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PDBsum entry 3df2
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protein dna_rna metals Protein-protein interface(s) links
Ribosome PDB id
3df2

 

 

 

 

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Contents
Protein chains
94 a.a. *
271 a.a. *
209 a.a. *
201 a.a. *
178 a.a. *
176 a.a. *
149 a.a. *
142 a.a. *
121 a.a. *
143 a.a. *
136 a.a. *
120 a.a. *
116 a.a. *
114 a.a. *
117 a.a. *
103 a.a. *
110 a.a. *
93 a.a. *
102 a.a. *
79 a.a. *
63 a.a. *
58 a.a. *
77 a.a. *
56 a.a. *
50 a.a. *
46 a.a. *
64 a.a. *
38 a.a. *
141 a.a. *
DNA/RNA
Metals
_MG ×110
_ZN
Waters ×506
* Residue conservation analysis
Obsolete entry
PDB id:
3df2
Name: Ribosome
Title: Crystal structure of the bacterial ribosome from escherichia coli in complex with hygromycin b. This file contains the 50s subunit of the first 70s ribosome. The entire crystal structure contains two 70s ribosomes.
Structure: 5s ribosomal RNA. Chain: a. 23s ribosomal RNA. Chain: b. 50s ribosomal protein l25. Chain: v. 50s ribosomal protein l2. Chain: c. 50s ribosomal protein l3.
Source: Escherichia coli. Organism_taxid: 562. Strain: mre600. Strain: mre600
Resolution:
3.50Å     R-factor:   0.269     R-free:   0.318
Authors: M.A.Borovinskaya,S.Shoji,K.Fredrick,J.H.D.Cate
Key ref: M.A.Borovinskaya et al. (2008). Structural basis for hygromycin B inhibition of protein biosynthesis. Rna, 14, 1590-1599. PubMed id: 18567815
Date:
11-Jun-08     Release date:   19-Aug-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P68919  (RL25_ECOLI) -  50S ribosomal protein L25 from Escherichia coli (strain K12)
Seq:
Struc: 		94 a.a.
94 a.a.
Protein chain
Pfam   ArchSchema ?
P60422  (RL2_ECOLI) -  50S ribosomal protein L2 from Escherichia coli (strain K12)
Seq:
Struc: 		273 a.a.
271 a.a.
Protein chain
Pfam   ArchSchema ?
P60438  (RL3_ECOLI) -  50S ribosomal protein L3 from Escherichia coli (strain K12)
Seq:
Struc: 		209 a.a.
209 a.a.
Protein chain
Pfam   ArchSchema ?
P60723  (RL4_ECOLI) -  50S ribosomal protein L4 from Escherichia coli (strain K12)
Seq:
Struc: 		201 a.a.
201 a.a.
Protein chain
Pfam   ArchSchema ?
P62399  (RL5_ECOLI) -  50S ribosomal protein L5 from Escherichia coli (strain K12)
Seq:
Struc: 		179 a.a.
178 a.a.
Protein chain
P02390  (RL6_ECOLI) - 
Protein chain
Pfam   ArchSchema ?
P0A7R1  (RL9_ECOLI) -  50S ribosomal protein L9 from Escherichia coli (strain K12)
Seq:
Struc: 		149 a.a.
149 a.a.
Protein chain
P02410  (RL13_ECOLI) - 
Protein chain
P02411  (RL14_ECOLI) - 
Protein chain
Pfam   ArchSchema ?
P02413  (RL15_ECOLI) -  50S ribosomal protein L15 from Escherichia coli (strain K12)
Seq:
Struc: 		144 a.a.
143 a.a.
Protein chain
P02414  (RL16_ECOLI) - 
Protein chain
P02416  (RL17_ECOLI) - 
Protein chain
Pfam   ArchSchema ?
P0C018  (RL18_ECOLI) -  50S ribosomal protein L18 from Escherichia coli (strain K12)
Seq:
Struc: 		117 a.a.
116 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7K6  (RL19_ECOLI) -  50S ribosomal protein L19 from Escherichia coli (strain K12)
Seq:
Struc: 		115 a.a.
114 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7L3  (RL20_ECOLI) -  50S ribosomal protein L20 from Escherichia coli (strain K12)
Seq:
Struc: 		118 a.a.
117 a.a.
Protein chain
P02422  (RL21_ECOLI) - 
Protein chain
Pfam   ArchSchema ?
P61175  (RL22_ECOLI) -  50S ribosomal protein L22 from Escherichia coli (strain K12)
Seq:
Struc: 		110 a.a.
110 a.a.
Protein chain
P02424  (RL23_ECOLI) - 
Protein chain
Pfam   ArchSchema ?
P60624  (RL24_ECOLI) -  50S ribosomal protein L24 from Escherichia coli (strain K12)
Seq:
Struc: 		104 a.a.
102 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7L8  (RL27_ECOLI) -  50S ribosomal protein L27 from Escherichia coli (strain K12)
Seq:
Struc: 		85 a.a.
79 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7M6  (RL29_ECOLI) -  50S ribosomal protein L29 from Escherichia coli (strain K12)
Seq:
Struc: 		63 a.a.
63 a.a.
Protein chain
P02430  (RL30_ECOLI) - 
Protein chain
Pfam   ArchSchema ?
P0A7M2  (RL28_ECOLI) -  50S ribosomal protein L28 from Escherichia coli (strain K12)
Seq:
Struc: 		78 a.a.
77 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7N4  (RL32_ECOLI) -  50S ribosomal protein L32 from Escherichia coli (strain K12)
Seq:
Struc: 		57 a.a.
56 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7N9  (RL33_ECOLI) -  50S ribosomal protein L33 from Escherichia coli (strain K12)
Seq:
Struc: 		55 a.a.
50 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7P5  (RL34_ECOLI) -  50S ribosomal protein L34 from Escherichia coli (strain K12)
Seq:
Struc: 		46 a.a.
46 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7Q1  (RL35_ECOLI) -  50S ribosomal protein L35 from Escherichia coli (strain K12)
Seq:
Struc: 		65 a.a.
64 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7Q6  (RL36_ECOLI) -  50S ribosomal protein L36 from Escherichia coli (strain K12)
Seq:
Struc: 		38 a.a.
38 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7J7  (RL11_ECOLI) -  50S ribosomal protein L11 from Escherichia coli (strain K12)
Seq:
Struc: 		142 a.a.
141 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

