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PDBsum entry 3izc

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protein Protein-protein interface(s) links
Ribosome PDB id
3izc
Jmol
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Superseded by: 3izs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
Pfam  
P53030  (RL1_YEAST) - 
Protein chain
Pfam  
P05736  (RL2_YEAST) - 
Protein chain
Pfam   ArchSchema ?
P14126  (RL3_YEAST) -  60S ribosomal protein L3
Seq:
Struc:
387 a.a.
388 a.a.
Protein chain
Pfam   ArchSchema ?
P0C0W9  (RL11A_YEAST) -  60S ribosomal protein L11-A
Seq:
Struc:
174 a.a.
168 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 ?
P05738  (RL9A_YEAST) -  60S ribosomal protein L9-A
Seq:
Struc:
191 a.a.
191 a.a.
Protein chain
Pfam   ArchSchema ?
P17076  (RL8A_YEAST) -  60S ribosomal protein L8-A
Seq:
Struc:
256 a.a.
197 a.a.
Protein chain
Pfam   ArchSchema ?
P41805  (RL10_YEAST) -  60S ribosomal protein L10
Seq:
Struc:
221 a.a.
189 a.a.
Protein chain
Pfam   ArchSchema ?
P05317  (RLA0_YEAST) -  60S acidic ribosomal protein P0
Seq:
Struc:
312 a.a.
257 a.a.
Protein chain
Pfam  
P17079  (RL12_YEAST) - 
Protein chain
Pfam   ArchSchema ?
P26784  (RL16A_YEAST) -  60S ribosomal protein L16-A
Seq:
Struc:
199 a.a.
199 a.a.
Protein chain
Pfam  
D6VXT1  (RL14A_YEAST) - 
Protein chain
Pfam  
P04451  (RL23_YEAST) - 
Protein chain
Pfam   ArchSchema ?
P05748  (RL15A_YEAST) -  60S ribosomal protein L15-A
Seq:
Struc:
204 a.a.
193 a.a.
Protein chain
Pfam   ArchSchema ?
P02406  (RL28_YEAST) -  60S ribosomal protein L28
Seq:
Struc:
149 a.a.
149 a.a.
Protein chain
Pfam  
P07279  (RL18_YEAST) - 
Protein chain
Pfam  
P05735  (RL19_YEAST) - 
Protein chain
Pfam   ArchSchema ?
Q02753  (RL21A_YEAST) -  60S ribosomal protein L21-A
Seq:
Struc:
160 a.a.
160 a.a.
Protein chain
Pfam   ArchSchema ?
P05749  (RL22A_YEAST) -  60S ribosomal protein L22-A
Seq:
Struc:
121 a.a.
105 a.a.
Protein chain
Pfam   ArchSchema ?
P05740  (RL17A_YEAST) -  60S ribosomal protein L17-A
Seq:
Struc:
184 a.a.
170 a.a.
Protein chain
Pfam   ArchSchema ?
P04456  (RL25_YEAST) -  60S ribosomal protein L25
Seq:
Struc:
142 a.a.
122 a.a.
Protein chain
Pfam   ArchSchema ?
P04449  (RL24A_YEAST) -  60S ribosomal protein L24-A
Seq:
Struc:
155 a.a.
73 a.a.
Protein chain
Pfam   ArchSchema ?
P05743  (RL26A_YEAST) -  60S ribosomal protein L26-A
Seq:
Struc:
127 a.a.
123 a.a.
Protein chain
Pfam   ArchSchema ?
P0C2H6  (RL27A_YEAST) -  60S ribosomal protein L27-A
Seq:
Struc:
136 a.a.
95 a.a.
Protein chain
Pfam   ArchSchema ?
P05747  (RL29_YEAST) -  60S ribosomal protein L29
Seq:
Struc:
59 a.a.
22 a.a.
Protein chain
Pfam  
P39741  (RL35_YEAST) - 
Protein chain
Pfam   ArchSchema ?
P14120  (RL30_YEAST) -  60S ribosomal protein L30
Seq:
Struc:
105 a.a.
105 a.a.
Protein chain
Pfam   ArchSchema ?
P05737  (RL7A_YEAST) -  60S ribosomal protein L7-A
Seq:
Struc:
244 a.a.
239 a.a.
Protein chain
Pfam   ArchSchema ?
P0C2H8  (RL31A_YEAST) -  60S ribosomal protein L31-A
Seq:
Struc:
113 a.a.
110 a.a.
Protein chain
Pfam   ArchSchema ?
P38061  (RL32_YEAST) -  60S ribosomal protein L32
Seq:
Struc:
130 a.a.
130 a.a.
Protein chain
Pfam   ArchSchema ?
P87262  (RL34A_YEAST) -  60S ribosomal protein L34-A
Seq:
Struc:
121 a.a.
118 a.a.
Protein chain
Pfam   ArchSchema ?
P05744  (RL33A_YEAST) -  60S ribosomal protein L33-A
Seq:
Struc:
107 a.a.
100 a.a.
Protein chain
Pfam   ArchSchema ?
P05745  (RL36A_YEAST) -  60S ribosomal protein L36-A
Seq:
Struc:
100 a.a.
77 a.a.
Protein chain
Pfam  
P49631  (RL43_YEAST) - 
Protein chain
Pfam   ArchSchema ?
P49166  (RL37A_YEAST) -  60S ribosomal protein L37-A
Seq:
Struc:
88 a.a.
88 a.a.
Protein chain
Pfam   ArchSchema ?
P49167  (RL38_YEAST) -  60S ribosomal protein L38
Seq:
Struc:
78 a.a.
78 a.a.
Protein chain
Pfam   ArchSchema ?
P04650  (RL39_YEAST) -  60S ribosomal protein L39
Seq:
Struc:
51 a.a.
51 a.a.
Protein chain
Pfam   ArchSchema ?
P0CH08  (RL401_YEAST) -  Ubiquitin-60S ribosomal protein L40
Seq:
Struc:
128 a.a.
40 a.a.
Protein chain
Pfam  
P05746  (RL41_YEAST) - 
Protein chain
Pfam  
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
Seq:
Struc:
106 a.a.
58 a.a.*
Protein chains
Pfam   ArchSchema ?
P05319  (RLA2_YEAST) -  60S acidic ribosomal protein P2-alpha
Seq:
Struc:
106 a.a.
58 a.a.
Protein chain
Pfam   ArchSchema ?
P26321  (RL5_YEAST) -  60S ribosomal protein L5
Seq:
Struc:
297 a.a.
297 a.a.*
Protein chain
Pfam   ArchSchema ?
P10664  (RL4A_YEAST) -  60S ribosomal protein L4-A
Seq:
Struc:
362 a.a.
329 a.a.
Protein chain
No UniProt id for this chain
Struc: 169 a.a.
Protein chain
Pfam   ArchSchema ?
Q0JJA0  (Q0JJA0_ORYSJ) -  60S ribosomal protein L18a
Seq:
Struc:
178 a.a.
167 a.a.
Key:    PfamA domain  PfamB 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.