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PDBsum entry 3iz5

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protein Protein-protein interface(s) links
Ribosome PDB id
3iz5
Jmol
Contents
Protein chains
216 a.a.
255 a.a.
170 a.a.
190 a.a.
201 a.a.
192 a.a.
140 a.a.
194 a.a.
144 a.a.
163 a.a.
304 a.a.
189 a.a.
164 a.a.
171 a.a.
122 a.a.
75 a.a.
130 a.a.
73 a.a.
23 a.a.
112 a.a.
120 a.a.
133 a.a.
94 a.a.
69 a.a.
51 a.a.
105 a.a.
25 a.a.
20 a.a.
14 a.a.
219 a.a.
182 a.a.
134 a.a.
167 a.a.
108 a.a.
99 a.a.
119 a.a.
104 a.a.
77 a.a.
41 a.a.
128 a.a.
58 a.a.
59 a.a.
124 a.a.
244 a.a.
262 a.a.
389 a.a.
372 a.a.
206 a.a.
92 a.a.
Superseded by: 3izr
PDB id:
3iz5
Name: Ribosome
Title: Localization of the large subunit ribosomal proteins into a cryo-em map of triticum aestivum translating 80s ribosome
Structure: 60s ribosomal protein l1 (l1p). Chain: a. 60s ribosomal protein l2 (l2p). Chain: b. 60s ribosomal protein l11 (l5p). Chain: e. 60s ribosomal protein l9 (l6p). Chain: f. 60s ribosomal protein l7a (l7ae).
Source: Triticum aestivum. Wheat. Organism_taxid: 4565. Organism_taxid: 4565
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,Mielk M.Thomm,O.Berninghausen,B.Beatrix,J.Soeding,E.Westhof,D.N.W R.Beckmann
Key ref: J.P.Armache et al. (2010). Localization of eukaryote-specific ribosomal proteins in a 5.5-Å cryo-EM map of the 80S eukaryotic ribosome. Proc Natl Acad Sci U S A, 107, 19754-19759. PubMed id: 20974910
Date:
30-Sep-10     Release date:   01-Dec-10    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q5I7L3  (Q5I7L3_WHEAT) -  Ribosomal protein
Seq:
Struc:
216 a.a.
216 a.a.
Protein chain
Pfam   ArchSchema ?
Q2QNF3  (Q2QNF3_ORYSJ) -  60S ribosomal protein L2, putative, expressed
Seq:
Struc:
261 a.a.
255 a.a.
Protein chain
Pfam   ArchSchema ?
Q5I7L2  (Q5I7L2_WHEAT) -  Ribosomal protein L11
Seq:
Struc:
180 a.a.
170 a.a.
Protein chain
Pfam   ArchSchema ?
P49210  (RL9_ORYSJ) -  60S ribosomal protein L9
Seq:
Struc:
190 a.a.
190 a.a.
Protein chain
Pfam   ArchSchema ?
P35685  (RL7A_ORYSJ) -  60S ribosomal protein L7a
Seq:
Struc:
258 a.a.
201 a.a.
Protein chain
Pfam   ArchSchema ?
Q0ITS8  (RL101_ORYSJ) -  60S ribosomal protein L10-1
Seq:
Struc:
224 a.a.
192 a.a.
Protein chain
Pfam   ArchSchema ?
Q5I7K4  (Q5I7K4_WHEAT) -  Ribosomal protein L17
Seq:
Struc:
140 a.a.
140 a.a.
Protein chain
Pfam   ArchSchema ?
Q8H8S1  (Q8H8S1_ORYSJ) -  Ribosomal protein L15
Seq:
Struc:
204 a.a.
194 a.a.
Protein chain
Pfam   ArchSchema ?
Q6EUQ7  (Q6EUQ7_ORYSJ) -  Os02g0175600 protein
Seq:
Struc:
144 a.a.
144 a.a.
Protein chain
Pfam   ArchSchema ?
Q5I7L0  (Q5I7L0_WHEAT) -  60S ribosomal protein L18
Seq:
Struc:
188 a.a.
163 a.a.
Protein chain
Pfam   ArchSchema ?
