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PDBsum entry 3o58

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protein dna_rna ligands Protein-protein interface(s) links
Ribosome PDB id
3o58
Jmol
Contents
Protein chains
213 a.a. *
234 a.a. *
364 a.a. *
268 a.a. *
287 a.a. *
176 a.a. *
215 a.a. *
173 a.a. *
191 a.a. *
208 a.a. *
165 a.a. *
120 a.a. *
187 a.a. *
196 a.a. *
154 a.a. *
143 a.a. *
188 a.a. *
119 a.a. *
129 a.a. *
59 a.a. *
94 a.a. *
107 a.a. *
149 a.a. *
98 a.a. *
86 a.a. *
125 a.a. *
68 a.a. *
72 a.a. *
48 a.a. *
95 a.a. *
83 a.a. *
44 a.a. *
12 a.a. *
21 a.a. *
16 a.a. *
19 a.a. *
27 a.a. *
20 a.a. *
17 a.a. *
23 a.a. *
DNA/RNA
Ligands
UNK-UNK-UNK-UNK-
UNK-UNK-UNK-UNK-
UNK
UNK-UNK-UNK-UNK-
UNK-UNK-UNK-UNK
* Residue conservation analysis
PDB id:
3o58
Name: Ribosome
Title: Yeast 80s ribosome. This entry consists of the 60s subunit o first 80s in the asymmetric unit.
Structure: 25s ribosomal RNA. Chain: 1. 5s ribosomal RNA. Chain: 2. 5.8s ribosomal RNA. Chain: 3. 60s ribosomal protein l1. Chain: a. Synonym: l10a.
Source: Saccharomyces cerevisiae s288c. Yeast. Organism_taxid: 559292. Saccharomyces cerevisiae. Organism_taxid: 4932. Organism_taxid: 4932
Resolution:
4.00Å     R-factor:   0.280     R-free:   0.341
Authors: A.Ben-Shem,L.Jenner,G.Yusupova,M.Yusupov
Key ref: A.Ben-Shem et al. (2010). Crystal structure of the eukaryotic ribosome. Science, 330, 1203-1209. PubMed id: 21109664
Date:
28-Jul-10     Release date:   15-Dec-10    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0CX43  (RL1A_YEAST) -  60S ribosomal protein L1-A
Seq:
Struc:
217 a.a.
213 a.a.
Protein chain
Pfam   ArchSchema ?
P0CX45  (RL2A_YEAST) -  60S ribosomal protein L2-A
Seq:
Struc:
254 a.a.
234 a.a.
Protein chain
Pfam   ArchSchema ?
P14126  (RL3_YEAST) -  60S ribosomal protein L3
Seq:
Struc:
387 a.a.
364 a.a.
Protein chain
Pfam   ArchSchema ?
P10664  (RL4A_YEAST) -  60S ribosomal protein L4-A
Seq:
Struc:
362 a.a.
268 a.a.
Protein chain
Pfam   ArchSchema ?
P26321  (RL5_YEAST) -  60S ribosomal protein L5
Seq:
Struc:
297 a.a.
287 a.a.*
Protein chain
Pfam   ArchSchema ?
Q02326  (RL6A_YEAST) -  60S ribosomal protein L6-A
Seq:
Struc:
176 a.a.
176 a.a.
Protein chain
Pfam   ArchSchema ?
P05737  (RL7A_YEAST) -  60S ribosomal protein L7-A
Seq:
Struc:
244 a.a.
215 a.a.
Protein chain
Pfam   ArchSchema ?
P17076  (RL8A_YEAST) -  60S ribosomal protein L8-A
Seq:
Struc:
256 a.a.
173 a.a.
Protein chain
Pfam   ArchSchema ?
P05738  (RL9A_YEAST) -  60S ribosomal protein L9-A
Seq:
Struc:
191 a.a.
191 a.a.
Protein chain
Pfam   ArchSchema ?
P41805  (RL10_YEAST) -  60S ribosomal protein L10
Seq:
Struc:
221 a.a.
208 a.a.
Protein chain
Pfam   ArchSchema ?
P0C0W9  (RL11A_YEAST) -  60S ribosomal protein L11-A
Seq:
Struc:
174 a.a.
165 a.a.
Protein chain
Pfam   ArchSchema ?
P36105  (RL14A_YEAST) -  60S ribosomal protein L14-A
Seq:
Struc:
138 a.a.
120 a.a.
Protein chain
