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PDBsum entry 3i9c

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protein dna_rna Protein-protein interface(s) links
Ribosome PDB id
3i9c
Jmol
Contents
Protein chains
272 a.a. *
205 a.a. *
208 a.a. *
181 a.a. *
170 a.a. *
146 a.a. *
138 a.a. *
122 a.a. *
150 a.a. *
141 a.a. *
117 a.a. *
111 a.a. *
137 a.a. *
117 a.a. *
101 a.a. *
113 a.a. *
92 a.a. *
102 a.a. *
176 a.a. *
80 a.a. *
97 a.a. *
69 a.a. *
59 a.a. *
71 a.a. *
59 a.a. *
48 a.a. *
49 a.a. *
64 a.a. *
DNA/RNA
* Residue conservation analysis
PDB id:
3i9c
Name: Ribosome
Title: Initiation complex of 70s ribosome with two trnas and mRNA. 3i9c contains 50s ribosomal subunit of molecule b. The 30s subunit can be found in PDB entry 3i9b. Molecule a in the s asymmetric unit is deposited as 3i9d (30s) and 3i9e (50s)
Structure: 23s ribosomal RNA. Chain: a. 5s ribosomal RNA. Chain: b. 50s ribosomal protein l2. Chain: d. 50s ribosomal protein l3. Chain: e. 50s ribosomal protein l4.
Source: Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Organism_taxid: 274. Strain: hb8
Resolution:
3.50Å     R-factor:   0.213     R-free:   0.252
Authors: L.B.Jenner,G.Yusupova,M.Yusupov
Key ref: L.B.Jenner et al. (2010). Structural aspects of messenger RNA reading frame maintenance by the ribosome. Nat Struct Mol Biol, 17, 555-560. PubMed id: 20400952
Date:
10-Jul-09     Release date:   21-Apr-10    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P60405  (RL2_THET8) -  50S ribosomal protein L2
Seq:
Struc:
276 a.a.
272 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHN8  (RL3_THET8) -  50S ribosomal protein L3
Seq:
Struc:
206 a.a.
205 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHN9  (RL4_THET8) -  50S ribosomal protein L4
Seq:
Struc:
210 a.a.
208 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHQ0  (RL5_THET8) -  50S ribosomal protein L5
Seq:
Struc:
182 a.a.
181 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHQ3  (RL6_THET8) -  50S ribosomal protein L6
Seq:
Struc:
180 a.a.
170 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SLQ1  (RL9_THET8) -  50S ribosomal protein L9
Seq:
Struc:
148 a.a.
146 a.a.
Protein chain
Pfam   ArchSchema ?
P60488  (RL13_THET8) -  50S ribosomal protein L13
Seq:
Struc:
140 a.a.
138 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHP8  (RL14_THET8) -  50S ribosomal protein L14
Seq:
Struc:
122 a.a.
122 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHQ7  (RL15_THET8) -  50S ribosomal protein L15
Seq:
Struc:
150 a.a.
150 a.a.
Protein chain
Pfam   ArchSchema ?
P60489  (RL16_THET8) -  50S ribosomal protein L16
Seq:
Struc:
141 a.a.
141 a.a.
Protein chain
Pfam   ArchSchema ?
Q9Z9H5  (RL17_THET8) -  50S ribosomal protein L17
Seq:
Struc:
118 a.a.
117 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHQ4  (RL18_THET8) -  50S ribosomal protein L18
Seq:
Struc:
112 a.a.
111 a.a.
Protein chain
Pfam   ArchSchema ?
P60490  (RL19_THET8) -  50S ribosomal protein L19
Seq:
Struc:
146 a.a.
137 a.a.
Protein chain
Pfam   ArchSchema ?
P60491  (RL20_THET8) -  50S ribosomal protein L20
Seq:
Struc:
118 a.a.
117 a.a.
Protein chain
Pfam   ArchSchema ?
P60492  (RL21_THET8) -  50S ribosomal protein L21
Seq:
Struc:
101 a.a.
101 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHP3  (RL22_THET8) -  50S ribosomal protein L22
Seq:
Struc:
113 a.a.
113 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHP0  (RL23_THET8) -  50S ribosomal protein L23
Seq:
Struc:
96 a.a.
92 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHP9  (RL24_THET8) -  50S ribosomal protein L24
Seq:
Struc:
110 a.a.
102 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHZ1  (RL25_THET8) -  50S ribosomal protein L25
Seq:
Struc:
206 a.a.
176 a.a.
Protein chain
Pfam   ArchSchema ?
P60493  (RL27_THET8) -  50S ribosomal protein L27
Seq:
Struc:
85 a.a.
80 a.a.
Protein chain
Pfam   ArchSchema ?
P60494  (RL28_THET8) -  50S ribosomal protein L28
Seq:
Struc:
98 a.a.
97 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHP6  (RL29_THET8) -  50S ribosomal protein L29
Seq:
Struc:
72 a.a.
69 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHQ6  (RL30_THET8) -  50S ribosomal protein L30
Seq:
Struc:
60 a.a.
59 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SJE1  (RL31_THET8) -  50S ribosomal protein L31
Seq:
Struc:
71 a.a.
71 a.a.
Protein chain
Pfam   ArchSchema ?
P80339  (RL32_THET8) -  50S ribosomal protein L32
Seq:
Struc:
60 a.a.
59 a.a.
Protein chain
Pfam   ArchSchema ?
P35871  (RL33_THET8) -  50S ribosomal protein L33
Seq:
Struc:
54 a.a.
48 a.a.
Protein chain
Pfam   ArchSchema ?
P80340  (RL34_THET8) -  50S ribosomal protein L34
Seq:
Struc:
49 a.a.
49 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SKU1  (RL35_THET8) -  50S ribosomal protein L35
Seq:
Struc:
65 a.a.
64 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   4 terms 
  Biological process     translation   1 term 
  Biochemical function     structural constituent of ribosome     8 terms  

