3G4S image
Deposition Date 2009-02-04
Release Date 2009-04-28
Last Version Date 2023-09-06
Entry Detail
PDB ID:
3G4S
Keywords:
RIBOSOME
Title:
Co-crystal structure of Tiamulin bound to the large ribosomal subunit
Biological Source:
Source Organism:
Haloarcula marismortui (Taxon ID: 2238)
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
3.20 Å
R-Value Free:
0.29
R-Value Work:
0.21
Space Group:
C 2 2 21
3G4S validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:A (auth: 0)
Chain Length:2923
Number of Molecules:1
Biological Source:Haloarcula marismortui
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L37e
Gene (Uniprot):rpl37e
Chain IDs:BA (auth: 1)
Chain Length:56
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P32410 Pfam ID:PF01907
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L39e
Gene (Uniprot):rpl39e
Chain IDs:CA (auth: 2)
Chain Length:50
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P22452 Pfam ID:PF00832
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L44E
Gene (Uniprot):rpl44e
Chain IDs:DA (auth: 3)
Chain Length:92
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P32411 Pfam ID:PF00935
Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:EA (auth: 9)
Chain Length:122
Number of Molecules:1
Biological Source:Haloarcula marismortui
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2P
Gene (Uniprot):rpl2
Chain IDs:B (auth: A)
Chain Length:237
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P20276 Pfam ID:PF00181, PF03947
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3P
Gene (Uniprot):rpl3
Chain IDs:C (auth: B)
Chain Length:337
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P20279 Pfam ID:PF00297
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4P
Gene (Uniprot):rpl4
Chain IDs:D (auth: C)
Chain Length:246
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P12735 Pfam ID:PF00573
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5P
Gene (Uniprot):rpl5
Chain IDs:E (auth: D)
Chain Length:177
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P14124 Pfam ID:PF00281, PF00673
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6P
Gene (Uniprot):rpl6
Chain IDs:F (auth: E)
Chain Length:172
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P14135 Pfam ID:PF00347
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L7Ae
Gene (Uniprot):rpl7ae
Chain IDs:G (auth: F)
Chain Length:119
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P12743 Pfam ID:PF01248
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L10
Gene (Uniprot):rpl10
Chain IDs:H (auth: G)
Chain Length:348
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P15825 Pfam ID:PF00466, PF17777
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L10e
Gene (Uniprot):rpl10e
Chain IDs:I (auth: H)
Chain Length:177
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P60617 Pfam ID:PF00252
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L11P
Gene (Uniprot):rpl11
Chain IDs:J (auth: I)
Chain Length:70
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P14122 Pfam ID:PF00298
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13P
Gene (Uniprot):rpl13
Chain IDs:K (auth: J)
Chain Length:142
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P29198 Pfam ID:PF00572
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14P
Gene (Uniprot):rpl14
Chain IDs:L (auth: K)
Chain Length:132
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P22450 Pfam ID:PF00238
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15P
Gene (Uniprot):rpl15
Chain IDs:M (auth: L)
Chain Length:165
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P12737 Pfam ID:PF00828
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15e
Gene (Uniprot):rpl15e
Chain IDs:N (auth: M)
Chain Length:194
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P60618 Pfam ID:PF00827
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18P
Gene (Uniprot):rpl18
Chain IDs:O (auth: N)
Chain Length:186
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P14123 Pfam ID:PF17144
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18e
Gene (Uniprot):rpl18e
Chain IDs:P (auth: O)
Chain Length:115
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P12733 Pfam ID:PF00828
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19e
Gene (Uniprot):rpl19e
Chain IDs:Q (auth: P)
Chain Length:143
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P14119 Pfam ID:PF01280
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21e
Gene (Uniprot):rpl21e
Chain IDs:R (auth: Q)
Chain Length:95
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P12734 Pfam ID:PF01157
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22P
Gene (Uniprot):rpl22
Chain IDs:S (auth: R)
Chain Length:150
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P10970 Pfam ID:PF00237
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23P
Gene (Uniprot):rpl23
Chain IDs:T (auth: S)
Chain Length:81
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P12732 Pfam ID:PF00276
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24P
Gene (Uniprot):rpl24
Chain IDs:U (auth: T)
Chain Length:119
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P10972 Pfam ID:PF16906, PF00467
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24e
Gene (Uniprot):rpl24e
Chain IDs:V (auth: U)
Chain Length:53
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P14116 Pfam ID:PF01246
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29P
Gene (Uniprot):rpl29
Chain IDs:W (auth: V)
Chain Length:65
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P10971 Pfam ID:PF00831
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30P
Gene (Uniprot):rpl30
Chain IDs:X (auth: W)
Chain Length:154
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P14121 Pfam ID:PF00327
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31e
Gene (Uniprot):rpl31e
Chain IDs:Y (auth: X)
Chain Length:82
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P18138 Pfam ID:PF01198
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32e
Gene (Uniprot):rpl32e
Chain IDs:Z (auth: Y)
Chain Length:142
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P12736 Pfam ID:PF01655
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L37Ae
Gene (Uniprot):rpl37ae
Chain IDs:AA (auth: Z)
Chain Length:73
Number of Molecules:1
Biological Source:Haloarcula marismortui
UniProt ID:P60619 Pfam ID:PF01780
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
1MA A A ?
OMG A G O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE
OMU A U O2'-METHYLURIDINE 5'-MONOPHOSPHATE
PSU A U PSEUDOURIDINE-5'-MONOPHOSPHATE
UR3 A U 3-METHYLURIDINE-5'-MONOPHOSHATE
Ligand Molecules
CD
CL
K
MG
MUL
NA
SR
Primary Citation
U2504 determines the species specificity of the A-site cleft antibiotics: the structures of tiamulin, homoharringtonine, and bruceantin bound to the ribosome.
J.Mol.Biol. 389 146 156 (2009)
PMID: 19362093 DOI: 10.1016/j.jmb.2009.04.005

Abstact

Structures have been obtained for the complexes that tiamulin, homoharringtonine, and bruceantin form with the large ribosomal subunit of Haloarcula marismortui at resolutions ranging from 2.65 to 3.2 A. They show that all these inhibitors block protein synthesis by competing with the amino acid side chains of incoming aminoacyl-tRNAs for binding in the A-site cleft in the peptidyl-transferase center, which is universally conserved. In addition, these structures support the hypothesis that the species specificity exhibited by the A-site cleft inhibitors is determined by the interactions they make, or fail to make, with a single nucleotide, U2504 (Escherichia coli). In the ribosome, the position of U2504 is controlled by its interactions with neighboring nucleotides, whose identities vary among kingdoms.

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Protein

Chemical

Disease

Primary Citation of related structures
3G6E
3G71