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protein dna_rna metals Protein-protein interface(s) links
Ribosome PDB id
1jj2
Jmol
Contents
Protein chains
237 a.a. *
337 a.a. *
246 a.a. *
140 a.a. *
172 a.a. *
119 a.a. *
29 a.a. *
156 a.a. *
142 a.a. *
132 a.a. *
145 a.a. *
194 a.a. *
186 a.a. *
115 a.a. *
143 a.a. *
95 a.a. *
150 a.a. *
81 a.a. *
119 a.a. *
53 a.a. *
65 a.a. *
154 a.a. *
82 a.a. *
142 a.a. *
73 a.a. *
56 a.a. *
46 a.a. *
92 a.a. *
DNA/RNA
Metals
_CL ×22
_NA ×86
_MG ×117
_CD ×5
__K ×2
Waters ×7893
* Residue conservation analysis
PDB id:
1jj2
Name: Ribosome
Title: Fully refined crystal structure of the haloarcula marismortui large ribosomal subunit at 2.4 angstrom resolution
Structure: 23s rrna. Chain: 0. 5s rrna. Chain: 9. Ribosomal protein l2. Chain: a. Synonym: 50s ribosomal protein l2p, hmal2, hl4. Ribosomal protein l3. Chain: b.
Source: Haloarcula marismortui. Organism_taxid: 2238. Organism_taxid: 2238
Biol. unit: 30mer (from PQS)
Resolution:
2.40Å     R-factor:   0.189     R-free:   0.222
Authors: D.J.Klein,T.M.Schmeing,P.B.Moore,T.A.Steitz
Key ref:
D.J.Klein et al. (2001). The kink-turn: a new RNA secondary structure motif. EMBO J, 20, 4214-4221. PubMed id: 11483524 DOI: 10.1093/emboj/20.15.4214
Date:
03-Jul-01     Release date:   01-Aug-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P20276  (RL2_HALMA) -  50S ribosomal protein L2P
Seq:
Struc: 		240 a.a.
237 a.a.*
Protein chain
Pfam   ArchSchema ?
P20279  (RL3_HALMA) -  50S ribosomal protein L3P
Seq:
Struc: 		338 a.a.
337 a.a.
Protein chain
Pfam   ArchSchema ?
P12735  (RL4_HALMA) -  50S ribosomal protein L4P
Seq:
Struc: 		246 a.a.
246 a.a.*
Protein chain
Pfam   ArchSchema ?
P14124  (RL5_HALMA) -  50S ribosomal protein L5P
Seq:
Struc: 		177 a.a.
140 a.a.
Protein chain
Pfam   ArchSchema ?
P14135  (RL6_HALMA) -  50S ribosomal protein L6P
Seq:
Struc: 		178 a.a.
172 a.a.
Protein chain
Pfam   ArchSchema ?
P12743  (RL7A_HALMA) -  50S ribosomal protein L7Ae
Seq:
Struc: 		120 a.a.
119 a.a.*
Protein chain
Pfam   ArchSchema ?
P15825  (RLA0_HALMA) -  50S ribosomal protein L10E
Seq:
Struc: 		348 a.a.
29 a.a.*
Protein chain
Pfam   ArchSchema ?
P60617  (RL10_HALMA) -  50S ribosomal protein L10e
Seq:
Struc: 		177 a.a.
156 a.a.*
Protein chain
Pfam   ArchSchema ?
P29198  (RL13_HALMA) -  50S ribosomal protein L13P
Seq:
Struc: 		145 a.a.
142 a.a.
Protein chain
Pfam   ArchSchema ?
P22450  (RL14_HALMA) -  50S ribosomal protein L14P
Seq:
Struc: 		132 a.a.
132 a.a.
Protein chain
Pfam   ArchSchema ?
P12737  (RL15_HALMA) -  50S ribosomal protein L15P
Seq:
Struc: 		165 a.a.
145 a.a.
Protein chain
Pfam   ArchSchema ?
P60618  (RL15E_HALMA) -  50S ribosomal protein L15e
Seq:
Struc: 		196 a.a.
194 a.a.*
Protein chain
Pfam   ArchSchema ?
P14123  (RL18_HALMA) -  50S ribosomal protein L18P
Seq:
Struc: 		187 a.a.
186 a.a.
Protein chain
Pfam   ArchSchema ?
P12733  (RL18E_HALMA) -  50S ribosomal protein L18e
Seq:
Struc: 		116 a.a.
115 a.a.
Protein chain
Pfam   ArchSchema ?
P14119  (RL19_HALMA) -  50S ribosomal protein L19e
Seq:
Struc: 		149 a.a.
143 a.a.*
Protein chain
Pfam   ArchSchema ?
P12734  (RL21_HALMA) -  50S ribosomal protein L21e
Seq:
Struc: 		96 a.a.
95 a.a.
Protein chain
Pfam   ArchSchema ?
P10970  (RL22_HALMA) -  50S ribosomal protein L22P
Seq:
Struc: 		155 a.a.
150 a.a.
Protein chain
Pfam   ArchSchema ?
P12732  (RL23_HALMA) -  50S ribosomal protein L23P
Seq:
Struc: 		85 a.a.
81 a.a.
Protein chain
Pfam   ArchSchema ?
P10972  (RL24_HALMA) -  50S ribosomal protein L24P
Seq:
Struc: 		120 a.a.
119 a.a.
Protein chain
Pfam   ArchSchema ?
P14116  (RL24E_HALMA) -  50S ribosomal protein L24e
Seq:
Struc: 		67 a.a.
53 a.a.
Protein chain
Pfam   ArchSchema ?
P10971  (RL29_HALMA) -  50S ribosomal protein L29P
Seq:
Struc: 		71 a.a.
65 a.a.
Protein chain
Pfam   ArchSchema ?
P14121  (RL30_HALMA) -  50S ribosomal protein L30P
Seq:
Struc: 		154 a.a.
154 a.a.
Protein chain
Pfam   ArchSchema ?
P18138  (RL31_HALMA) -  50S ribosomal protein L31e
Seq:
Struc: 		92 a.a.
82 a.a.
Protein chain
Pfam   ArchSchema ?
P12736  (RL32_HALMA) -  50S ribosomal protein L32e
Seq:
Struc: 		241 a.a.
142 a.a.
Protein chain
Pfam   ArchSchema ?
P60619  (RL37A_HALMA) -  50S ribosomal protein L37Ae
Seq:
Struc: 		92 a.a.
73 a.a.*
Protein chain
Pfam   ArchSchema ?
P32410  (RL37_HALMA) -  50S ribosomal protein L37e
Seq:
Struc: 		57 a.a.
56 a.a.
Protein chain
Pfam   ArchSchema ?
P22452  (RL39_HALMA) -  50S ribosomal protein L39e
Seq:
Struc: 		50 a.a.
46 a.a.*
Protein chain
Pfam   ArchSchema ?
P32411  (RL44_HALMA) -  50S ribosomal protein L44E
Seq:
Struc: 		92 a.a.
92 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 185 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   4 terms 
  Biological process     ribosome biogenesis   3 terms 
  Biochemical function     structural constituent of ribosome     9 terms  

