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PDBsum entry 3izb

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protein Protein-protein interface(s) links
Ribosome PDB id
3izb
Jmol
Contents
Protein chains
319 a.a. *
252 a.a. *
204 a.a. *
200 a.a. *
197 a.a. *
254 a.a. *
143 a.a. *
199 a.a. *
130 a.a. *
126 a.a. *
113 a.a. *
119 a.a. *
145 a.a. *
140 a.a. *
48 a.a. *
121 a.a. *
136 a.a. *
85 a.a. *
88 a.a. *
144 a.a. *
87 a.a. *
85 a.a. *
92 a.a. *
50 a.a. *
60 a.a. *
63 a.a. *
36 a.a. *
25 a.a. *
96 a.a. *
* Residue conservation analysis
PDB id:
3izb
Name: Ribosome
Title: Localization of the small subunit ribosomal proteins into a cryo-em map of saccharomyces cerevisiae translating 80s rib
Structure: 40s ribosomal protein rack1 (rack1). Chain: a. 40s ribosomal protein rps0 (s2p). Chain: a. 40s ribosomal protein rps3 (s3p). Chain: b. 40s ribosomal protein rps4 (s4e). Chain: d. 40s ribosomal protein rps9 (s4p).
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
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P38011  (GBLP_YEAST) -  Guanine nucleotide-binding protein subunit beta-like protein
Seq:
Struc:
319 a.a.
319 a.a.
Protein chain
Pfam   ArchSchema ?
P32905  (RSSA1_YEAST) -  40S ribosomal protein S0-A
Seq:
Struc:
252 a.a.
252 a.a.
Protein chain
Pfam   ArchSchema ?
P05750  (RS3_YEAST) -  40S ribosomal protein S3
Seq:
Struc:
240 a.a.
204 a.a.
Protein chain
Pfam   ArchSchema ?
P0CX35  (RS4A_YEAST) -  40S ribosomal protein S4-A
Seq:
Struc:
261 a.a.
200 a.a.
Protein chain
Pfam   ArchSchema ?
O13516  (RS9A_YEAST) -  40S ribosomal protein S9-A
Seq:
Struc:
197 a.a.
197 a.a.
Protein chain
Pfam   ArchSchema ?
P25443  (RS2_YEAST) -  40S ribosomal protein S2
Seq:
Struc:
254 a.a.
254 a.a.
Protein chain
No UniProt id for this chain
Struc: 143 a.a.
Protein chain
Pfam   ArchSchema ?
P26783  (RS5_YEAST) -  40S ribosomal protein S5
Seq:
Struc:
225 a.a.
199 a.a.
Protein chain
Pfam   ArchSchema ?
P0C0W1  (RS22A_YEAST) -  40S ribosomal protein S22-A
Seq:
Struc:
130 a.a.
130 a.a.
Protein chain
Pfam   ArchSchema ?
P0CX51  (RS16A_YEAST) -  40S ribosomal protein S16-A
Seq:
Struc:
143 a.a.
126 a.a.
Protein chain
Pfam   ArchSchema ?
P38701  (RS20_YEAST) -  40S ribosomal protein S20
Seq:
Struc:
121 a.a.
113 a.a.
Protein chain
Pfam   ArchSchema ?
P06367  (RS14A_YEAST) -  40S ribosomal protein S14-A
Seq:
Struc:
137 a.a.
119 a.a.
Protein chain
Pfam   ArchSchema ?
P0CX29  (RS23A_YEAST) -  40S ribosomal protein S23-A
Seq:
Struc:
145 a.a.
145 a.a.
Protein chain
Pfam   ArchSchema ?
P0CX55  (RS18A_YEAST) -  40S ribosomal protein S18-A
Seq:
Struc:
146 a.a.
140 a.a.
Protein chain
Pfam   ArchSchema ?
P41057  (RS29A_YEAST) -  40S ribosomal protein S29-A
Seq:
Struc:
56 a.a.
48 a.a.
Protein chain
Pfam   ArchSchema ?
P05756  (RS13_YEAST) -  40S ribosomal protein S13
Seq:
Struc:
151 a.a.
121 a.a.
Protein chain
Pfam   ArchSchema ?
P02407  (RS17A_YEAST) -  40S ribosomal protein S17-A
Seq:
Struc:
136 a.a.
136 a.a.
Protein chain
Pfam   ArchSchema ?
P0CX47  (RS11A_YEAST) -  40S ribosomal protein S11-A
Seq:
Struc:
156 a.a.
85 a.a.
Protein chain
Pfam   ArchSchema ?
Q01855  (RS15_YEAST) -  40S ribosomal protein S15
Seq:
Struc:
142 a.a.
88 a.a.
Protein chain
Pfam   ArchSchema ?
P07280  (RS19A_YEAST) -  40S ribosomal protein S19-A
Seq:
Struc:
144 a.a.
144 a.a.
Protein chain
Pfam   ArchSchema ?
P0C0V8  (RS21A_YEAST) -  40S ribosomal protein S21-A
Seq:
Struc:
87 a.a.
87 a.a.
Protein chain
Pfam   ArchSchema ?
Q3E792  (RS25A_YEAST) -  40S ribosomal protein S25-A
Seq:
Struc:
108 a.a.
85 a.a.
Protein chain
No UniProt id for this chain
Struc: 92 a.a.
Protein chain
Pfam   ArchSchema ?
P35997  (RS27_YEAST) -  40S ribosomal protein S27-A
Seq:
Struc:
82 a.a.
50 a.a.
Protein chain
Pfam   ArchSchema ?
Q3E7X9  (RS28A_YEAST) -  40S ribosomal protein S28-A
Seq:
Struc:
67 a.a.
60 a.a.
Protein chain
Pfam   ArchSchema ?
P0CX33  (RS30A_YEAST) -  40S ribosomal protein S30-A
Seq:
Struc:
63 a.a.
63 a.a.
Protein chain
No UniProt id for this chain
Struc: 36 a.a.
Protein chain
No UniProt id for this chain
Struc: 25 a.a.
Protein chain
Pfam   ArchSchema ?
P0CX31  (RS24A_YEAST) -  40S ribosomal protein S24-A
Seq:
Struc:
135 a.a.
96 a.a.
Key:    PfamA domain  Secondary structure

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   11 terms 
  Biological process     cytoplasmic translation   20 terms 
  Biochemical function     structural constituent of ribosome     14 terms  

 

 
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.