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PDBsum entry 3u5e
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protein metals Protein-protein interface(s) links
Ribosome PDB id
3u5e

 

 

 

 

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JSmol PyMol  
Contents
Protein chains
252 a.a.
386 a.a.
361 a.a.
296 a.a.
156 a.a.
222 a.a.
233 a.a.
191 a.a.
211 a.a.
169 a.a.
193 a.a.
136 a.a.
203 a.a.
217 a.a.
183 a.a.
185 a.a.
188 a.a.
172 a.a.
159 a.a.
100 a.a.
136 a.a.
98 a.a.
121 a.a.
126 a.a.
135 a.a.
148 a.a.
58 a.a.
97 a.a.
109 a.a.
127 a.a.
106 a.a.
112 a.a.
119 a.a.
99 a.a.
87 a.a.
77 a.a.
50 a.a.
52 a.a.
25 a.a.
105 a.a.
91 a.a.
Metals
_ZN ×4
Obsolete entry
PDB id:
3u5e
Name: Ribosome
Title: The structure of the eukaryotic ribosome at 3.0 a resolution. This entry contains proteins of the 60s subunit, ribosome a
Structure: 60s ribosomal protein l2-a. Chain: a. Synonym: l5, rp8, yl6. 60s ribosomal protein l3. Chain: b. Synonym: maintenance of killer protein 8, rp1, trichodermin resistance protein, yl1. 60s ribosomal protein l4-a. Chain: c.
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 559292. Strain: atcc 204508 / s288c. Strain: atcc 204508 / s288c
Resolution:
3.00Å     R-factor:   0.182     R-free:   0.229
Authors: A.Ben-Shem,N.Garreau De Loubresse,S.Melnikov,L.Jenner,G.Yusupova, M.Yusupov
Key ref: A.Ben-Shem et al. (2011). The structure of the eukaryotic ribosome at 3.0 Å resolution. Science, 334, 1524-1529. PubMed id: 22096102
Date:
11-Oct-11     Release date:   21-Dec-11    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0CX45  (RL2A_YEAST) -  60S ribosomal protein L2-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		254 a.a.
252 a.a.
Protein chain
Pfam   ArchSchema ?
P14126  (RL3_YEAST) -  60S ribosomal protein L3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		387 a.a.
386 a.a.
Protein chain
Pfam   ArchSchema ?
P10664  (RL4A_YEAST) -  60S ribosomal protein L4-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		362 a.a.
361 a.a.
Protein chain
Pfam   ArchSchema ?
P26321  (RL5_YEAST) -  60S ribosomal protein L5 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		297 a.a.
296 a.a.
Protein chain
Pfam   ArchSchema ?
Q02326  (RL6A_YEAST) -  60S ribosomal protein L6-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		176 a.a.
156 a.a.
Protein chain
Pfam   ArchSchema ?
P05737  (RL7A_YEAST) -  60S ribosomal protein L7-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		244 a.a.
222 a.a.
Protein chain
Pfam   ArchSchema ?
P17076  (RL8A_YEAST) -  60S ribosomal protein L8-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		256 a.a.
233 a.a.
Protein chain
Pfam   ArchSchema ?
P05738  (RL9A_YEAST) -  60S ribosomal protein L9-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		191 a.a.
191 a.a.
Protein chain
Pfam   ArchSchema ?
P41805  (RL10_YEAST) -  60S ribosomal protein L10 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		221 a.a.
211 a.a.
Protein chain
Pfam   ArchSchema ?
P0C0W9  (RL11A_YEAST) -  60S ribosomal protein L11-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		174 a.a.
169 a.a.
Protein chain
Pfam   ArchSchema ?
Q12690  (RL13A_YEAST) -  60S ribosomal protein L13-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		199 a.a.
193 a.a.
Protein chain
Pfam   ArchSchema ?
P36105  (RL14A_YEAST) -  60S ribosomal protein L14-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		138 a.a.
136 a.a.
Protein chain
Pfam   ArchSchema ?
P05748  (RL15A_YEAST) -  60S ribosomal protein L15-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		204 a.a.
203 a.a.
Protein chain
Pfam   ArchSchema ?
P26784  (RL16A_YEAST) -  60S ribosomal protein L16-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		199 a.a.
217 a.a.*
Protein chain
Pfam   ArchSchema ?
P26785  (RL16B_YEAST) -  60S ribosomal protein L16-B from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		198 a.a.
217 a.a.*
Protein chain
Pfam   ArchSchema ?
P05740  (RL17A_YEAST) -  60S ribosomal protein L17-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		184 a.a.
183 a.a.
Protein chain
Pfam   ArchSchema ?
P0CX49  (RL18A_YEAST) -  60S ribosomal protein L18-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		186 a.a.
185 a.a.
Protein chain
Pfam   ArchSchema ?
P0CX82  (RL19A_YEAST) -  60S ribosomal protein L19-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		189 a.a.
188 a.a.
Protein chain
Pfam   ArchSchema ?
P0CX23  (RL20A_YEAST) -  60S ribosomal protein L20-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		172 a.a.
172 a.a.
Protein chain
Pfam   ArchSchema ?
Q02753  (RL21A_YEAST) -  60S ribosomal protein L21-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		160 a.a.
159 a.a.
Protein chain
Pfam   ArchSchema ?
P05749  (RL22A_YEAST) -  60S ribosomal protein L22-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		121 a.a.
100 a.a.
Protein chain
Pfam   ArchSchema ?
P0CX41  (RL23A_YEAST) -  60S ribosomal protein L23-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		137 a.a.
136 a.a.
Protein chain
Pfam   ArchSchema ?
P04449  (RL24A_YEAST) -  60S ribosomal protein L24-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		155 a.a.
98 a.a.
Protein chain
Pfam   ArchSchema ?
P04456  (RL25_YEAST) -  60S ribosomal protein L25 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		142 a.a.
121 a.a.
Protein chain
Pfam   ArchSchema ?
P05743  (RL26A_YEAST) -  60S ribosomal protein L26-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		127 a.a.
126 a.a.
Protein chain
Pfam   ArchSchema ?
P0C2H6  (RL27A_YEAST) -  60S ribosomal protein L27-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		136 a.a.
135 a.a.
Protein chain
Pfam   ArchSchema ?
P02406  (RL28_YEAST) -  60S ribosomal protein L28 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		149 a.a.
148 a.a.
Protein chain
Pfam   ArchSchema ?
P05747  (RL29_YEAST) -  60S ribosomal protein L29 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		59 a.a.
58 a.a.
Protein chain
Pfam   ArchSchema ?
P14120  (RL30_YEAST) -  60S ribosomal protein L30 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		105 a.a.
97 a.a.
Protein chain
Pfam   ArchSchema ?
P0C2H8  (RL31A_YEAST) -  60S ribosomal protein L31-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		113 a.a.
109 a.a.
Protein chain
Pfam   ArchSchema ?
P38061  (RL32_YEAST) -  60S ribosomal protein L32 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		130 a.a.
127 a.a.
Protein chain
Pfam   ArchSchema ?
P05744  (RL33A_YEAST) -  60S ribosomal protein L33-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		107 a.a.
106 a.a.
Protein chain
Pfam   ArchSchema ?
P87262  (RL34A_YEAST) -  60S ribosomal protein L34-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		121 a.a.
112 a.a.
Protein chain
Pfam   ArchSchema ?
P0CX84  (RL35A_YEAST) -  60S ribosomal protein L35-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		120 a.a.
119 a.a.
Protein chain
Pfam   ArchSchema ?
P05745  (RL36A_YEAST) -  60S ribosomal protein L36-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		100 a.a.
99 a.a.
Protein chain
Pfam   ArchSchema ?
P49166  (RL37A_YEAST) -  60S ribosomal protein L37-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		88 a.a.
87 a.a.
Protein chain
Pfam   ArchSchema ?
P49167  (RL38_YEAST) -  60S ribosomal protein L38 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		78 a.a.
77 a.a.
Protein chain
Pfam   ArchSchema ?
P04650  (RL39_YEAST) -  60S ribosomal protein L39 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		51 a.a.
50 a.a.
Protein chain
Pfam   ArchSchema ?
P0CH08  (RL40A_YEAST) -  Ubiquitin-60S ribosomal protein L40 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		128 a.a.
52 a.a.
Protein chain
Pfam   ArchSchema ?
P0CX86  (RL41A_YEAST) -  60S ribosomal protein L41-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		25 a.a.
25 a.a.
Protein chain
Pfam   ArchSchema ?
P0CX27  (RL44A_YEAST) -  60S ribosomal protein L42-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		106 a.a.
105 a.a.
Protein chain
Pfam   ArchSchema ?
P0CX25  (RL43A_YEAST) -  60S ribosomal protein L43-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		92 a.a.
91 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 50 residue positions (black crosses)