Q8L4L4  (RL52_ORYSJ) -  60S ribosomal protein L5-2
Seq:
Struc:
304 a.a.
304 a.a.
Protein chain
Pfam   ArchSchema ?
Q7XY20  (Q7XY20_WHEAT) -  Ribosomal protein L19
Seq:
Struc:
209 a.a.
189 a.a.*
Protein chain
Pfam   ArchSchema ?
Q7XYC9  (Q7XYC9_WHEAT) -  60s ribosomal protein L21 (Fragment)
Seq:
Struc:
172 a.a.
164 a.a.*
Protein chain
Pfam   ArchSchema ?
Q6K1W6  (Q6K1W6_ORYSJ) -  Os09g0258600 protein
Seq:
Struc:
171 a.a.
171 a.a.
Protein chain
Pfam   ArchSchema ?
Q94CM9  (Q94CM9_ORYSJ) -  Os01g0348700 protein
Seq:
Struc:
152 a.a.
122 a.a.
Protein chain
Pfam   ArchSchema ?
Q5N754  (Q5N754_ORYSJ) -  Os01g0815800 protein
Seq:
Struc:
162 a.a.
75 a.a.
Protein chain
Pfam   ArchSchema ?
Q2QXN5  (Q2QXN5_ORYSJ) -  60S ribosomal protein L26-1, putative, expressed
Seq:
Struc:
150 a.a.
130 a.a.
Protein chain
Pfam   ArchSchema ?
Q5TKP3  (Q5TKP3_ORYSJ) -  Putative 60S ribosomal L28 protein
Seq:
Struc:
147 a.a.
73 a.a.
Protein chain
Pfam   ArchSchema ?
Q9FP55  (Q9FP55_ORYSJ) -  Os01g0304000 protein
Seq:
Struc:
60 a.a.
23 a.a.
Protein chain
Pfam   ArchSchema ?
Q5I7K9  (RL30_WHEAT) -  60S ribosomal protein L30
Seq:
Struc:
112 a.a.
112 a.a.
Protein chain
Pfam   ArchSchema ?
Q6ZGV5  (Q6ZGV5_ORYSJ) -  Putative 60S ribosomal protein L31
Seq:
Struc:
123 a.a.
120 a.a.
Protein chain
Pfam   ArchSchema ?
Q3MST7  (Q3MST7_ORYSI) -  Ribosomal L32
Seq:
Struc:
133 a.a.
133 a.a.
Protein chain
Pfam   ArchSchema ?
Q6Z8Y5  (Q6Z8Y5_ORYSJ) -  Ribosomal protein L37
Seq:
Struc:
94 a.a.
94 a.a.
Protein chain
Pfam   ArchSchema ?
Q8GVY2  (Q8GVY2_ORYSJ) -  60S ribosomal protein L38, putative, expressed
Seq:
Struc:
69 a.a.
69 a.a.
Protein chain
Pfam   ArchSchema ?
Q5I7K7  (Q5I7K7_WHEAT) -  Ribosomal protein L39
Seq:
Struc:
51 a.a.
51 a.a.
Protein chain
Pfam   ArchSchema ?
Q8H5N0  (Q8H5N0_ORYSJ) -  Os07g0450000 protein
Seq:
Struc:
105 a.a.
105 a.a.
Protein chain
Pfam   ArchSchema ?
Q8GVZ2  (Q8GVZ2_ORYSJ) -  Putative uncharacterized protein OJ1417_E01.123
Seq:
Struc:
85 a.a.
25 a.a.
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 chain
Pfam   ArchSchema ?
Q5I7L4  (Q5I7L4_WHEAT) -  60S ribosomal protein L6
Seq:
Struc:
219 a.a.
219 a.a.
Protein chain
No UniProt id for this chain
Struc: 182 a.a.
Protein chain
Pfam   ArchSchema ?
Q6K1Q6  (Q6K1Q6_ORYSJ) -  Putative hydroxyproline-rich glycoprotein 1
Seq:
Struc:
134 a.a.
134 a.a.
Protein chain
Pfam   ArchSchema ?
