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PDBsum entry 3ohy
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protein dna_rna metals Protein-protein interface(s) links
Ribosome/antibiotic PDB id
3ohy

 

 

 

 

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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. *
115 a.a. *
60 a.a. *
88 a.a. *
84 a.a. *
100 a.a. *
70 a.a. *
79 a.a. *
99 a.a. *
25 a.a. *
DNA/RNA
Metals
_MG ×51
_ZN ×2
* Residue conservation analysis
Obsolete entry
PDB id:
3ohy
Name: Ribosome/antibiotic
Title: Structure of the thermus thermophilus 70s ribosome complexed with azithromycin. This file contains the 30s subunit of one 70s ribosome. The entire crystal structure contains two 70s ribosomes.
Structure: 16s rrna. 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. Organism_taxid: 300852. Strain: hb8. Strain: hb8
Resolution:
3.00Å     R-factor:   0.235     R-free:   0.269
Authors: D.P.Bulkley,C.A.Innis,G.Blaha,T.A.Steitz
Key ref: D.Bulkley et al. (2010). Revisiting the structures of several antibiotics bound to the bacterial ribosome. Proc Natl Acad Sci U S A, 107, 17158-17163. PubMed id: 20876130
Date:
18-Aug-10     Release date:   20-Oct-10    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P80371  (RS2_THET8) -  Small ribosomal subunit protein uS2 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		256 a.a.
235 a.a.
Protein chain
Pfam   ArchSchema ?
P80372  (RS3_THET8) -  Small ribosomal subunit protein uS3 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		239 a.a.
207 a.a.
Protein chain
Pfam   ArchSchema ?
P80373  (RS4_THET8) -  Small ribosomal subunit protein uS4 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		209 a.a.
208 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHQ5  (RS5_THET8) -  Small ribosomal subunit protein uS5 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		162 a.a.
151 a.a.
Protein chain
Q5SLP8  (RS6_THET8) -  Small ribosomal subunit protein bS6 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		101 a.a.
101 a.a.
Protein chain
Pfam   ArchSchema ?
P17291  (RS7_THET8) -  Small ribosomal subunit protein uS7 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		156 a.a.
155 a.a.
Protein chain
Q5SHQ2  (RS8_THET8) - 
Protein chain
Pfam   ArchSchema ?
P80374  (RS9_THET8) -  Small ribosomal subunit protein uS9 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		128 a.a.
127 a.a.*
Protein chain
Pfam   ArchSchema ?
Q5SHN7  (RS10_THET8) -  Small ribosomal subunit protein uS10 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		105 a.a.
99 a.a.
Protein chain
Pfam   ArchSchema ?
P80376  (RS11_THET8) -  Small ribosomal subunit protein uS11 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		129 a.a.
119 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHN3  (RS12_THET8) -  Small ribosomal subunit protein uS12 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		132 a.a.
125 a.a.
Protein chain
Pfam   ArchSchema ?
P80377  (RS13_THET8) -  Small ribosomal subunit protein uS13 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		126 a.a.
115 a.a.
Protein chain
Q5SHQ1  (RS14Z_THET8) - 
Protein chain
Pfam   ArchSchema ?
Q5SJ76  (RS15_THET8) -  Small ribosomal subunit protein uS15 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		89 a.a.
88 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SJH3  (RS16_THET8) -  Small ribosomal subunit protein bS16 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		88 a.a.
84 a.a.
Protein chain
Q5SHP7  (RS17_THET8) - 
Protein chain
Pfam   ArchSchema ?
Q5SLQ0  (RS18_THET8) -  Small ribosomal subunit protein bS18 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		88 a.a.
70 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHP2  (RS19_THET8) -  Small ribosomal subunit protein uS19 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		93 a.a.
79 a.a.
Protein chain
Pfam   ArchSchema ?
P80380  (RS20_THET8) -  Small ribosomal subunit protein bS20 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		106 a.a.
99 a.a.
Protein chain
Q5SIH3  (RSHX_THET8) -  Small ribosomal subunit protein bTHX from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		27 a.a.
25 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chain
  U-G-G-A-G-A-G-U-U-U-G-A-U-C-C-U-G-G-C-U-C-A-G-G-G-U-G-A-A-C-G-C-U-G-G-C-G-G-C- ... 1504 bases

 

 
Proc Natl Acad Sci U S A 107:17158-17163 (2010)
PubMed id: 20876130  
 
 
Revisiting the structures of several antibiotics bound to the bacterial ribosome.
D.Bulkley, C.A.Innis, G.Blaha, T.A.Steitz.
 
  ABSTRACT  
 
No abstract given.

 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21368151 F.Yan, and D.G.Fujimori (2011).
RNA methylation by Radical SAM enzymes RlmN and Cfr proceeds via methylene transfer and hydride shift.
  Proc Natl Acad Sci U S A, 108, 3930-3934.  
21286630 G.D.Wright (2011).
Molecular mechanisms of antibiotic resistance.
  Chem Commun (Camb), 47, 4055-4061.  
21342782 L.R.Cruz-Vera, M.S.Sachs, C.L.Squires, and C.Yanofsky (2011).
Nascent polypeptide sequences that influence ribosome function.
  Curr Opin Microbiol, 14, 160-166.  
21383133 S.Chiba, T.Kanamori, T.Ueda, Y.Akiyama, K.Pogliano, and K.Ito (2011).
Recruitment of a species-specific translational arrest module to monitor different cellular processes.
  Proc Natl Acad Sci U S A, 108, 6073-6078.  
  21320180 T.Siibak, L.Peil, A.Dönhöfer, A.Tats, M.Remm, D.N.Wilson, T.Tenson, and J.Remme (2011).
Antibiotic-induced ribosomal assembly defects result from changes in the synthesis of ribosomal proteins.
  Mol Microbiol, 80, 54-67.  
20876111 S.Douthwaite (2010).
Designer drugs for discerning bugs.
  Proc Natl Acad Sci U S A, 107, 17065-17066.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.

 

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