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PDBsum entry 2wwq

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protein dna_rna Protein-protein interface(s) links
Ribosome PDB id
2wwq
Jmol
Contents
Protein chains
77 a.a. *
63 a.a. *
58 a.a. *
56 a.a. *
50 a.a. *
234 a.a. *
46 a.a. *
64 a.a. *
38 a.a. *
271 a.a. *
209 a.a. *
201 a.a. *
178 a.a. *
175 a.a. *
149 a.a. *
141 a.a. *
142 a.a. *
121 a.a. *
143 a.a. *
136 a.a. *
120 a.a. *
116 a.a. *
114 a.a. *
117 a.a. *
103 a.a. *
110 a.a. *
93 a.a. *
99 a.a. *
94 a.a. *
79 a.a. *
20 a.a. *
DNA/RNA
* Residue conservation analysis
PDB id:
2wwq
Name: Ribosome
Title: E.Coli 70s ribosome stalled during translation of tnac leader peptide. This file contains the 50s, the p-site tRNA and the tnac leader peptide (part 2 of 2).
Structure: 23s ribosomal RNA. Chain: b. 5s ribosomal RNA. Chain: a. 50s ribosomal protein l1. Chain: 5. 50s ribosomal protein l2. Chain: c. 50s ribosomal protein l3.
Source: Escherichia coli. Organism_taxid: 562. Organism_taxid: 562
Authors: B.Seidelt,C.A.Innis,D.N.Wilson,M.Gartmann,J.Armache,E.Villa, L.G.Trabuco,T.Becker,T.Mielke,K.Schulten,T.A.Steitz, R.Beckmann
Key ref: B.Seidelt et al. (2009). Structural insight into nascent polypeptide chain-mediated translational stalling. Science, 326, 1412-1415. PubMed id: 19933110
Date:
26-Oct-09     Release date:   14-Apr-10    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0A7M2  (RL28_ECOLI) -  50S ribosomal protein L28
Seq:
Struc:
78 a.a.
77 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7M6  (RL29_ECOLI) -  50S ribosomal protein L29
Seq:
Struc:
63 a.a.
63 a.a.
Protein chain
Pfam   ArchSchema ?
P0AG51  (RL30_ECOLI) -  50S ribosomal protein L30
Seq:
Struc:
59 a.a.
58 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7N4  (RL32_ECOLI) -  50S ribosomal protein L32
Seq:
Struc:
57 a.a.
56 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7N9  (RL33_ECOLI) -  50S ribosomal protein L33
Seq:
Struc:
55 a.a.
50 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7L0  (RL1_ECOLI) -  50S ribosomal protein L1
Seq:
Struc:
234 a.a.
234 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7P5  (RL34_ECOLI) -  50S ribosomal protein L34
Seq:
Struc:
46 a.a.
46 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7Q1  (RL35_ECOLI) -  50S ribosomal protein L35
Seq:
Struc:
65 a.a.
64 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7Q6  (RL36_ECOLI) -  50S ribosomal protein L36
Seq:
Struc:
38 a.a.
38 a.a.
Protein chain
Pfam   ArchSchema ?
P60422  (RL2_ECOLI) -  50S ribosomal protein L2
Seq:
Struc:
273 a.a.
271 a.a.
Protein chain
Pfam   ArchSchema ?
P60438  (RL3_ECOLI) -  50S ribosomal protein L3
Seq:
Struc:
209 a.a.
209 a.a.
Protein chain
Pfam   ArchSchema ?
P60723  (RL4_ECOLI) -  50S ribosomal protein L4
Seq:
Struc:
201 a.a.
201 a.a.
Protein chain
Pfam   ArchSchema ?
P62399  (RL5_ECOLI) -  50S ribosomal protein L5
Seq:
Struc:
179 a.a.
178 a.a.
Protein chain
Pfam   ArchSchema ?
P0AG55  (RL6_ECOLI) -  50S ribosomal protein L6
Seq:
Struc:
177 a.a.
175 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7R1  (RL9_ECOLI) -  50S ribosomal protein L9
Seq:
Struc:
149 a.a.
149 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7J7  (RL11_ECOLI) -  50S ribosomal protein L11
Seq:
Struc:
142 a.a.
141 a.a.
Protein chain
Pfam   ArchSchema ?
P0AA10  (RL13_ECOLI) -  50S ribosomal protein L13
Seq:
Struc:
142 a.a.
142 a.a.
Protein chain
Pfam   ArchSchema ?
P0ADY3  (RL14_ECOLI) -  50S ribosomal protein L14
Seq:
Struc:
123 a.a.
121 a.a.
Protein chain
Pfam   ArchSchema ?
P02413  (RL15_ECOLI) -  50S ribosomal protein L15
Seq:
Struc:
144 a.a.
143 a.a.
Protein chain
Pfam   ArchSchema ?
P0ADY7  (RL16_ECOLI) -  50S ribosomal protein L16
Seq:
Struc:
136 a.a.
136 a.a.
Protein chain
Pfam   ArchSchema ?
P0AG44  (RL17_ECOLI) -  50S ribosomal protein L17
Seq:
Struc:
127 a.a.
120 a.a.
Protein chain
Pfam   ArchSchema ?
P0C018  (RL18_ECOLI) -  50S ribosomal protein L18
Seq:
Struc:
117 a.a.
116 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7K6  (RL19_ECOLI) -  50S ribosomal protein L19
Seq:
Struc:
115 a.a.
114 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7L3  (RL20_ECOLI) -  50S ribosomal protein L20
Seq:
Struc:
118 a.a.
117 a.a.
Protein chain
Pfam   ArchSchema ?
P0AG48  (RL21_ECOLI) -  50S ribosomal protein L21
Seq:
Struc:
103 a.a.
103 a.a.
Protein chain
Pfam   ArchSchema ?
P61175  (RL22_ECOLI) -  50S ribosomal protein L22
Seq:
Struc:
110 a.a.
110 a.a.
Protein chain
Pfam   ArchSchema ?
P0ADZ0  (RL23_ECOLI) -  50S ribosomal protein L23
Seq:
Struc:
100 a.a.
93 a.a.
Protein chain
Pfam   ArchSchema ?
P60624  (RL24_ECOLI) -  50S ribosomal protein L24
Seq:
Struc:
104 a.a.
99 a.a.
Protein chain
Pfam   ArchSchema ?
P68919  (RL25_ECOLI) -  50S ribosomal protein L25
Seq:
Struc:
94 a.a.
94 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7L8  (RL27_ECOLI) -  50S ribosomal protein L27
Seq:
Struc:
85 a.a.
79 a.a.
Protein chain
No UniProt id for this chain
Struc: 20 a.a.
Key:    PfamA domain  Secondary structure