DNA/RNA chains
  G-C-C-U-G-G-C-G-G-C-C-G-U-A-G-C-G-C-G-G-U-G-G-U-C-C-C-A-C-C-U-G-A-C-C-C-C-A-U- 117 bases
  G-G-U-U-A-A-G-C-G-A-C-U-A-A-G-C-G-U-A-C-A-C-G-G-U-G-G-A-U-G-C-C-C-U-G-G-C-A-G- ... 2841 bases

 

 
Rna 14:1590-1599 (2008)
PubMed id: 18567815  
 
 
Structural basis for hygromycin B inhibition of protein biosynthesis.
M.A.Borovinskaya, S.Shoji, K.Fredrick, J.H.Cate.
 
  ABSTRACT  
 
Aminoglycosides are one of the most widely used and clinically important classes of antibiotics that target the ribosome. Hygromycin B is an atypical aminoglycoside antibiotic with unique structural and functional properties. Here we describe the structure of the intact Escherichia coli 70S ribosome in complex with hygromycin B. The antibiotic binds to the mRNA decoding center in the small (30S) ribosomal subunit of the 70S ribosome and induces a localized conformational change, in contrast to its effects observed in the structure of the isolated 30S ribosomal subunit in complex with the drug. The conformational change in the ribosome caused by hygromycin B binding differs from that induced by other aminoglycosides. Also, in contrast to other aminoglycosides, hygromycin B potently inhibits spontaneous reverse translocation of tRNAs and mRNA on the ribosome in vitro. These structural and biochemical results help to explain the unique mode of translation inhibition by hygromycin B.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21399643 D.N.Ermolenko, and H.F.Noller (2011).
mRNA translocation occurs during the second step of ribosomal intersubunit rotation.
  Nat Struct Mol Biol, 18, 457-462.  
20838678 E.Gaggelli, N.Gaggelli, E.Molteni, G.Valensin, D.Balenci, M.Wrońska, W.Szczepanik, J.Nagaj, J.Skała, and M.Jeżowska-Bojczuk (2010).
Coordination pattern, solution structure and DNA damage studies of the copper(II) complex with the unusual aminoglycoside antibiotic hygromycin B.
  Dalton Trans, 39, 9830-9837.  
20494981 H.David-Eden, A.S.Mankin, and Y.Mandel-Gutfreund (2010).
Structural signatures of antibiotic binding sites on the ribosome.
  Nucleic Acids Res, 38, 5982-5994.  
20087596 J.Kurepa, C.Karangwa, L.S.Duke, and J.A.Smalle (2010).
Arabidopsis sensitivity to protein synthesis inhibitors depends on 26S proteasome activity.
  Plant Cell Rep, 29, 249-259.  
20154709 R.E.Stanley, G.Blaha, R.L.Grodzicki, M.D.Strickler, and T.A.Steitz (2010).
The structures of the anti-tuberculosis antibiotics viomycin and capreomycin bound to the 70S ribosome.
  Nat Struct Mol Biol, 17, 289-293.
PDB codes: 3knh 3kni 3knj 3knk 3knl 3knm 3knn 3kno
20215440 S.M.Dibrov, J.Parsons, and T.Hermann (2010).
A model for the study of ligand binding to the ribosomal RNA helix h44.
  Nucleic Acids Res, 38, 4458-4465.
PDB code: 3loa
  19929179 D.N.Wilson (2009).
The A-Z of bacterial translation inhibitors.
  Crit Rev Biochem Mol Biol, 44, 393-433.  
  19173642 S.Shoji, S.E.Walker, and K.Fredrick (2009).
Ribosomal translocation: one step closer to the molecular mechanism.
  ACS Chem Biol, 4, 93.  
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. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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