Pfam   ArchSchema ?
P05748  (RL15A_YEAST) -  60S ribosomal protein L15-A
Seq:
Struc:
204 a.a.
187 a.a.
Protein chain
Pfam   ArchSchema ?
P26784  (RL16A_YEAST) -  60S ribosomal protein L16-A
Seq:
Struc:
199 a.a.
196 a.a.
Protein chain
Pfam   ArchSchema ?
P05740  (RL17A_YEAST) -  60S ribosomal protein L17-A
Seq:
Struc:
184 a.a.
154 a.a.
Protein chain
Pfam   ArchSchema ?
P0CX49  (RL18A_YEAST) -  60S ribosomal protein L18-A
Seq:
Struc:
186 a.a.
143 a.a.
Protein chain
Pfam   ArchSchema ?
P0CX82  (RL19A_YEAST) -  60S ribosomal protein L19-A
Seq:
Struc:
189 a.a.
188 a.a.
Protein chain
Pfam   ArchSchema ?
Q02753  (RL21A_YEAST) -  60S ribosomal protein L21-A
Seq:
Struc:
160 a.a.
119 a.a.
Protein chain
Pfam   ArchSchema ?
P0CX41  (RL23A_YEAST) -  60S ribosomal protein L23-A
Seq:
Struc:
137 a.a.
129 a.a.
Protein chain
Pfam   ArchSchema ?
P04449  (RL24A_YEAST) -  60S ribosomal protein L24-A
Seq:
Struc:
155 a.a.
59 a.a.
Protein chain
Pfam   ArchSchema ?
P04456  (RL25_YEAST) -  60S ribosomal protein L25
Seq:
Struc:
142 a.a.
94 a.a.
Protein chain
Pfam   ArchSchema ?
P05743  (RL26A_YEAST) -  60S ribosomal protein L26-A
Seq:
Struc:
127 a.a.
107 a.a.
Protein chain
Pfam   ArchSchema ?
P02406  (RL28_YEAST) -  60S ribosomal protein L28
Seq:
Struc:
149 a.a.
149 a.a.*
Protein chain
Pfam   ArchSchema ?
P14120  (RL30_YEAST) -  60S ribosomal protein L30
Seq:
Struc:
105 a.a.
98 a.a.
Protein chain
Pfam   ArchSchema ?
P0C2H8  (RL31A_YEAST) -  60S ribosomal protein L31-A
Seq:
Struc:
113 a.a.
86 a.a.
Protein chain
Pfam   ArchSchema ?
P38061  (RL32_YEAST) -  60S ribosomal protein L32
Seq:
Struc:
130 a.a.
125 a.a.
Protein chain
Pfam   ArchSchema ?
P0CX84  (RL35A_YEAST) -  60S ribosomal protein L35-A
Seq:
Struc:
120 a.a.
68 a.a.
Protein chain
Pfam   ArchSchema ?
P49166  (RL37A_YEAST) -  60S ribosomal protein L37-A
Seq:
Struc:
88 a.a.
72 a.a.
Protein chain
Pfam   ArchSchema ?
P04650  (RL39_YEAST) -  60S ribosomal protein L39
Seq:
Struc:
51 a.a.
48 a.a.
Protein chain
Pfam   ArchSchema ?
P0CX27  (RL44A_YEAST) -  60S ribosomal protein L42-A
Seq:
Struc:
106 a.a.
95 a.a.
Protein chain
Pfam   ArchSchema ?
P0CX25  (RL43A_YEAST) -  60S ribosomal protein L43-A
Seq:
Struc:
92 a.a.
83 a.a.
Protein chain
No UniProt id for this chain
Struc: 44 a.a.
Protein chain
No UniProt id for this chain
Struc: 12 a.a.
Protein chain
No UniProt id for this chain
Struc: 21 a.a.
Protein chain
No UniProt id for this chain
Struc: 16 a.a.
Protein chain
No UniProt id for this chain
Struc: 19 a.a.
Protein chain
No UniProt id for this chain
Struc: 27 a.a.
Protein chain
No UniProt id for this chain
Struc: 20 a.a.
Protein chain
No UniProt id for this chain
Struc: 17 a.a.
Protein chain
No UniProt id for this chain
Struc: 23 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   8 terms 
  Biological process     cytoplasmic translation   14 terms 
  Biochemical function     structural constituent of ribosome     8 terms  

