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

 

 

 

 

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Contents
Protein chains
218 a.a. *
206 a.a. *
205 a.a. *
150 a.a. *
100 a.a. *
150 a.a. *
129 a.a. *
127 a.a. *
98 a.a. *
117 a.a. *
123 a.a. *
113 a.a. *
95 a.a. *
88 a.a. *
80 a.a. *
80 a.a. *
55 a.a. *
79 a.a. *
85 a.a. *
51 a.a. *
DNA/RNA
Metals
_MG ×42
Waters ×207
* Residue conservation analysis
Obsolete entry
PDB id:
3ofb
Name: Ribosome/antibiotic
Title: Crystal structure of the e. Coli ribosome bound to chloramphenicol. This file contains the 30s subunit of the second 70s ribosome.
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: Escherichia coli. Organism_taxid: 562. Organism_taxid: 83333. Strain: k-12. Strain: k-12
Resolution:
3.19Å     R-factor:   0.192     R-free:   0.252
Authors: J.A.Dunkle,L.Xiong,A.S.Mankin,J.H.D.Cate
Key ref: J.A.Dunkle et al. (2010). Structures of the Escherichia coli ribosome with antibiotics bound near the peptidyl transferase center explain spectra of drug action. Proc Natl Acad Sci U S A, 107, 17152-17157. PubMed id: 20876128
Date:
14-Aug-10     Release date:   20-Oct-10    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0A7V0  (RS2_ECOLI) -  30S ribosomal protein S2 from Escherichia coli (strain K12)
Seq:
Struc: 		241 a.a.
218 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7V3  (RS3_ECOLI) -  30S ribosomal protein S3 from Escherichia coli (strain K12)
Seq:
Struc: 		233 a.a.
206 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7V8  (RS4_ECOLI) -  30S ribosomal protein S4 from Escherichia coli (strain K12)
Seq:
Struc: 		206 a.a.
205 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7W1  (RS5_ECOLI) -  30S ribosomal protein S5 from Escherichia coli (strain K12)
Seq:
Struc: 		167 a.a.
150 a.a.
Protein chain
Pfam   ArchSchema ?
P02358  (RS6_ECOLI) -  30S ribosomal protein S6 from Escherichia coli (strain K12)
Seq:
Struc: 		135 a.a.
100 a.a.
Protein chain
Pfam   ArchSchema ?
P02359  (RS7_ECOLI) -  30S ribosomal protein S7 from Escherichia coli (strain K12)
Seq:
Struc: 		179 a.a.
150 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7W7  (RS8_ECOLI) -  30S ribosomal protein S8 from Escherichia coli (strain K12)
Seq:
Struc: 		130 a.a.
129 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7X3  (RS9_ECOLI) -  30S ribosomal protein S9 from Escherichia coli (strain K12)
Seq:
Struc: 		130 a.a.
127 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7R5  (RS10_ECOLI) -  30S ribosomal protein S10 from Escherichia coli (strain K12)
Seq:
Struc: 		103 a.a.
98 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7R9  (RS11_ECOLI) -  30S ribosomal protein S11 from Escherichia coli (strain K12)
Seq:
Struc: 		129 a.a.
117 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7S3  (RS12_ECOLI) -  30S ribosomal protein S12 from Escherichia coli (strain K12)
Seq:
Struc: 		124 a.a.
123 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7S9  (RS13_ECOLI) -  30S ribosomal protein S13 from Escherichia coli (strain K12)
Seq:
Struc: 		118 a.a.
113 a.a.
Protein chain
Pfam   ArchSchema ?
P0AG59  (RS14_ECOLI) -  30S ribosomal protein S14 from Escherichia coli (strain K12)
Seq:
Struc: 		101 a.a.
95 a.a.
Protein chain
Pfam   ArchSchema ?
P0ADZ4  (RS15_ECOLI) -  30S ribosomal protein S15 from Escherichia coli (strain K12)
Seq:
Struc: 		89 a.a.
88 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7T3  (RS16_ECOLI) -  30S ribosomal protein S16 from Escherichia coli (strain K12)
Seq:
Struc: 		82 a.a.
80 a.a.
Protein chain
Pfam   ArchSchema ?
P0AG63  (RS17_ECOLI) -  30S ribosomal protein S17 from Escherichia coli (strain K12)
Seq:
Struc: 		84 a.a.
80 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7T7  (RS18_ECOLI) -  30S ribosomal protein S18 from Escherichia coli (strain K12)
Seq:
Struc: 		75 a.a.
55 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7U3  (RS19_ECOLI) -  30S ribosomal protein S19 from Escherichia coli (strain K12)
Seq:
Struc: 		92 a.a.
79 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7U7  (RS20_ECOLI) -  30S ribosomal protein S20 from Escherichia coli (strain K12)
Seq:
Struc: 		87 a.a.
85 a.a.
Protein chain
Pfam   ArchSchema ?
P68679  (RS21_ECOLI) -  30S ribosomal protein S21 from Escherichia coli (strain K12)
Seq:
Struc: 		71 a.a.
51 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

DNA/RNA chain
  U-G-A-A-G-A-G-U-U-U-G-A-U-C-A-U-G-G-C-U-C-A-G-A-U-U-G-A-A-C-G-C-U-G-G-C-G-G-C- ... 1530 bases

 

 
Proc Natl Acad Sci U S A 107:17152-17157 (2010)
PubMed id: 20876128  
 
 
Structures of the Escherichia coli ribosome with antibiotics bound near the peptidyl transferase center explain spectra of drug action.
J.A.Dunkle, L.Xiong, A.S.Mankin, J.H.Cate.
 
  ABSTRACT  
 
No abstract given.

 

Literature references that cite this PDB file's key reference

  PubMed id Reference
22407015 L.Wang, F.Yang, D.Zhang, Z.Chen, R.M.Xu, K.H.Nierhaus, W.Gong, and Y.Qin (2012).
A conserved proline switch on the ribosome facilitates the recruitment and binding of trGTPases.
  Nat Struct Mol Biol, 19, 403-410.  
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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