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PDBsum entry 2gyc
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protein dna_rna Protein-protein interface(s) links
Ribosome PDB id
2gyc

 

 

 

 

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Contents
Protein chains
222 a.a. *
119 a.a. *
227 a.a. *
209 a.a. *
198 a.a. *
177 a.a. *
167 a.a. *
149 a.a. *
139 a.a. *
142 a.a. *
122 a.a. *
140 a.a. *
131 a.a. *
114 a.a. *
113 a.a. *
114 a.a. *
115 a.a. *
106 a.a. *
92 a.a. *
99 a.a. *
94 a.a. *
84 a.a. *
60 a.a. *
56 a.a. *
29 a.a. *
52 a.a. *
DNA/RNA
* Residue conservation analysis
PDB id:
2gyc
Name: Ribosome
Title: Structure of the 50s subunit of a secm-stalled e. Coli ribosome complex obtained by fitting atomic models for RNA and protein components into cryo-em map emd-1143
Structure: 23s ribosomal RNA. Chain: 0. 5s ribosomal RNA. Chain: 9. 50s ribosomal protein l1. Chain: 2. 50s ribosomal protein l7/l12. Chain: 3, 5. 50s ribosomal protein l2.
Source: Escherichia coli. Organism_taxid: 562. Organism_taxid: 562
Biol. unit: 29mer (from PQS)
Authors: K.Mitra,J.Frank
Key ref:
K.Mitra et al. (2006). Elongation arrest by SecM via a cascade of ribosomal RNA rearrangements. Mol Cell, 22, 533-543. PubMed id: 16713583 DOI: 10.1016/j.molcel.2006.05.003
Date:
09-May-06     Release date:   26-Sep-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0A7L0  (RL1_ECOLI) -  50S ribosomal protein L1 from Escherichia coli (strain K12)
Seq:
Struc: 		234 a.a.
222 a.a.
Protein chains
Pfam   ArchSchema ?
P0A7K2  (RL7_ECOLI) -  50S ribosomal protein L7/L12 from Escherichia coli (strain K12)
Seq:
Struc: 		121 a.a.
119 a.a.
Protein chain
Pfam   ArchSchema ?
P60422  (RL2_ECOLI) -  50S ribosomal protein L2 from Escherichia coli (strain K12)
Seq:
Struc: 		273 a.a.
227 a.a.
Protein chain
Pfam   ArchSchema ?
P60438  (RL3_ECOLI) -  50S ribosomal protein L3 from Escherichia coli (strain K12)
Seq:
Struc: 		209 a.a.
209 a.a.
Protein chain
Pfam   ArchSchema ?
P60723  (RL4_ECOLI) -  50S ribosomal protein L4 from Escherichia coli (strain K12)
Seq:
Struc: 		201 a.a.
198 a.a.
Protein chain
Pfam   ArchSchema ?
P62399  (RL5_ECOLI) -  50S ribosomal protein L5 from Escherichia coli (strain K12)
Seq:
Struc: 		179 a.a.
177 a.a.
Protein chain
Pfam   ArchSchema ?
P0AG55  (RL6_ECOLI) -  50S ribosomal protein L6 from Escherichia coli (strain K12)
Seq:
Struc: 		177 a.a.
167 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7R1  (RL9_ECOLI) -  50S ribosomal protein L9 from Escherichia coli (strain K12)
Seq:
Struc: 		149 a.a.
149 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7J7  (RL11_ECOLI) -  50S ribosomal protein L11 from Escherichia coli (strain K12)
Seq:
Struc: 		142 a.a.
139 a.a.
Protein chain
Pfam   ArchSchema ?
P0AA10  (RL13_ECOLI) -  50S ribosomal protein L13 from Escherichia coli (strain K12)
Seq:
Struc: 		142 a.a.
142 a.a.
Protein chain
Pfam   ArchSchema ?
P0ADY3  (RL14_ECOLI) -  50S ribosomal protein L14 from Escherichia coli (strain K12)
Seq:
Struc: 		123 a.a.
122 a.a.
Protein chain
Pfam   ArchSchema ?
P02413  (RL15_ECOLI) -  50S ribosomal protein L15 from Escherichia coli (strain K12)
Seq:
Struc: 		144 a.a.
140 a.a.
Protein chain
Pfam   ArchSchema ?
P0ADY7  (RL16_ECOLI) -  50S ribosomal protein L16 from Escherichia coli (strain K12)
Seq:
Struc: 		136 a.a.
131 a.a.
Protein chain
Pfam   ArchSchema ?
P0AG44  (RL17_ECOLI) -  50S ribosomal protein L17 from Escherichia coli (strain K12)
Seq:
Struc: 		127 a.a.
114 a.a.
Protein chain
Pfam   ArchSchema ?
P0C018  (RL18_ECOLI) -  50S ribosomal protein L18 from Escherichia coli (strain K12)
Seq:
Struc: 		117 a.a.
113 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7K6  (RL19_ECOLI) -  50S ribosomal protein L19 from Escherichia coli (strain K12)
Seq:
Struc: 		115 a.a.
114 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7L3  (RL20_ECOLI) -  50S ribosomal protein L20 from Escherichia coli (strain K12)
Seq:
Struc: 		118 a.a.
115 a.a.
Protein chain
Pfam   ArchSchema ?
P61175  (RL22_ECOLI) -  50S ribosomal protein L22 from Escherichia coli (strain K12)
Seq:
Struc: 		110 a.a.
106 a.a.
Protein chain
Pfam   ArchSchema ?
P0ADZ0  (RL23_ECOLI) -  50S ribosomal protein L23 from Escherichia coli (strain K12)
Seq:
Struc: 		100 a.a.
92 a.a.
Protein chain
Pfam   ArchSchema ?
P60624  (RL24_ECOLI) -  50S ribosomal protein L24 from Escherichia coli (strain K12)
Seq:
Struc: 		104 a.a.
99 a.a.
Protein chain
Pfam   ArchSchema ?
P68919  (RL25_ECOLI) -  50S ribosomal protein L25 from Escherichia coli (strain K12)
Seq:
Struc: 		94 a.a.
94 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7L8  (RL27_ECOLI) -  50S ribosomal protein L27 from Escherichia coli (strain K12)
Seq:
Struc: 		85 a.a.
84 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7M6  (RL29_ECOLI) -  50S ribosomal protein L29 from Escherichia coli (strain K12)
Seq:
Struc: 		63 a.a.
60 a.a.
Protein chain
Pfam   ArchSchema ?
P0AG51  (RL30_ECOLI) -  50S ribosomal protein L30 from Escherichia coli (strain K12)
Seq:
Struc: 		59 a.a.
56 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7N4  (RL32_ECOLI) -  50S ribosomal protein L32 from Escherichia coli (strain K12)
Seq:
Struc: 		57 a.a.
29 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7N9  (RL33_ECOLI) -  50S ribosomal protein L33 from Escherichia coli (strain K12)
Seq:
Struc: 		55 a.a.
52 a.a.
Key:    PfamA domain  Secondary structure