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   5 terms 
  Biological process     response to antibiotic   11 terms 
  Biochemical function     structural constituent of ribosome     12 terms  

 

 
Science 326:1412-1415 (2009)
PubMed id: 19933110  
 
 
Structural insight into nascent polypeptide chain-mediated translational stalling.
B.Seidelt, C.A.Innis, D.N.Wilson, M.Gartmann, J.P.Armache, E.Villa, L.G.Trabuco, T.Becker, T.Mielke, K.Schulten, T.A.Steitz, R.Beckmann.
 
  ABSTRACT  
 
Expression of the Escherichia coli tryptophanase operon depends on ribosome stalling during translation of the upstream TnaC leader peptide, a process for which interactions between the TnaC nascent chain and the ribosomal exit tunnel are critical. We determined a 5.8 angstrom-resolution cryo-electron microscopy and single-particle reconstruction of a ribosome stalled during translation of the tnaC leader gene. The nascent chain was extended within the exit tunnel, making contacts with ribosomal components at distinct sites. Upon stalling, two conserved residues within the peptidyltransferase center adopted conformations that preclude binding of release factors. We propose a model whereby interactions within the tunnel are relayed to the peptidyltransferase center to inhibit translation. Moreover, we show that nascent chains adopt distinct conformations within the ribosomal exit tunnel.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
22868764 K.S.Keating, and A.M.Pyle (2012).
RCrane: semi-automated RNA model building.
  Acta Crystallogr D Biol Crystallogr, 68, 985-995.  
21112769 A.Gershenson, and L.M.Gierasch (2011).
Protein folding in the cell: challenges and progress.
  Curr Opin Struct Biol, 21, 32-41.  
21240267 C.C.Liu, L.Qi, C.Yanofsky, and A.P.Arkin (2011).
Regulation of transcription by unnatural amino acids.
  Nat Biotechnol, 29, 164-168.  
21292157 D.N.Wilson (2011).
Peptides in the ribosomal tunnel talk back.
  Mol Cell, 41, 247-248.  
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.  
21370971 D.V.Fedyukina, and S.Cavagnero (2011).
Protein folding at the exit tunnel.
  Annu Rev Biophys, 40, 337-359.  
21251100 G.Horiguchi, A.Mollá-Morales, J.M.Pérez-Pérez, K.Kojima, P.Robles, M.R.Ponce, J.L.Micol, and H.Tsukaya (2011).
Differential contributions of ribosomal protein genes to Arabidopsis thaliana leaf development.
  Plant J, 65, 724-736.  
21111607 G.Zhang, and Z.Ignatova (2011).
Folding at the birth of the nascent chain: coordinating translation with co-translational folding.
  Curr Opin Struct Biol, 21, 25-31.  
21292164 H.Ramu, N.Vázquez-Laslop, D.Klepacki, Q.Dai, J.Piccirilli, R.Micura, and A.S.Mankin (2011).
Nascent peptide in the ribosome exit tunnel affects functional properties of the A-site of the peptidyl transferase center.
  Mol Cell, 41, 321-330.  
21499241 J.Frauenfeld, J.Gumbart, E.O.Sluis, S.Funes, M.Gartmann, B.Beatrix, T.Mielke, O.Berninghausen, T.Becker, K.Schulten, and R.Beckmann (2011).
Cryo-EM structure of the ribosome-SecYE complex in the membrane environment.
  Nat Struct Mol Biol, 18, 614-621.
PDB codes: 3j00 3j01
21342782 L.R.Cruz-Vera, M.S.Sachs, C.L.Squires, and C.Yanofsky (2011).
Nascent polypeptide sequences that influence ribosome function.
  Curr Opin Microbiol, 14, 160-166.  
21336521 M.Valle (2011).
Almost lost in translation. Cryo-EM of a dynamic macromolecular complex: the ribosome.
  Eur Biophys J, 40, 589-597.  
21464303 N.Vázquez-Laslop, and A.S.Mankin (2011).