 

 
Science 334:1524-1529 (2011)
PubMed id: 22096102  
 
 
The structure of the eukaryotic ribosome at 3.0 Å resolution.
A.Ben-Shem, N.Garreau de Loubresse, S.Melnikov, L.Jenner, G.Yusupova, M.Yusupov.
 
  ABSTRACT  
 
No abstract given.

 

Literature references that cite this PDB file's key reference

  PubMed id Reference
23262488 M.E.Filbin, B.S.Vollmar, D.Shi, T.Gonen, and J.S.Kieft (2013).
HCV IRES manipulates the ribosome to promote the switch from translation initiation to elongation.
  Nat Struct Mol Biol, 20, 150-158.  
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
23142985 B.J.Greber, D.Boehringer, C.Montellese, and N.Ban (2012).
Cryo-EM structures of Arx1 and maturation factors Rei1 and Jjj1 bound to the 60S ribosomal subunit.
  Nat Struct Mol Biol, 19, 1228-1233.
PDB codes: 4b6a 4b6b
22664984 C.E.Aitken, and J.R.Lorsch (2012).
A mechanistic overview of translation initiation in eukaryotes.
  Nat Struct Mol Biol, 19, 568-576.  
23072885 M.Graille, and B.Séraphin (2012).
Surveillance pathways rescuing eukaryotic ribosomes lost in translation.
  Nat Rev Mol Cell Biol, 13, 727-735.  
23104056 S.Ferreira-Cerca, V.Sagar, T.Schäfer, M.Diop, A.M.Wesseling, H.Lu, E.Chai, E.Hurt, and N.Laronde-Leblanc (2012).
ATPase-dependent role of the atypical kinase Rio2 on the evolving pre-40S ribosomal subunit.
  Nat Struct Mol Biol, 19, 1316-1323.
PDB codes: 4gyg 4gyi
22751017 S.Lebaron, C.Schneider, R.W.van Nues, A.Swiatkowska, D.Walsh, B.Böttcher, S.Granneman, N.J.Watkins, and D.Tollervey (2012).
Proofreading of pre-40S ribosome maturation by a translation initiation factor and 60S subunits.
  Nat Struct Mol Biol, 19, 744-753.  
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.  
22617470 S.Xue, and M.Barna (2012).
Specialized ribosomes: a new frontier in gene regulation and organismal biology.
  Nat Rev Mol Cell Biol, 13, 355-369.  
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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