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PDBsum entry 2bcw
Go to PDB code: 
protein links
Ribosome PDB id
2bcw
Contents
Protein chains
65 a.a.* *
68 a.a.* *
58 a.a.* *
* Residue conservation analysis
* C-alpha coords only
PDB id:
2bcw
Name: Ribosome
Title: Coordinates of the n-terminal domain of ribosomal protein l11,c- terminal domain of ribosomal protein l7/l12 and a portion of the g' domain of elongation factor g, as fitted into cryo-em map of an escherichia coli 70s Ef-g Gdp Fusidic acid complex
Structure: 50s ribosomal protein l11. Chain: a. Fragment: n-terminal domain. 50s ribosomal protein l7/l12. Chain: b. Fragment: c-terminal domain. Synonym: l8. Elongation factor g. Chain: c.
Source: Thermotoga maritima. Organism_taxid: 2336. Escherichia coli. Organism_taxid: 562. Thermus thermophilus. Organism_taxid: 274
Biol. unit: Trimer (from PQS)
Authors: P.P.Datta,M.R.Sharma,L.Qi,J.Frank,R.K.Agrawal
Key ref:
P.P.Datta et al. (2005). Interaction of the G' domain of elongation factor G and the C-terminal domain of ribosomal protein L7/L12 during translocation as revealed by cryo-EM. Mol Cell, 20, 723-731. PubMed id: 16337596 DOI: 10.1016/j.molcel.2005.10.028
Date:
19-Oct-05     Release date:   20-Dec-05    
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P29395  (RL11_THEMA) -  Large ribosomal subunit protein uL11 from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)
Seq:
Struc: 		141 a.a.
65 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7K2  (RL7_ECOLI) -  Large ribosomal subunit protein bL12 from Escherichia coli (strain K12)
Seq:
Struc: 		121 a.a.
68 a.a.
Protein chain
Pfam   ArchSchema ?
P13551  (EFG_THETH) -  Elongation factor G from Thermus thermophilus
Seq:
Struc: 		 
Seq:
Struc: 		691 a.a.
58 a.a.
Key:    PfamA domain  Secondary structure

 Enzyme reactions 
   Enzyme class: Chains A, B, C: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1016/j.molcel.2005.10.028 Mol Cell 20:723-731 (2005)
PubMed id: 16337596  
 
 
Interaction of the G' domain of elongation factor G and the C-terminal domain of ribosomal protein L7/L12 during translocation as revealed by cryo-EM.
P.P.Datta, M.R.Sharma, L.Qi, J.Frank, R.K.Agrawal.
 
  ABSTRACT  
 
During tRNA translocation on the ribosome, an arc-like connection (ALC) is formed between the G' domain of elongation factor G (EF-G) and the L7/L12-stalk base of the large ribosomal subunit in the GDP state. To delineate the boundary of EF-G within the ALC, we tagged an amino acid residue near the tip of the G' domain of EF-G with undecagold, which was then visualized with three-dimensional cryo-electron microscopy (cryo-EM). Two distinct positions for the undecagold, observed in the GTP-state and GDP-state cryo-EM maps of the ribosome bound EF-G, allowed us to determine the movement of the labeled amino acid. Molecular analyses of the cryo-EM maps show: (1) that three structural components, the N-terminal domain of ribosomal protein L11, the C-terminal domain of ribosomal protein L7/L12, and the G' domain of EF-G, participate in formation of the ALC; and (2) that both EF-G and the ribosomal protein L7/L12 undergo large conformational changes to form the ALC.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Localization of Amino Acid 209C in EF-G 		Figure 3.
Figure 3. Participation of EF-G in ALC Formation
 
  The above figures are reprinted by permission from Cell Press: Mol Cell (2005, 20, 723-731) copyright 2005.  
  Figures were selected by an automated process.  