DNA/RNA chains
  C-G-U-A-C-A-C-G-G-U-G-G-A-U-G-C-C-C-U-G-G-C-A-G-U-C-A-A-G-G-C-G-A-U-G-A-A-G-G- ... 2740 bases
  G-G-C-G-G-C-C-G-U-A-G-C-G-C-G-G-U-G-G-U-C-C-C-A-C-C-U-G-A-C-C-C-C-A-U-G-C-C-G- 108 bases

 

 
DOI no: 10.1016/j.molcel.2006.05.003 Mol Cell 22:533-543 (2006)
PubMed id: 16713583  
 
 
Elongation arrest by SecM via a cascade of ribosomal RNA rearrangements.
K.Mitra, C.Schaffitzel, F.Fabiola, M.S.Chapman, N.Ban, J.Frank.
 
  ABSTRACT  
 
In E. coli, the SecM nascent polypeptide causes elongation arrest, while interacting with 23S RNA bases A2058 and A749-753 in the exit tunnel of the large ribosomal subunit. We compared atomic models fitted by real-space refinement into cryo-electron microscopy reconstructions of a pretranslocational and SecM-stalled E. coli ribosome complex. A cascade of RNA rearrangements propagates from the exit tunnel throughout the large subunit, affecting intersubunit bridges and tRNA positions, which in turn reorient small subunit RNA elements. Elongation arrest could result from the inhibition of mRNA.(tRNAs) translocation, E site tRNA egress, and perhaps translation factor activation at the GTPase-associated center. Our study suggests that the specific secondary and tertiary arrangement of ribosomal RNA provides the basis for internal signal transduction within the ribosome. Thus, the ribosome may itself have the ability to regulate its progression through translation by modulating its structure and consequently its receptivity to activation by cofactors.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Overview and Interconnectivity of rRNA Elements in Relation to the Interaction Sites with the SecM Nascent Polypeptide 		Figure 4.
Figure 4. Flowchart of SecM Nascent Polypeptide-Induced rRNA Rearrangements in the Ribosome
 
