL2 Chain: A
Molecule details ›
Chain: A
Length: 237 amino acids
Theoretical weight: 24.98 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P20276 (Residues: 2-238; Coverage: 99%)
Gene names: rpl2, rrnAC1608
Sequence domains:
Structure domains:
Large ribosomal subunit protein uL3 Chain: B
Molecule details ›
Chain: B
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: C
Molecule details ›
Chain: C
Length: 246 amino acids
Theoretical weight: 26.46 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: 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
Sequence domains:
Structure domains: 50s Ribosomal Protein L5; Chain: A,
Large ribosomal subunit protein uL6 Chain: E
Molecule details ›
Chain: E
Length: 172 amino acids
Theoretical weight: 19.32 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P14135 (Residues: 2-173; Coverage: 97%)
Gene names: rpl6, rrnAC1596
Sequence domains: Ribosomal protein L6
Structure domains: Ribosomal protein L6, alpha-beta domain
Large ribosomal subunit protein eL8 Chain: F
Molecule details ›
Chain: F
Length: 119 amino acids
Theoretical weight: 12.66 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: G
Molecule details ›
Chain: G
Length: 348 amino acids
Theoretical weight: 37.17 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: 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
Sequence domains: Ribosomal protein L16p/L10e
Structure domains: Ribosomal protein L10e/L16
Large ribosomal subunit protein uL11 Chain: I
Molecule details ›
Chain: I
Length: 70 amino acids
Theoretical weight: 7.41 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P14122 (Residues: 67-136; Coverage: 43%)
Gene names: rpl11, rrnAC1414
Sequence domains: Ribosomal protein L11, RNA binding domain
Structure domains: Ribosomal protein L11, C-terminal domain
Large ribosomal subunit protein uL13 Chain: J
Molecule details ›
Chain: J
Length: 142 amino acids
Theoretical weight: 15.93 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P29198 (Residues: 4-145; Coverage: 98%)
Gene names: rpl13, rrnAC0065
Sequence domains: Ribosomal protein L13
Structure domains: Ribosomal protein L13
Large ribosomal subunit protein uL14 Chain: K
Molecule details ›
Chain: K
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: 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
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Structure domains:
Large ribosomal subunit protein eL15 Chain: M
Molecule details ›
Chain: M
Length: 194 amino acids
Theoretical weight: 22.14 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P60618 (Residues: 2-195; Coverage: 99%)
Gene names: rpl15e, rrnAC2065
Sequence domains: Ribosomal L15
Structure domains: Ribosomal protein l15e
Large ribosomal subunit protein uL18 Chain: N
Molecule details ›
Chain: N
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: O
Molecule details ›
Chain: O
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: P
Molecule details ›
Chain: P
Length: 143 amino acids
Theoretical weight: 16.17 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P14119 (Residues: 2-144; Coverage: 96%)
Gene names: rpl19e, rrnAC1594
Sequence domains: Ribosomal protein L19e
Structure domains:
Large ribosomal subunit protein eL21 Chain: Q
Molecule details ›
Chain: Q
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: R
Molecule details ›
Chain: R
Length: 150 amino acids
Theoretical weight: 16.36 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P10970 (Residues: 2-151; Coverage: 97%)
Gene names: rpl22, rrnAC1606
Sequence domains: Ribosomal protein L22p/L17e
Structure domains: Ribosomal protein L22/L17
Large ribosomal subunit protein uL23 Chain: S
Molecule details ›
Chain: S
Length: 81 amino acids
Theoretical weight: 9.18 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P12732 (Residues: 2-82; Coverage: 95%)
Gene names: rpl23, rrnAC1609
Sequence domains: Ribosomal protein L23
Structure domains: Alpha-Beta Plaits
Large ribosomal subunit protein uL24 Chain: T
Molecule details ›
Chain: T
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: U
Molecule details ›
Chain: U
Length: 53 amino acids
Theoretical weight: 5.92 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P14116 (Residues: 5-57; Coverage: 79%)
Gene names: rpl24e, rrnAC0104
Sequence domains: Ribosomal protein L24e
Structure domains: Ribosomal protein L24e
Large ribosomal subunit protein uL29 Chain: V
Molecule details ›
Chain: V
Length: 65 amino acids
Theoretical weight: 7.15 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P10971 (Residues: 2-66; Coverage: 92%)
Gene names: rpl29, rrnAC1604
Sequence domains: Ribosomal L29 protein
Structure domains: Helix Hairpins
Large ribosomal subunit protein uL30 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
Sequence domains: Ribosomal protein L30p/L7e
Structure domains:
Large ribosomal subunit protein eL31 Chain: X
Molecule details ›
Chain: X
Length: 82 amino acids
Theoretical weight: 9.32 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P18138 (Residues: 8-89; Coverage: 89%)
Gene names: rpl31e, rrnAC3113
Sequence domains: Ribosomal protein L31e
Structure domains: Ribosomal Protein L31e; Chain: W;
Large ribosomal subunit protein eL32 Chain: Y
Molecule details ›
Chain: Y
Length: 142 amino acids
Theoretical weight: 16.08 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P12736 (Residues: 96-237; Coverage: 59%)
Gene names: rpl32e, rrnAC1595
Sequence domains: Ribosomal protein L32
Large ribosomal subunit protein eL43 Chain: Z
Molecule details ›
Chain: Z
Length: 73 amino acids
Theoretical weight: 8.22 KDa
Source organism: Haloarcula marismortui
UniProt:
  • Canonical: P60619 (Residues: 10-82; Coverage: 79%)
Gene names: rpl37ae, rrnAC1669
Sequence domains: Ribosomal L37ae protein family
Structure domains: N-terminal domain of TfIIb
Large ribosomal subunit protein eL37 Chain: 1
Molecule details ›
Chain: 1
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: 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
Sequence domains: Ribosomal L39 protein
Structure domains: Ribosomal protein L39e
Large ribosomal subunit protein eL42 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
Sequence domains: Ribosomal protein L44
Structure domains: Nuclear Transport Factor 2; Chain: A,
23S ribosomal RNA Chain: 0
Molecule details ›
Chain: 0
Length: 2923 nucleotides
Theoretical weight: 946.46 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

7 bound ligands:
Ligand MG 93 x MG
Ligand K 2 x K
Ligand NA 75 x NA
Ligand CL 22 x CL
Ligand SR 108 x SR
Ligand WIN 1 x WIN
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: APS BEAMLINE 24-ID-C
Spacegroup: C2221
Unit cell:
a: 212.207Å b: 299.544Å c: 574.251Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.186 0.186 0.233

Quick links

Citations

29 review citations

The A-Z of bacterial translation inhibitors.
Wilson DN. (2009)
28 more

4 mentions without citation

U2504 determines the species specificity of the A-site cleft antibiotics: the structures of tiamulin, homoharringtonine, and bruceantin bound to the ribosome.
Gürel et al. (2009)
3 more