 

 
Science 330:1203-1209 (2010)
PubMed id: 21109664  
 
 
Crystal structure of the eukaryotic ribosome.
A.Ben-Shem, L.Jenner, G.Yusupova, M.Yusupov.
 
  ABSTRACT  
 
No abstract given.

 

Literature references that cite this PDB file's key reference

  PubMed id Reference
23395961 Y.Hashem, A.des Georges, J.Fu, S.N.Buss, F.Jossinet, A.Jobe, Q.Zhang, H.Y.Liao, R.A.Grassucci, C.Bajaj, E.Westhof, S.Madison-Antenucci, and J.Frank (2013).
High-resolution cryo-electron microscopy structure of the Trypanosoma brucei ribosome.
  Nature, 494, 385-389.
PDB codes: 3zeq 3zex 3zey 3zf7
23142978 B.Bradatsch, C.Leidig, S.Granneman, M.Gnädig, D.Tollervey, B.Böttcher, R.Beckmann, and E.Hurt (2012).
Structure of the pre-60S ribosomal subunit with nuclear export factor Arx1 bound at the exit tunnel.
  Nat Struct Mol Biol, 19, 1234-1241.
PDB code: 3j2i
22447243 E.Schmitt, M.Panvert, C.Lazennec-Schurdevin, P.D.Coureux, J.Perez, A.Thompson, and Y.Mechulam (2012).
Structure of the ternary initiation complex aIF2-GDPNP-methionylated initiator tRNA.
  Nat Struct Mol Biol, 19, 450-454.
PDB code: 3v11
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.  
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.  
22002225 B.S.Shin, J.R.Kim, S.E.Walker, J.Dong, J.R.Lorsch, and T.E.Dever (2011).
Initiation factor eIF2γ promotes eIF2-GTP-Met-tRNAi(Met) ternary complex binding to the 40S ribosome.
  Nat Struct Mol Biol, 18, 1227-1234.  
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.  
21419622 F.A.Rey, and W.I.Sundquist (2011).
Macromolecular assemblages.
  Curr Opin Struct Biol, 21, 221-222.  
21205638 J.Rabl, M.Leibundgut, S.F.Ataide, A.Haag, and N.Ban (2011).
Crystal structure of the eukaryotic 40S ribosomal subunit in complex with initiation factor 1.
  Science, 331, 730-736.
PDB codes: 2xzm 2xzn
21623367 T.Becker, J.P.Armache, A.Jarasch, A.M.Anger, E.Villa, H.Sieber, B.A.Motaal, T.Mielke, O.Berninghausen, and R.Beckmann (2011).
Structure of the no-go mRNA decay complex Dom34-Hbs1 bound to a stalled 80S ribosome.
  Nat Struct Mol Biol, 18, 715-720.
PDB code: 3izq
21448132 V.P.Pisareva, M.A.Skabkin, C.U.Hellen, T.V.Pestova, and A.V.Pisarev (2011).
Dissociation by Pelota, Hbs1 and ABCE1 of mammalian vacant 80S ribosomes and stalled elongation complexes.
  EMBO J, 30, 1804-1817.  
21310988 V.Ramakrishnan (2011).
Molecular biology. The eukaryotic ribosome.
  Science, 331, 681-682.  
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.