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PDBsum entry 3j39

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protein Protein-protein interface(s) links
Ribosome PDB id
3j39
Jmol
Contents
Protein chains
217 a.a.
223 a.a.
158 a.a.
205 a.a.
210 a.a.
134 a.a.
159 a.a.
149 a.a.
203 a.a.
217 a.a.
290 a.a.
187 a.a.
203 a.a.
253 a.a.
173 a.a.
158 a.a.
185 a.a.
116 a.a.
120 a.a.
131 a.a.
130 a.a.
134 a.a.
134 a.a.
123 a.a.
75 a.a.
414 a.a.
229 a.a.
100 a.a.
111 a.a.
132 a.a.
157 a.a.
113 a.a.
113 a.a.
92 a.a.
70 a.a.
50 a.a.
392 a.a.
52 a.a.
25 a.a.
91 a.a.
104 a.a.
182 a.a.
190 a.a.
228 a.a.
241 a.a.
PDB id:
3j39
Name: Ribosome
Title: Structure of the d. Melanogaster 60s ribosomal proteins
Structure: 60s ribosomal protein l10a-2. Chain: z. 60s acidic ribosomal protein p0. Chain: q. Fragment: see remark 999. Synonym: 60s ribosomal protein l10e. 60s ribosomal protein l12. Chain: k. 60s ribosomal protein l13a.
Source: Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Organism_taxid: 7227
Authors: A.M.Anger,J.-P.Armache,O.Berninghausen,M.Habeck,M.Subklewe, D.N.Wilson,R.Beckmann
Key ref: A.M.Anger et al. (2013). Structures of the human and Drosophila 80S ribosome. Nature, 497, 80-85. PubMed id: 23636399 DOI: 10.1038/nature12104
Date:
27-Feb-13     Release date:   01-May-13    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9VTP4  (R10AB_DROME) -  60S ribosomal protein L10a-2
Seq:
Struc:
217 a.a.
217 a.a.
Protein chain
Pfam   ArchSchema ?
P05388  (RLA0_HUMAN) -  60S acidic ribosomal protein P0
Seq:
Struc:
317 a.a.
223 a.a.*
Protein chain
Pfam   ArchSchema ?
Q9W1B9  (Q9W1B9_DROME) -  RE28824p
Seq:
Struc:
165 a.a.
158 a.a.
Protein chain
Pfam   ArchSchema ?
Q9VNE9  (RL13A_DROME) -  60S ribosomal protein L13a
Seq:
Struc:
205 a.a.
205 a.a.
Protein chain
Pfam   ArchSchema ?
P41126  (RL13_DROME) -  60S ribosomal protein L13
Seq:
Struc:
218 a.a.
210 a.a.
Protein chain
Pfam   ArchSchema ?
P48159  (RL23_DROME) -  60S ribosomal protein L23
Seq:
Struc:
140 a.a.
134 a.a.
Protein chain
Pfam   ArchSchema ?
P55841  (RL14_DROME) -  60S ribosomal protein L14
Seq:
Struc:
166 a.a.
159 a.a.
Protein chain
Pfam   ArchSchema ?
P41092  (RL27A_DROME) -  60S ribosomal protein L27a
Seq:
Struc:
149 a.a.
149 a.a.
Protein chain
Pfam   ArchSchema ?
O17445  (RL15_DROME) -  60S ribosomal protein L15
Seq:
Struc:
204 a.a.
203 a.a.
Protein chain
Pfam   ArchSchema ?
O61231  (RL10_DROME) -  60S ribosomal protein L10
Seq:
Struc:
218 a.a.
217 a.a.
Protein chain
Pfam   ArchSchema ?
Q9W5R8  (RL5_DROME) -  60S ribosomal protein L5
Seq:
Struc:
299 a.a.
290 a.a.
Protein chain
Pfam   ArchSchema ?
Q9VS34  (RL18_DROME) -  60S ribosomal protein L18
Seq:
Struc:
188 a.a.
187 a.a.
Protein chain
Pfam   ArchSchema ?
P36241  (RL19_DROME) -  60S ribosomal protein L19
Seq:
Struc:
203 a.a.
203 a.a.
Protein chain
Pfam   ArchSchema ?
Q9V3G1  (RL8_DROME) -  60S ribosomal protein L8
Seq:
Struc:
256 a.a.
253 a.a.
Protein chain
Pfam   ArchSchema ?
P41093  (RL18A_DROME) -  60S ribosomal protein L18a
Seq:
Struc:
177 a.a.
173 a.a.
Protein chain
Pfam   ArchSchema ?
Q9V9M7  (Q9V9M7_DROME) -  RE62581p
Seq:
Struc:
159 a.a.
158 a.a.
Protein chain
Pfam   ArchSchema ?
Q9W3W8  (RL17_DROME) -  60S ribosomal protein L17
Seq:
Struc:
186 a.a.
185 a.a.
Protein chain
Pfam   ArchSchema ?
P50887  (RL22_DROME) -  60S ribosomal protein L22
Seq:
Struc:
299 a.a.
116 a.a.
Protein chain
Pfam   ArchSchema ?
Q9W0A8  (Q9W0A8_DROME) -  FI01658p
Seq:
Struc:
277 a.a.
120 a.a.
Protein chain
Pfam   ArchSchema ?
Q9VVU2  (Q9VVU2_DROME) -  RE17611p
Seq:
Struc:
149 a.a.
131 a.a.
Protein chain
Pfam   ArchSchema ?
Q9VJY6  (RL24_DROME) -  60S ribosomal protein L24
Seq:
Struc:
155 a.a.
130 a.a.
Protein chain
Pfam   ArchSchema ?
Q9VBN5  (Q9VBN5_DROME) -  60S ribosomal protein L27
Seq:
Struc:
135 a.a.
134 a.a.
Protein chain
Pfam   ArchSchema ?
Q9VZS5  (RL28_DROME) -  60S ribosomal protein L28
Seq:
Struc:
144 a.a.