 

 
DOI no: 10.1093/emboj/20.15.4214 EMBO J 20:4214-4221 (2001)
PubMed id: 11483524  
 
 
The kink-turn: a new RNA secondary structure motif.
D.J.Klein, T.M.Schmeing, P.B.Moore, T.A.Steitz.
 
  ABSTRACT  
 
Analysis of the Haloarcula marismortui large ribosomal subunit has revealed a common RNA structure that we call the kink-turn, or K-turn. The six K-turns in H.marismortui 23S rRNA superimpose with an r.m.s.d. of 1.7 A. There are two K-turns in the structure of Thermus thermophilus 16S rRNA, and the structures of U4 snRNA and L30e mRNA fragments form K-turns. The structure has a kink in the phosphodiester backbone that causes a sharp turn in the RNA helix. Its asymmetric internal loop is flanked by C-G base pairs on one side and sheared G-A base pairs on the other, with an A-minor interaction between these two helical stems. A derived consensus secondary structure for the K-turn includes 10 consensus nucleotides out of 15, and predicts its presence in the 5'-UTR of L10 mRNA, helix 78 in Escherichia coli 23S rRNA and human RNase MRP. Five K-turns in 23S rRNA interact with nine proteins. While the observed K-turns interact with proteins of unrelated structures in different ways, they interact with L7Ae and two homologous proteins in the same way.
 
  Selected figure(s)  
 
Figure 4.
Figure 4 (A) Stereo view of the three-stranded K-turn located around nucleotide 46 in H.marismortui 23S rRNA. (B) Stereo image of KT-7 shown in the same relative orientation. 		Figure 9.
Figure 9 Location of the K-turns in the H.marismortui 50S structure. (A) The 50S particle shown in the crown view. (B) The back side of the subunit, rotated 180° around the vertical axis from the crown view. K-turns are in blue, with sugars and phosphates in dark blue, and bases in light blue. The remaining RNA has sugars and phosphates in orange, and bases in yellow. (C) The positions of K-turns in the schematic secondary structure diagram of 23S rRNA. K-turns are highlighted in blue.
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2001, 20, 4214-4221) copyright 2001.  
  Figures were selected by the author.  

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