  The above figures are reprinted by permission from Cell Press: Mol Cell (2006, 22, 533-543) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
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.  
20117091 K.Ito, S.Chiba, and K.Pogliano (2010).
Divergent stalling sequences sense and control cellular physiology.
  Biochem Biophys Res Commun, 393, 1-5.  
19952067 K.Réblová, F.Rázga, W.Li, H.Gao, J.Frank, and J.Sponer (2010).
Dynamics of the base of ribosomal A-site finger revealed by molecular dynamics simulations and Cryo-EM.
  Nucleic Acids Res, 38, 1325-1340.  
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
19656820 A.Yonath (2009).
Large facilities and the evolving ribosome, the cellular machine for genetic-code translation.
  J R Soc Interface, 6, S575-S585.  
19933110 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, and R.Beckmann (2009).
Structural insight into nascent polypeptide chain-mediated translational stalling.
  Science, 326, 1412-1415.
PDB codes: 2wwl 2wwq
19840930 D.R.Tanner, D.A.Cariello, C.J.Woolstenhulme, M.A.Broadbent, and A.R.Buskirk (2009).
Genetic identification of nascent peptides that induce ribosome stalling.
  J Biol Chem, 284, 34809-34818.  
19170872 H.Ramu, A.Mankin, and N.Vazquez-Laslop (2009).
Programmed drug-dependent ribosome stalling.
  Mol Microbiol, 71, 811-824.  
19394297 M.N.Yap, and H.D.Bernstein (2009).
The plasticity of a translation arrest motif yields insights into nascent polypeptide recognition inside the ribosome tunnel.
  Mol Cell, 34, 201-211.  
18462672 L.G.Trabuco, E.Villa, K.Mitra, J.Frank, and K.Schulten (2008).
Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics.
  Structure, 16, 673-683.  
18369182 M.Beringer (2008).
Modulating the activity of the peptidyl transferase center of the ribosome.
  RNA, 14, 795-801.  
18586934 M.G.Lawrence, L.Lindahl, and J.M.Zengel (2008).
Effects on translation pausing of alterations in protein and RNA components of the ribosome exit tunnel.
  J Bacteriol, 190, 5862-5869.  
18439898 N.Vazquez-Laslop, C.Thum, and A.S.Mankin (2008).
Molecular mechanism of drug-dependent ribosome stalling.
  Mol Cell, 30, 190-202.  
18221556 S.L.Liu, and K.Adams (2008).
Molecular adaptation and expression evolution following duplication of genes for organellar ribosomal protein S13 in rosids.
  BMC Evol Biol, 8, 25.  
18391966 T.Bornemann, J.Jöckel, M.V.Rodnina, and W.Wintermeyer (2008).
Signal sequence-independent membrane targeting of ribosomes containing short nascent peptides within the exit tunnel.
  Nat Struct Mol Biol, 15, 494-499.  
17532253 B.Felden (2007).
RNA structure: experimental analysis.
  Curr Opin Microbiol, 10, 286-291.  
17456564 J.F.Atkins, N.M.Wills, G.Loughran, C.Y.Wu, K.Parsawar, M.D.Ryan, C.H.Wang, and C.C.Nelson (2007).
A case for "StopGo": reprogramming translation to augment codon meaning of GGN by promoting unconventional termination (Stop) after addition of glycine and then allowing continued translation (Go).
  RNA, 13, 803-810.  
17996252 N.Gao, A.V.Zavialov, M.Ehrenberg, and J.Frank (2007).
Specific interaction between EF-G and RRF and its implication for GTP-dependent ribosome splitting into subunits.
  J Mol Biol, 374, 1345-1358.
PDB code: 2rdo
17291191 S.D.Moore, and R.T.Sauer (2007).
The tmRNA system for translational surveillance and ribosome rescue.
  Annu Rev Biochem, 76, 101-124.  
17664317 S.J.Schroeder, G.Blaha, and P.B.Moore (2007).
Negamycin binds to the wall of the nascent chain exit tunnel of the 50S ribosomal subunit.
  Antimicrob Agents Chemother, 51, 4462-4465.
PDB code: 2qex
17956547 S.Zaman, M.Fitzpatrick, L.Lindahl, and J.Zengel (2007).
Novel mutations in ribosomal proteins L4 and L22 that confer erythromycin resistance in Escherichia coli.
  Mol Microbiol, 66, 1039-1050.  
18046402 T.A.Rapoport (2007).
Protein translocation across the eukaryotic endoplasmic reticulum and bacterial plasma membranes.
  Nature, 450, 663-669.  
16968693 F.Garza-Sánchez, B.D.Janssen, and C.S.Hayes (2006).
Prolyl-tRNA(Pro) in the A-site of SecM-arrested ribosomes inhibits the recruitment of transfer-messenger RNA.
  J Biol Chem, 281, 34258-34268.  
17082791 K.Mitra, J.Frank, and A.Driessen (2006).
Co- and post-translational translocation through the protein-conducting channel: analogous mechanisms at work?
  Nat Struct Mol Biol, 13, 957-964.  
17000775 R.Rakauskaite, and J.D.Dinman (2006).
An arc of unpaired "hinge bases" facilitates information exchange among functional centers of the ribosome.
  Mol Cell Biol, 26, 8992-9002.  
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.

 

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