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.  
21152561 K.Mikulík, J.Bobek, A.Ziková, M.Smětáková, and S.Bezoušková (2011).
Phosphorylation of ribosomal proteins influences subunit association and translation of poly (U) in Streptomyces coelicolor.
  Mol Biosyst, 7, 817-823.  
21453772 M.J.Han, H.Cimen, J.L.Miller-Lee, H.Koc, and E.C.Koc (2011).
Purification of human mitochondrial ribosomal L7/L12 stalk proteins and reconstitution of functional hybrid ribosomes in Escherichia coli.
  Protein Expr Purif, 78, 48-54.  
20348921 N.Clementi, A.Chirkova, B.Puffer, R.Micura, and N.Polacek (2010).
Atomic mutagenesis reveals A2660 of 23S ribosomal RNA as key to EF-G GTPase activation.
  Nat Chem Biol, 6, 344-351.  
20004163 D.J.Taylor, B.Devkota, A.D.Huang, M.Topf, E.Narayanan, A.Sali, S.C.Harvey, and J.Frank (2009).
Comprehensive molecular structure of the eukaryotic ribosome.
  Structure, 17, 1591-1604.
PDB codes: 3jyv 3jyw 3jyx
19469554 G.Y.Soung, J.L.Miller, H.Koc, and E.C.Koc (2009).
Comprehensive analysis of phosphorylated proteins of Escherichia coli ribosomes.
  J Proteome Res, 8, 3390-3402.  
19702336 J.L.Miller, H.Cimen, H.Koc, and E.C.Koc (2009).
Phosphorylated proteins of the mammalian mitochondrial ribosome: implications in protein synthesis.
  J Proteome Res, 8, 4789-4798.  
19073700 P.H.Too, M.K.Ma, A.N.Mak, Y.T.Wong, C.K.Tung, G.Zhu, S.W.Au, K.B.Wong, and P.C.Shaw (2009).
The C-terminal fragment of the ribosomal P protein complexed to trichosanthin reveals the interaction between the ribosome-inactivating protein and the ribosome.
  Nucleic Acids Res, 37, 602-610.
PDB codes: 2jdl 2jjr 2vs6
18936095 T.Miyoshi, T.Nomura, and T.Uchiumi (2009).
Engineering and Characterization of the Ribosomal L10{middle dot}L12 Stalk Complex: A STRUCTURAL ELEMENT RESPONSIBLE FOR HIGH TURNOVER OF THE ELONGATION FACTOR G-DEPENDENT GTPase.
  J Biol Chem, 284, 85-92.  
19833919 Y.G.Gao, M.Selmer, C.M.Dunham, A.Weixlbaumer, A.C.Kelley, and V.Ramakrishnan (2009).
The structure of the ribosome with elongation factor G trapped in the posttranslocational state.
  Science, 326, 694-699.
PDB codes: 2wri 2wrj 2wrk 2wrl
18406324 J.M.Harms, D.N.Wilson, F.Schluenzen, S.R.Connell, T.Stachelhaus, Z.Zaborowska, C.M.Spahn, and P.Fucini (2008).
Translational regulation via L11: molecular switches on the ribosome turned on and off by thiostrepton and micrococcin.
  Mol Cell, 30, 26-38.
PDB codes: 2zjp 2zjq 2zjr 3cf5
18006331 M.Hu, L.Qian, R.P.Briñas, E.S.Lymar, L.Kuznetsova, and J.F.Hainfeld (2008).
Gold nanoparticle-protein arrays improve resolution for cryo-electron microscopy.
  J Struct Biol, 161, 83-91.  
19029596 O.Kurkcuoglu, P.Doruker, T.Z.Sen, A.Kloczkowski, and R.L.Jernigan (2008).
The ribosome structure controls and directs mRNA entry, translocation and exit dynamics.
  Phys Biol, 5, 046005.  
18400176 P.Chandramouli, M.Topf, J.F.Ménétret, N.Eswar, J.J.Cannone, R.R.Gutell, A.Sali, and C.W.Akey (2008).
Structure of the mammalian 80S ribosome at 8.7 A resolution.
  Structure, 16, 535-548.
PDB codes: 2zkq 2zkr
18362332 R.N.Evans, G.Blaha, S.Bailey, and T.A.Steitz (2008).
The structure of LepA, the ribosomal back translocase.
  Proc Natl Acad Sci U S A, 105, 4673-4678.
PDB code: 3cb4
17940088 A.García-Marcos, A.Morreale, E.Guarinos, E.Briones, M.Remacha, A.R.Ortiz, and J.P.Ballesta (2007).
In vivo assembling of bacterial ribosomal protein L11 into yeast ribosomes makes the particles sensitive to the prokaryotic specific antibiotic thiostrepton.
  Nucleic Acids Res, 35, 7109-7117.  
17643374 C.Barat, P.P.Datta, V.S.Raj, M.R.Sharma, H.Kaji, A.Kaji, and R.K.Agrawal (2007).
Progression of the ribosome recycling factor through the ribosome dissociates the two ribosomal subunits.
  Mol Cell, 27, 250-261.  
17292917 D.Lee, J.D.Walsh, P.Yu, M.A.Markus, T.Choli-Papadopoulou, C.D.Schwieters, S.Krueger, D.E.Draper, and Y.X.Wang (2007).
The structure of free L11 and functional dynamics of L11 in free, L11-rRNA(58 nt) binary and L11-rRNA(58 nt)-thiostrepton ternary complexes.
  J Mol Biol, 367, 1007-1022.
PDB codes: 2e34 2e35 2e36 2h8w
17317625 D.Pan, S.V.Kirillov, and B.S.Cooperman (2007).
Kinetically competent intermediates in the translocation step of protein synthesis.
  Mol Cell, 25, 519-529.  
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
17932030 R.Nechifor, M.Murataliev, and K.S.Wilson (2007).
Functional Interactions between the G' Subdomain of Bacterial Translation Factor EF-G and Ribosomal Protein L7/L12.
  J Biol Chem, 282, 36998-37005.  
17349960 S.R.Connell, C.Takemoto, D.N.Wilson, H.Wang, K.Murayama, T.Terada, M.Shirouzu, M.Rost, M.Schüler, J.Giesebrecht, M.Dabrowski, T.Mielke, P.Fucini, S.Yokoyama, and C.M.Spahn (2007).
Structural basis for interaction of the ribosome with the switch regions of GTP-bound elongation factors.
  Mol Cell, 25, 751-764.
PDB code: 2om7
17574829 V.Berk, and J.H.Cate (2007).
Insights into protein biosynthesis from structures of bacterial ribosomes.
  Curr Opin Struct Biol, 17, 302-309.  
17804412 Y.Maki, T.Hashimoto, M.Zhou, T.Naganuma, J.Ohta, T.Nomura, C.V.Robinson, and T.Uchiumi (2007).
Three binding sites for stalk protein dimers are generally present in ribosomes from archaeal organism.
  J Biol Chem, 282, 32827-32833.  
17040491 D.Qiu, P.Parada, A.G.Marcos, D.Cárdenas, M.Remacha, and J.P.Ballesta (2006).
Different roles of P1 and P2 Saccharomyces cerevisiae ribosomal stalk proteins revealed by cross-linking.
  Mol Microbiol, 62, 1191-1202.  
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.

 

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