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PDBsum entry 3jyw

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protein Protein-protein interface(s) links
Ribosome PDB id
3jyw
Jmol
Contents
Protein chains
109 a.a. *
48 a.a. *
98 a.a. *
118 a.a. *
72 a.a. *
213 a.a. *
243 a.a. *
362 a.a. *
257 a.a. *
237 a.a. *
213 a.a. *
113 a.a. *
179 a.a. *
165 a.a. *
151 a.a. *
138 a.a. *
192 a.a. *
178 a.a. *
150 a.a. *
121 a.a. *
176 a.a. *
116 a.a. *
131 a.a. *
45 a.a. *
80 a.a. *
116 a.a. *
142 a.a. *
79 a.a. *
86 a.a. *
52 a.a. *
92 a.a. *
* Residue conservation analysis
PDB id:
3jyw
Name: Ribosome
Title: Structure of the 60s proteins for eukaryotic ribosome based map of thermomyces lanuginosus ribosome at 8.9a resolution
Structure: 60s ribosomal protein l32. Chain: 0. 60s ribosomal protein l39. Chain: 1. 60s ribosomal protein l30e. Chain: 2. 60s ribosomal protein lp0. Chain: 8. 60s ribosomal protein l43.
Source: Thermomyces lanuginosus. Organism_taxid: 5541. Organism_taxid: 5541
Authors: D.J.Taylor,B.Devkota,A.D.Huang,M.Topf,E.Narayanan,A.Sali,S.C J.Frank
Key ref: D.J.Taylor et al. (2009). Comprehensive molecular structure of the eukaryotic ribosome. Structure, 17, 1591-1604. PubMed id: 20004163
Date:
22-Sep-09     Release date:   22-Dec-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
No UniProt id for this chain
Struc: 109 a.a.
Protein chain
No UniProt id for this chain
Struc: 48 a.a.
Protein chain
No UniProt id for this chain
Struc: 98 a.a.
Protein chain
No UniProt id for this chain
Struc: 118 a.a.
Protein chain
No UniProt id for this chain
Struc: 72 a.a.
Protein chain
Pfam   ArchSchema ?
P0CX43  (RL1A_YEAST) -  60S ribosomal protein L1-A
Seq:
Struc:
217 a.a.
213 a.a.
Protein chain
No UniProt id for this chain
Struc: 243 a.a.
Protein chain
No UniProt id for this chain
Struc: 362 a.a.
Protein chain
No UniProt id for this chain
Struc: 257 a.a.
Protein chain
No UniProt id for this chain
Struc: 237 a.a.
Protein chain
No UniProt id for this chain
Struc: 213 a.a.
Protein chain
No UniProt id for this chain
Struc: 113 a.a.
Protein chain
No UniProt id for this chain
Struc: 179 a.a.
Protein chain
No UniProt id for this chain
Struc: 165 a.a.
Protein chain
No UniProt id for this chain
Struc: 151 a.a.
Protein chain
No UniProt id for this chain
Struc: 138 a.a.
Protein chain
No UniProt id for this chain
Struc: 192 a.a.
Protein chain
No UniProt id for this chain
Struc: 178 a.a.
Protein chain
No UniProt id for this chain
Struc: 150 a.a.
Protein chain
No UniProt id for this chain
Struc: 121 a.a.
Protein chain
No UniProt id for this chain
Struc: 176 a.a.
Protein chain
No UniProt id for this chain
Struc: 116 a.a.
Protein chain
No UniProt id for this chain
Struc: 131 a.a.
Protein chain
No UniProt id for this chain
Struc: 45 a.a.
Protein chain
No UniProt id for this chain
Struc: 80 a.a.
Protein chain
No UniProt id for this chain
Struc: 116 a.a.
Protein chain
No UniProt id for this chain
Struc: 142 a.a.
Protein chain
No UniProt id for this chain
Struc: 79 a.a.
Protein chain
No UniProt id for this chain
Struc: 86 a.a.
Protein chain
No UniProt id for this chain
Struc: 52 a.a.
Protein chain
No UniProt id for this chain
Struc: 92 a.a.
Key:    PfamA domain  Secondary structure

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   6 terms 
  Biological process     cytoplasmic translation   5 terms 
  Biochemical function     structural constituent of ribosome     6 terms  

 

 
Structure 17:1591-1604 (2009)
PubMed id: 20004163  
 
 
Comprehensive molecular structure of the eukaryotic ribosome.
D.J.Taylor, B.Devkota, A.D.Huang, M.Topf, E.Narayanan, A.Sali, S.C.Harvey, J.Frank.
 