Q0JJA0  (Q0JJA0_ORYSJ) -  60S ribosomal protein L18a
Seq:
Struc:
178 a.a.
167 a.a.
Protein chain
Pfam   ArchSchema ?
Q6YSX0  (Q6YSX0_ORYSJ) -  Os07g0674200 protein
Seq:
Struc:
130 a.a.
108 a.a.
Protein chain
Pfam   ArchSchema ?
Q7XC31  (Q7XC31_ORYSJ) -  60S ribosomal protein L27
Seq:
Struc:
136 a.a.
99 a.a.
Protein chain
Pfam   ArchSchema ?
Q5I7K8  (Q5I7K8_WHEAT) -  Ribosomal protein l34
Seq:
Struc:
119 a.a.
119 a.a.
Protein chain
Pfam   ArchSchema ?
Q6I608  (Q6I608_ORYSJ) -  Os05g0556900 protein
Seq:
Struc:
111 a.a.
104 a.a.
Protein chain
Pfam   ArchSchema ?
Q5I7L5  (Q5I7L5_WHEAT) -  60S ribosomal protein L36
Seq:
Struc:
112 a.a.
77 a.a.
Protein chain
Pfam   ArchSchema ?
Q10PH1  (Q10PH1_ORYSJ) -  Os03g0234200 protein
Seq:
Struc:
129 a.a.
41 a.a.
Protein chain
Pfam   ArchSchema ?
Q0JAI2  (Q0JAI2_ORYSJ) -  OSJNba0093F12.16 protein
Seq:
Struc:
166 a.a.
128 a.a.
Protein chains
Pfam   ArchSchema ?
Q5I7K5  (Q5I7K5_WHEAT) -  Ribosomal protein P1
Seq:
Struc:
110 a.a.
58 a.a.
Protein chains
Pfam   ArchSchema ?
Q7X729  (Q7X729_WHEAT) -  Acidic ribosomal protein P2 (Fragment)
Seq:
Struc:
112 a.a.
59 a.a.
Protein chain
Pfam   ArchSchema ?
Q8L805  (RL35_WHEAT) -  60S ribosomal protein L35
Seq:
Struc:
124 a.a.
124 a.a.
Protein chain
Pfam   ArchSchema ?
Q5I7K6  (Q5I7K6_WHEAT) -  Ribosomal protein L7
Seq:
Struc:
244 a.a.
244 a.a.
Protein chain
Pfam   ArchSchema ?
P41095  (RLA0_ORYSJ) -  60S acidic ribosomal protein P0
Seq:
Struc:
319 a.a.
262 a.a.
Protein chain
Pfam   ArchSchema ?
Q7X744  (Q7X744_WHEAT) -  Ribosomal protein L3
Seq:
Struc:
389 a.a.
389 a.a.
Protein chain
Pfam   ArchSchema ?
Q6ZLB8  (Q6ZLB8_ORYSJ) -  Putative 60S ribosomal protein L4/L1
Seq:
Struc:
405 a.a.
372 a.a.
Protein chain
Pfam   ArchSchema ?
Q5I7L1  (Q5I7L1_WHEAT) -  Ribosomal protein L13a
Seq:
Struc:
206 a.a.
206 a.a.
Protein chain
Pfam   ArchSchema ?
Q5QM99  (RL37A_ORYSJ) -  60S ribosomal protein L37a
Seq:
Struc:
92 a.a.
92 a.a.
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 

 
Proc Natl Acad Sci U S A 107:19754-19759 (2010)
PubMed id: 20974910  
 
 
Localization of eukaryote-specific ribosomal proteins in a 5.5-Å cryo-EM map of the 80S eukaryotic ribosome.
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
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
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
21138957 M.G.Kearse, A.S.Chen, and V.C.Ware (2011).
Expression of ribosomal protein L22e family members in Drosophila melanogaster: rpL22-like is differentially expressed and alternatively spliced.
  Nucleic Acids Res, 39, 2701-2716.  
21333526 N.Grigorieff, and S.C.Harrison (2011).
Near-atomic resolution reconstructions of icosahedral viruses from electron cryo-microscopy.
  Curr Opin Struct Biol, 21, 265-273.  
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.