 

 
Nat Struct Mol Biol 17:555-560 (2010)
PubMed id: 20400952  
 
 
Structural aspects of messenger RNA reading frame maintenance by the ribosome.
L.B.Jenner, N.Demeshkina, G.Yusupova, M.Yusupov.
 
  ABSTRACT  
 
One key question in protein biosynthesis is how the ribosome couples mRNA and tRNA movements to prevent disruption of weak codon-anticodon interactions and loss of the translational reading frame during translocation. Here we report the complete path of mRNA on the 70S ribosome at the atomic level (3.1-A resolution), and we show that one of the conformational rearrangements that occurs upon transition from initiation to elongation is a narrowing of the downstream mRNA tunnel. This rearrangement triggers formation of a network of interactions between the mRNA downstream of the A-site codon and the elongating ribosome. Our data elucidate the mechanism by which hypermodified nucleoside 2-methylthio-N6 isopentenyl adenosine at position 37 (ms(2)i(6)A37) in tRNA(Phe)(GAA) stabilizes mRNA-tRNA interactions in all three tRNA binding sites. Another network of contacts is formed between this tRNA modification and ribosomal elements surrounding the mRNA E/P kink, resulting in the anchoring of P-site tRNA. These data allow rationalization of how modification deficiencies of ms(2)i(6)A37 in tRNAs may lead to shifts of the translational reading frame.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
22407015 L.Wang, F.Yang, D.Zhang, Z.Chen, R.M.Xu, K.H.Nierhaus, W.Gong, and Y.Qin (2012).
A conserved proline switch on the ribosome facilitates the recruitment and binding of trGTPases.
  Nat Struct Mol Biol, 19, 403-410.  
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.  
21397180 A.Guelorget, and B.Golinelli-Pimpaneau (2011).
Mechanism-based strategies for trapping and crystallizing complexes of RNA-modifying enzymes.
  Structure, 19, 282-291.  
21267063 S.Bhushan, T.Hoffmann, B.Seidelt, J.Frauenfeld, T.Mielke, O.Berninghausen, D.N.Wilson, and R.Beckmann (2011).
SecM-stalled ribosomes adopt an altered geometry at the peptidyl transferase center.
  PLoS Biol, 9, e1000581.  
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
21448132 V.P.Pisareva, M.A.Skabkin, C.U.Hellen, T.V.Pestova, and A.V.Pisarev (2011).
Dissociation by Pelota, Hbs1 and ABCE1 of mammalian vacant 80S ribosomes and stalled elongation complexes.
  EMBO J, 30, 1804-1817.  
21109664 A.Ben-Shem, L.Jenner, G.Yusupova, and M.Yusupov (2010).
Crystal structure of the eukaryotic ribosome.
  Science, 330, 1203-1209.
PDB codes: 3o2z 3o30 3o58 3o5h
21143320 A.Devaraj, and K.Fredrick (2010).
Short spacing between the Shine-Dalgarno sequence and P codon destabilizes codon-anticodon pairing in the P site to promote +1 programmed frameshifting.
  Mol Microbiol, 78, 1500-1509.  
20974910 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, and R.Beckmann (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.
PDB codes: 3iz5 3iz6 3iz7 3iz9 3izr
20694005 L.Jenner, N.Demeshkina, G.Yusupova, and M.Yusupov (2010).
Structural rearrangements of the ribosome at the tRNA proofreading step.
  Nat Struct Mol Biol, 17, 1072-1078.  
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 code is shown on the right.