Picky nascent peptides do not talk to foreign ribosomes.
  Proc Natl Acad Sci U S A, 108, 5931-5932.  
21177642 O.L.Gurvich, S.J.Näsvall, P.V.Baranov, G.R.Björk, and J.F.Atkins (2011).
Two groups of phenylalanine biosynthetic operon leader peptides genes: a high level of apparently incidental frameshifting in decoding Escherichia coli pheL.
  Nucleic Acids Res, 39, 3079-3092.  
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.  
21383133 S.Chiba, T.Kanamori, T.Ueda, Y.Akiyama, K.Pogliano, and K.Ito (2011).
Recruitment of a species-specific translational arrest module to monitor different cellular processes.
  Proc Natl Acad Sci U S A, 108, 6073-6078.  
20534348 A.L.Starosta, V.V.Karpenko, A.V.Shishkina, A.Mikolajka, N.V.Sumbatyan, F.Schluenzen, G.A.Korshunova, A.A.Bogdanov, and D.N.Wilson (2010).
Interplay between the ribosomal tunnel, nascent chain, and macrolides influences drug inhibition.
  Chem Biol, 17, 504-514.  
20439768 C.Eichmann, S.Preissler, R.Riek, and E.Deuerling (2010).
Cotranslational structure acquisition of nascent polypeptides monitored by NMR spectroscopy.
  Proc Natl Acad Sci U S A, 107, 9111-9116.  
20525967 D.Graber, H.Moroder, J.Steger, K.Trappl, N.Polacek, and R.Micura (2010).
Reliable semi-synthesis of hydrolysis-resistant 3'-peptidyl-tRNA conjugates containing genuine tRNA modifications.
  Nucleic Acids Res, 38, 6796-6802.  
20975935 D.Lucent, C.D.Snow, C.E.Aitken, and V.S.Pande (2010).
Non-bulk-like solvent behavior in the ribosome exit tunnel.
  PLoS Comput Biol, 6, e1000963.  
  21072331 J.Frank (2010).
The Ribosome Comes Alive.
  Isr J Chem, 50, 95-98.  
20183845 J.Hsin, D.E.Chandler, J.Gumbart, C.B.Harrison, M.Sener, J.Strumpfer, and K.Schulten (2010).
Self-assembly of photosynthetic membranes.
  Chemphyschem, 11, 1154-1159.  
20980660 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).
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.
PDB codes: 3izb 3izc 3izd 3ize 3izf 3izs
20117091 K.Ito, S.Chiba, and K.Pogliano (2010).
Divergent stalling sequences sense and control cellular physiology.
  Biochem Biophys Res Commun, 393, 1-5.  
20462496 L.G.Trabuco, C.B.Harrison, E.Schreiner, and K.Schulten (2010).
Recognition of the regulatory nascent chain TnaC by the ribosome.
  Structure, 18, 627-637.  
20676057 N.Vázquez-Laslop, H.Ramu, D.Klepacki, K.Kannan, and A.S.Mankin (2010).
The key function of a conserved and modified rRNA residue in the ribosomal response to the nascent peptide.
  EMBO J, 29, 3108-3117.  
20932481 S.Bhushan, H.Meyer, A.L.Starosta, T.Becker, T.Mielke, O.Berninghausen, M.Sattler, D.N.Wilson, and R.Beckmann (2010).
Structural basis for translational stalling by human cytomegalovirus and fungal arginine attenuator peptide.
  Mol Cell, 40, 138-146.
PDB code: 2xl1
21124925 S.L.Hutson, E.Mui, K.Kinsley, W.H.Witola, M.S.Behnke, K.El Bissati, S.P.Muench, B.Rohrman, S.R.Liu, R.Wollmann, Y.Ogata, A.Sarkeshik, J.R.Yates, and R.McLeod (2010).
T. gondii RP promoters & knockdown reveal molecular pathways associated with proliferation and cell-cycle arrest.
  PLoS One, 5, e14057.  
20511136 X.Agirrezabala, and J.Frank (2010).
From DNA to proteins via the ribosome: structural insights into the workings of the translation machinery.
  Hum Genomics, 4, 226-237.  
19965743 M.Kampmann, and G.Blobel (2009).
Biochemistry. Nascent proteins caught in the act.
  Science, 326, 1352-1353.  
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.