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PDBsum entry 4b3s

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protein dna_rna ligands metals Protein-protein interface(s) links
Ribosome PDB id
4b3s
Jmol
Contents
Protein chains
235 a.a.
207 a.a.
208 a.a.
151 a.a.
101 a.a.
155 a.a.
138 a.a.
127 a.a.
99 a.a.
119 a.a.
125 a.a.
125 a.a.
60 a.a.
88 a.a.
84 a.a.
104 a.a.
73 a.a.
81 a.a.
99 a.a.
25 a.a.
DNA/RNA
Ligands
RPO
Metals
_MG ×166
_ZN ×2
__K ×13
PDB id:
4b3s
Name: Ribosome
Title: Crystal structure of the 30s ribosome in complex with compou
Structure: 16s ribosomal RNA. Chain: a. 30s ribosomal protein s2. Chain: b. 30s ribosomal protein s3. Chain: c. 30s ribosomal protein s4. Chain: d. 30s ribosomal protein s5.
Source: Thermus thermophilus hb8. Organism_taxid: 300852. Organism_taxid: 300852
Resolution:
3.15Å     R-factor:   0.210     R-free:   0.247
Authors: C.L.Ng,K.Lang,D.Shcherbakov,T.Matt,D.Perez-Fernandez,R.Patak S.Duscha,R.Akbergenov,H.Boukari,P.Freihofer,I.Kudyba,M.S.K. R.S.Nandurikar,V.Ramakrishnan,A.Vasella,E.C.Bottger
Key ref: D.Perez-Fernandez et al. (2014). 4'-O-substitutions determine selectivity of aminoglycoside antibiotics. Nat Commun, 5, 3112. PubMed id: 24473108 DOI: 10.1038/ncomms4112
Date:
26-Jul-12     Release date:   07-Aug-13    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P80371  (RS2_THET8) -  30S ribosomal protein S2
Seq:
Struc:
256 a.a.
235 a.a.
Protein chain
Pfam   ArchSchema ?
P80372  (RS3_THET8) -  30S ribosomal protein S3
Seq:
Struc:
239 a.a.
207 a.a.
Protein chain
Pfam   ArchSchema ?
P80373  (RS4_THET8) -  30S ribosomal protein S4
Seq:
Struc:
209 a.a.
208 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHQ5  (RS5_THET8) -  30S ribosomal protein S5
Seq:
Struc:
162 a.a.
151 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SLP8  (RS6_THET8) -  30S ribosomal protein S6
Seq:
Struc:
101 a.a.
101 a.a.
Protein chain
Pfam   ArchSchema ?
P17291  (RS7_THET8) -  30S ribosomal protein S7
Seq:
Struc:
156 a.a.
155 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHQ2  (RS8_THET8) -  30S ribosomal protein S8
Seq:
Struc:
138 a.a.
138 a.a.
Protein chain
Pfam   ArchSchema ?
P80374  (RS9_THET8) -  30S ribosomal protein S9
Seq:
Struc:
128 a.a.
127 a.a.*
Protein chain
Pfam   ArchSchema ?
Q5SHN7  (RS10_THET8) -  30S ribosomal protein S10
Seq:
Struc:
105 a.a.
99 a.a.
Protein chain
Pfam   ArchSchema ?
P80376  (RS11_THET8) -  30S ribosomal protein S11
Seq:
Struc:
129 a.a.
119 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHN3  (RS12_THET8) -  30S ribosomal protein S12
Seq:
Struc:
132 a.a.
125 a.a.
Protein chain
Pfam   ArchSchema ?
P80377  (RS13_THET8) -  30S ribosomal protein S13
Seq:
Struc:
126 a.a.
125 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHQ1  (RS14Z_THET8) -  30S ribosomal protein S14 type Z
Seq:
Struc:
61 a.a.
60 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SJ76  (RS15_THET8) -  30S ribosomal protein S15
Seq:
Struc:
89 a.a.
88 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SJH3  (RS16_THET8) -  30S ribosomal protein S16
Seq:
Struc:
88 a.a.
84 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHP7  (RS17_THET8) -  30S ribosomal protein S17
Seq:
Struc:
105 a.a.
104 a.a.*
Protein chain
Pfam   ArchSchema ?
Q5SLQ0  (RS18_THET8) -  30S ribosomal protein S18
Seq:
Struc:
88 a.a.
73 a.a.*
Protein chain
Pfam   ArchSchema ?
Q5SHP2  (RS19_THET8) -  30S ribosomal protein S19
Seq:
Struc:
93 a.a.
81 a.a.
Protein chain
Pfam   ArchSchema ?
P80380  (RS20_THET8) -  30S ribosomal protein S20
Seq:
Struc:
106 a.a.
99 a.a.*
Protein chain
Pfam   ArchSchema ?
Q5SIH3  (RSHX_THET8) -  30S ribosomal protein Thx
Seq:
Struc:
27 a.a.
25 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   4 terms 
  Biological process     translation   1 term 
  Biochemical function     structural constituent of ribosome     8 terms  

 

 
DOI no: 10.1038/ncomms4112 Nat Commun 5:3112 (2014)
PubMed id: 24473108  
 
 
4'-O-substitutions determine selectivity of aminoglycoside antibiotics.
D.Perez-Fernandez, D.Shcherbakov, T.Matt, N.C.Leong, I.Kudyba, S.Duscha, H.Boukari, R.Patak, S.R.Dubbaka, K.Lang, M.Meyer, R.Akbergenov, P.Freihofer, S.Vaddi, P.Thommes, V.Ramakrishnan, A.Vasella, E.C.Böttger.
 
  ABSTRACT  
 
Clinical use of 2-deoxystreptamine aminoglycoside antibiotics, which target the bacterial ribosome, is compromised by adverse effects related to limited drug selectivity. Here we present a series of 4',6'-O-acetal and 4'-O-ether modifications on glucopyranosyl ring I of aminoglycosides. Chemical modifications were guided by measuring interactions between the compounds synthesized and ribosomes harbouring single point mutations in the drug-binding site, resulting in aminoglycosides that interact poorly with the drug-binding pocket of eukaryotic mitochondrial or cytosolic ribosomes. Yet, these compounds largely retain their inhibitory activity for bacterial ribosomes and show antibacterial activity. Our data indicate that 4'-O-substituted aminoglycosides possess increased selectivity towards bacterial ribosomes and little activity for any of the human drug-binding pockets.