134 a.a.
Protein chain
Pfam   ArchSchema ?
Q9W499  (Q9W499_DROME) -  FI02809p
Seq:
Struc:
123 a.a.
123 a.a.
Protein chain
Pfam   ArchSchema ?
Q24154  (RL29_DROME) -  60S ribosomal protein L29
Seq:
Struc:
76 a.a.
75 a.a.
Protein chain
Pfam   ArchSchema ?
O16797  (RL3_DROME) -  60S ribosomal protein L3
Seq:
Struc:
416 a.a.
414 a.a.
Protein chain
Pfam   ArchSchema ?
P32100  (RL7_DROME) -  60S ribosomal protein L7
Seq:
Struc:
252 a.a.
229 a.a.
Protein chain
Pfam   ArchSchema ?
Q9VJ19  (Q9VJ19_DROME) -  RE25263p
Seq:
Struc:
111 a.a.
100 a.a.
Protein chain
Pfam   ArchSchema ?
Q9V597  (RL31_DROME) -  60S ribosomal protein L31
Seq:
Struc:
124 a.a.
111 a.a.
Protein chain
Pfam   ArchSchema ?
P04359  (RL32_DROME) -  60S ribosomal protein L32
Seq:
Struc:
134 a.a.
132 a.a.
Protein chain
Pfam   ArchSchema ?
Q9VNB9  (Q9VNB9_DROME) -  RE17737p
Seq:
Struc:
157 a.a.
157 a.a.
Protein chain
Pfam   ArchSchema ?
Q9VBH8  (Q9VBH8_DROME) -  FI02850p
Seq:
Struc:
162 a.a.
113 a.a.
Protein chain
Pfam   ArchSchema ?
P49630  (RL36_DROME) -  60S ribosomal protein L36
Seq:
Struc:
115 a.a.
113 a.a.
Protein chain
Pfam   ArchSchema ?
Q9VXX8  (RL371_DROME) -  Probable 60S ribosomal protein L37-A
Seq:
Struc:
93 a.a.
92 a.a.
Protein chain
Pfam   ArchSchema ?
Q9W5N2  (RL38_DROME) -  60S ribosomal protein L38
Seq:
Struc:
70 a.a.
70 a.a.
Protein chain
Pfam   ArchSchema ?
O16130  (RL39_DROME) -  60S ribosomal protein L39
Seq:
Struc:
51 a.a.
50 a.a.
Protein chain
Pfam   ArchSchema ?
P09180  (RL4_DROME) -  60S ribosomal protein L4
Seq:
Struc:
401 a.a.
392 a.a.
Protein chain
Pfam   ArchSchema ?
P18101  (RL40_DROME) -  Ubiquitin-60S ribosomal protein L40
Seq:
Struc:
128 a.a.
52 a.a.
Protein chain
Pfam   ArchSchema ?
Q962S2  (Q962S2_DROME) -  RE63504p
Seq:
Struc:
25 a.a.
25 a.a.
Protein chain
Pfam   ArchSchema ?
Q9VMU4  (RL37A_DROME) -  60S ribosomal protein L37a
Seq:
Struc:
92 a.a.
91 a.a.
Protein chain
Pfam   ArchSchema ?
Q9VLT7  (Q9VLT7_DROME) -  IP17351p
Seq:
Struc:
104 a.a.
104 a.a.
Protein chain
Pfam   ArchSchema ?
P46222  (RL11_DROME) -  60S ribosomal protein L11
Seq:
Struc:
184 a.a.
182 a.a.
Protein chain
Pfam   ArchSchema ?
P50882  (RL9_DROME) -  60S ribosomal protein L9
Seq:
Struc:
190 a.a.
190 a.a.
Protein chain
Pfam   ArchSchema ?
Q9V9W2  (Q9V9W2_DROME) -  Ribosomal protein L6, isoform A
Seq:
Struc:
243 a.a.
228 a.a.
Protein chain
Pfam   ArchSchema ?
P46223  (RL7A_DROME) -  60S ribosomal protein L7a
Seq:
Struc:
271 a.a.
241 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure
* PDB and UniProt seqs differ at 14 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cellular_component   12 terms 
  Biological process     growth   18 terms 
  Biochemical function     structural constituent of ribosome     9 terms  

 

 
DOI no: 10.1038/nature12104 Nature 497:80-85 (2013)
PubMed id: 23636399  
 
 
Structures of the human and Drosophila 80S ribosome.
A.M.Anger, J.P.Armache, O.Berninghausen, M.Habeck, M.Subklewe, D.N.Wilson, R.Beckmann.
 
  ABSTRACT  
 
Protein synthesis in all cells is carried out by macromolecular machines called ribosomes. Although the structures of prokaryotic, yeast and protist ribosomes have been determined, the more complex molecular architecture of metazoan 80S ribosomes has so far remained elusive. Here we present structures of Drosophila melanogaster and Homo sapiens 80S ribosomes in complex with the translation factor eEF2, E-site transfer RNA and Stm1-like proteins, based on high-resolution cryo-electron-microscopy density maps. These structures not only illustrate the co-evolution of metazoan-specific ribosomal RNA with ribosomal proteins but also reveal the presence of two additional structural layers in metazoan ribosomes, a well-ordered inner layer covered by a flexible RNA outer layer. The human and Drosophila ribosome structures will provide the basis for more detailed structural, biochemical and genetic experiments.