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

 

 

 

 

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Contents
Protein chains
217 a.a.
254 a.a.
388 a.a.
168 a.a.
176 a.a.
191 a.a.
197 a.a.
189 a.a.
257 a.a.
127 a.a.
199 a.a.
138 a.a.
131 a.a.
193 a.a.
149 a.a.
161 a.a.
189 a.a.
160 a.a.
105 a.a.
170 a.a.
122 a.a.
73 a.a.
123 a.a.
95 a.a.
22 a.a.
118 a.a.
105 a.a.
239 a.a.
110 a.a.
130 a.a.
118 a.a.
100 a.a.
77 a.a.
92 a.a.
88 a.a.
78 a.a.
51 a.a.
40 a.a.
25 a.a.
106 a.a.
20 a.a.
14 a.a.
58 a.a.
58 a.a.
297 a.a.
329 a.a.
169 a.a.
167 a.a.
Superseded by: 3izs
PDB id:
3izc
Name: Ribosome
Title: Localization of the large subunit ribosomal proteins into a cryo-em map of saccharomyces cerevisiae translating 80s rib
Structure: 60s ribosomal protein rpl1 (l1p). Chain: a. 60s ribosomal protein rpl2 (l2p). Chain: b. 60s ribosomal protein rpl3 (l3p). Chain: c. 60s ribosomal protein rpl11 (l5p). Chain: e. 60s ribosomal protein rpl6 (l6e).
Source: Saccharomyces cerevisiae. Yeast. Organism_taxid: 4932. Organism_taxid: 4932
Authors: 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.Mie M.Thomm,O.Berninghausen,B.Beatrix,J.Soeding,E.Westhof,D.N.W R.Beckmann
Key ref: J.P.Armache et al. (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. PubMed id: 20980660
Date:
12-Oct-10     Release date:   01-Dec-10    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
P53030  (RL1_YEAST) - 
Protein chain
P05736  (RL2_YEAST) - 
Protein chain
Pfam   ArchSchema ?
P14126  (RL3_YEAST) -  60S ribosomal protein L3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		387 a.a.
388 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.
168 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.
176 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 ?
P17076  (RL8A_YEAST) -  60S ribosomal protein L8-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		256 a.a.
197 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.
189 a.a.
Protein chain
Pfam   ArchSchema ?
P05317  (RLA0_YEAST) -  60S acidic ribosomal protein P0 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		312 a.a.
257 a.a.
Protein chain
P17079  (RL12_YEAST) - 
Protein chain
Pfam   ArchSchema ?
P26784  (RL16A_YEAST) -  60S ribosomal protein L16-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		199 a.a.
199 a.a.
Protein chain
D6VXT1  (RL14A_YEAST) - 
Protein chain
P04451  (RL23_YEAST) - 
Protein chain
Pfam   ArchSchema ?
P05748  (RL15A_YEAST) -  60S ribosomal protein L15-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		204 a.a.
193 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.
149 a.a.
Protein chain
P07279  (RL18_YEAST) - 
Protein chain
P05735  (RL19_YEAST) - 
Protein chain
Pfam   ArchSchema ?
Q02753  (RL21A_YEAST) -  60S ribosomal protein L21-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		160 a.a.
160 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.
105 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.
170 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.
122 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.
73 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.
123 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.
95 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.
22 a.a.
Protein chain
P39741  (RL35_YEAST) - 
Protein chain
Pfam   ArchSchema ?
P14120  (RL30_YEAST) -  60S ribosomal protein L30 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		105 a.a.
105 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.
239 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.
110 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.
130 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.
118 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.
100 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.
77 a.a.
Protein chain
P49631  (RL43_YEAST) - 
Protein chain
Pfam   ArchSchema ?
P49166  (RL37A_YEAST) -  60S ribosomal protein L37-A from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		88 a.a.
88 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.
78 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.
51 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.
40 a.a.
Protein chain
P05746  (RL41_YEAST) - 
Protein chain
P02405  (RL44_YEAST) - 
Protein chains
No UniProt id for this chain
Struc: 20 a.a.
Protein chain
No UniProt id for this chain
Struc: 14 a.a.
Protein chains
Pfam   ArchSchema ?
P05318  (RLA1_YEAST) -  60S acidic ribosomal protein P1-alpha from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		106 a.a.
58 a.a.*
Protein chains
Pfam   ArchSchema ?
P05319  (RLA2_YEAST) -  60S acidic ribosomal protein P2-alpha from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		106 a.a.
58 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.
297 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.
329 a.a.
Protein chain
No UniProt id for this chain
Struc: 169 a.a.
Protein chain
Q0JJA0  (Q0JJA0_ORYSJ) - 
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 

 
Proc Natl Acad Sci U S A 107:19748-19753 (2010)
PubMed id: 20980660  
 
 
Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-A resolution.
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, R.Beckmann.
 
  ABSTRACT  
 
No abstract given.

 

Literature references that cite this PDB file's key reference

  PubMed id Reference
23202586 C.Leidig, G.Bange, J.Kopp, S.Amlacher, A.Aravind, S.Wickles, G.Witte, E.Hurt, R.Beckmann, and I.Sinning (2013).
Structural characterization of a eukaryotic chaperone-the ribosome-associated complex.
  Nat Struct Mol Biol, 20, 23-28.
PDB codes: 4gmq 4gni
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
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.  
22358840 T.Becker, S.Franckenberg, S.Wickles, C.J.Shoemaker, A.M.Anger, J.P.Armache, H.Sieber, C.Ungewickell, O.Berninghausen, I.Daberkow, A.Karcher, M.Thomm, K.P.Hopfner, R.Green, and R.Beckmann (2012).
Structural basis of highly conserved ribosome recycling in eukaryotes and archaea.
  Nature, 482, 501-506.
PDB codes: 3j15 3j16
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.  
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
21529712 N.Kondrashov, A.Pusic, C.R.Stumpf, K.Shimizu, A.C.Hsieh, S.Xue, J.Ishijima, T.Shiroishi, and M.Barna (2011).
Ribosome-mediated specificity in Hox mRNA translation and vertebrate tissue patterning.
  Cell, 145, 383-397.  
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
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.

 

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