  ABSTRACT  
 
Despite the emergence of a large number of X-ray crystallographic models of the bacterial 70S ribosome over the past decade, an accurate atomic model of the eukaryotic 80S ribosome is still not available. Eukaryotic ribosomes possess more ribosomal proteins and ribosomal RNA than do bacterial ribosomes, which are implicated in extraribosomal functions in the eukaryotic cells. By combining cryo-EM with RNA and protein homology modeling, we obtained an atomic model of the yeast 80S ribosome complete with all ribosomal RNA expansion segments and all ribosomal proteins for which a structural homolog can be identified. Mutation or deletion of 80S ribosomal proteins can abrogate maturation of the ribosome, leading to several human diseases. We have localized one such protein unique to eukaryotes, rpS19e, whose mutations are associated with Diamond-Blackfan anemia in humans. Additionally, we characterize crucial interactions between the dynamic stalk base of the ribosome with eukaryotic elongation factor 2.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
22664983 S.Melnikov, A.Ben-Shem, N.Garreau de Loubresse, L.Jenner, G.Yusupova, and M.Yusupov (2012).
One core, two shells: bacterial and eukaryotic ribosomes.
  Nat Struct Mol Biol, 19, 560-567.  
21320770 A.Stein, R.Mosca, and P.Aloy (2011).
Three-dimensional modeling of protein interactions and complexes is going 'omics.
  Curr Opin Struct Biol, 21, 200-208.  
21316217 D.N.Wilson, and R.Beckmann (2011).
The ribosomal tunnel as a functional environment for nascent polypeptide folding and translational stalling.
  Curr Opin Struct Biol, 21, 274-282.  
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.  
21283762 M.G.Campbell, and K.Karbstein (2011).
Protein-protein interactions within late pre-40S ribosomes.
  PLoS One, 6, e16194.  
20459660 A.M.Lopes, R.N.Miguel, C.A.Sargent, P.J.Ellis, A.Amorim, and N.A.Affara (2010).
The human RPS4 paralogue on Yq11.223 encodes a structurally conserved ribosomal protein and is preferentially expressed during spermatogenesis.
  BMC Mol Biol, 11, 33.  
20660012 A.Meskauskas, and J.D.Dinman (2010).
A molecular clamp ensures allosteric coordination of peptidyltransfer and ligand binding to the ribosomal A-site.
  Nucleic Acids Res, 38, 7800-7813.  
20974910 J.P.Armache, A.Jarasch, A.M.Anger, E.Villa, T.Becker, S.Bhushan, F.Jossinet, M.Habeck, G.Dindar, S.Franckenberg, V.Marquez, T.Mielke, M.Thomm, O.Berninghausen, B.Beatrix, J.Söding, E.Westhof, D.N.Wilson, and R.Beckmann (2010).
Localization of eukaryote-specific ribosomal proteins in a 5.5-Å cryo-EM map of the 80S eukaryotic ribosome.
  Proc Natl Acad Sci U S A, 107, 19754-19759.
PDB codes: 3iz5 3iz6 3iz7 3iz9 3izr
20980660 J.P.Armache, A.Jarasch, A.M.Anger, E.Villa, T.Becker, S.Bhushan, F.Jossinet, M.Habeck, G.Dindar, S.Franckenberg, V.Marquez, T.Mielke, M.Thomm, O.Berninghausen, B.Beatrix, J.Söding, E.Westhof, D.N.Wilson, and R.Beckmann (2010).
Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-A resolution.
  Proc Natl Acad Sci U S A, 107, 19748-19753.
PDB codes: 3izb 3izc 3izd 3ize 3izf 3izs
20876129 K.Kobayashi, I.Kikuno, K.Kuroha, K.Saito, K.Ito, R.Ishitani, T.Inada, and O.Nureki (2010).
Structural basis for mRNA surveillance by archaeal Pelota and GTP-bound EF1α complex.
  Proc Natl Acad Sci U S A, 107, 17575-17579.
PDB codes: 3agj 3wxm
21072063 K.Kuroha, M.Akamatsu, L.Dimitrova, T.Ito, Y.Kato, K.Shirahige, and T.Inada (2010).
Receptor for activated C kinase 1 stimulates nascent polypeptide-dependent translation arrest.
  EMBO Rep, 11, 956-961.  
20679478 L.Cuchalová, T.Kouba, A.Herrmannová, I.Dányi, W.L.Chiu, and L.Valásek (2010).
The RNA recognition motif of eukaryotic translation initiation factor 3g (eIF3g) is required for resumption of scanning of posttermination ribosomes for reinitiation on GCN4 and together with eIF3i stimulates linear scanning.
  Mol Cell Biol, 30, 4671-4686.  
20819938 M.F.O'Donohue, V.Choesmel, M.Faubladier, G.Fichant, and P.E.Gleizes (2010).
Functional dichotomy of ribosomal proteins during the synthesis of mammalian 40S ribosomal subunits.
  J Cell Biol, 190, 853-866.  
20705654 M.H.Rhodin, and J.D.Dinman (2010).
A flexible loop in yeast ribosomal protein L11 coordinates P-site tRNA binding.
  Nucleic Acids Res, 38, 8377-8389.  
  20836845 M.J.Raupach, J.J.Astrin, K.Hannig, M.K.Peters, M.Y.Stoeckle, and J.W.Wägele (2010).
Molecular species identification of Central European ground beetles (Coleoptera: Carabidae) using nuclear rDNA expansion segments and DNA barcodes.
  Front Zool, 7, 26.  
20699223 N.Nemoto, C.R.Singh, T.Udagawa, S.Wang, E.Thorson, Z.Winter, T.Ohira, M.Ii, L.Valásek, S.J.Brown, and K.Asano (2010).
Yeast 18 S rRNA is directly involved in the ribosomal response to stringent AUG selection during translation initiation.
  J Biol Chem, 285, 32200-32212.  
20584985 W.L.Chiu, S.Wagner, A.Herrmannová, L.Burela, F.Zhang, A.K.Saini, L.Valásek, and A.G.Hinnebusch (2010).
The C-terminal region of eukaryotic translation initiation factor 3a (eIF3a) promotes mRNA recruitment, scanning, and, together with eIF3j and the eIF3b RNA recognition motif, selection of AUG start codons.
  Mol Cell Biol, 30, 4415-4434.  
20511136 X.Agirrezabala, and J.Frank (2010).
From DNA to proteins via the ribosome: structural insights into the workings of the translation machinery.
  Hum Genomics, 4, 226-237.  
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.