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PDBsum entry 3fih

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protein dna_rna ligands Protein-protein interface(s) links
Ribosome PDB id
3fih
Jmol
Contents
Protein chains
98 a.a. *
117 a.a. *
123 a.a. *
113 a.a. *
96 a.a. *
88 a.a. *
80 a.a. *
80 a.a. *
55 a.a. *
79 a.a. *
85 a.a. *
51 a.a. *
218 a.a. *
206 a.a. *
205 a.a. *
150 a.a. *
100 a.a. *
150 a.a. *
129 a.a. *
127 a.a. *
393 a.a. *
DNA/RNA
Ligands
GDP
* Residue conservation analysis
PDB id:
3fih
Name: Ribosome
Title: Ternary complex-bound e.Coli 70s ribosome. This entry consis 30s subunit, trnas and the ternary complex.
Structure: 30s ribosomal protein s10. Chain: j. 30s ribosomal protein s11. Chain: k. 30s ribosomal protein s12. Chain: l. 30s ribosomal protein s13. Chain: m. 30s ribosomal protein s14.
Source: Escherichia coli. Organism_taxid: 562. Synthetic: yes. Other_details: this sequence occurs naturally in yeast.. Other_details: mRNA was synthetically contstructed. Organism_taxid: 562
Authors: E.Villa,J.Sengupta,L.G.Trabuco,J.Lebarron,W.T.Baxter,T.R.Sha R.A.Grassucci,P.Nissen,M.Ehrenberg,K.Schulten,J.Frank
Key ref:
E.Villa et al. (2009). Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis. Proc Natl Acad Sci U S A, 106, 1063-1068. PubMed id: 19122150 DOI: 10.1073/pnas.0811370106
Date:
11-Dec-08     Release date:   03-Mar-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0A7R5  (RS10_ECOLI) -  30S ribosomal protein S10
Seq:
Struc:
103 a.a.
98 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7R9  (RS11_ECOLI) -  30S ribosomal protein S11
Seq:
Struc:
129 a.a.
117 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7S3  (RS12_ECOLI) -  30S ribosomal protein S12
Seq:
Struc:
124 a.a.
123 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7S9  (RS13_ECOLI) -  30S ribosomal protein S13
Seq:
Struc:
118 a.a.
113 a.a.
Protein chain
Pfam   ArchSchema ?
P0AG59  (RS14_ECOLI) -  30S ribosomal protein S14
Seq:
Struc:
101 a.a.
96 a.a.
Protein chain
Pfam   ArchSchema ?
P0ADZ4  (RS15_ECOLI) -  30S ribosomal protein S15
Seq:
Struc:
89 a.a.
88 a.a.*
Protein chain
Pfam   ArchSchema ?
P0A7T3  (RS16_ECOLI) -  30S ribosomal protein S16
Seq:
Struc:
82 a.a.
80 a.a.
Protein chain
Pfam   ArchSchema ?
P0AG63  (RS17_ECOLI) -  30S ribosomal protein S17
Seq:
Struc:
84 a.a.
80 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7T7  (RS18_ECOLI) -  30S ribosomal protein S18
Seq:
Struc:
75 a.a.
55 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7U3  (RS19_ECOLI) -  30S ribosomal protein S19
Seq:
Struc:
92 a.a.
79 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7U7  (RS20_ECOLI) -  30S ribosomal protein S20
Seq:
Struc:
87 a.a.
85 a.a.
Protein chain
Pfam   ArchSchema ?
P68679  (RS21_ECOLI) -  30S ribosomal protein S21
Seq:
Struc:
71 a.a.
51 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7V0  (RS2_ECOLI) -  30S ribosomal protein S2
Seq:
Struc:
241 a.a.
218 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7V3  (RS3_ECOLI) -  30S ribosomal protein S3
Seq:
Struc:
233 a.a.
206 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7V8  (RS4_ECOLI) -  30S ribosomal protein S4
Seq:
Struc:
206 a.a.
205 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7W1  (RS5_ECOLI) -  30S ribosomal protein S5
Seq:
Struc:
167 a.a.
150 a.a.
Protein chain
Pfam   ArchSchema ?
P02358  (RS6_ECOLI) -  30S ribosomal protein S6
Seq:
Struc:
135 a.a.
100 a.a.
Protein chain
Pfam   ArchSchema ?
P02359  (RS7_ECOLI) -  30S ribosomal protein S7
Seq:
Struc:
179 a.a.
150 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7W7  (RS8_ECOLI) -  30S ribosomal protein S8
Seq:
Struc:
130 a.a.
129 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7X3  (RS9_ECOLI) -  30S ribosomal protein S9
Seq:
Struc:
130 a.a.
127 a.a.
Protein chain
Pfam   ArchSchema ?
P0CE48  (EFTU2_ECOLI) -  Elongation factor Tu 2
Seq:
Struc:
394 a.a.
393 a.a.
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   8 terms 
  Biological process     nucleic acid phosphodiester bond hydrolysis   20 terms 
  Biochemical function     structural constituent of ribosome     21 terms  

 

 
DOI no: 10.1073/pnas.0811370106 Proc Natl Acad Sci U S A 106:1063-1068 (2009)
PubMed id: 19122150  
 
 
Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis.
E.Villa, J.Sengupta, L.G.Trabuco, J.Lebarron, W.T.Baxter, T.R.Shaikh, R.A.Grassucci, P.Nissen, M.Ehrenberg, K.Schulten, J.Frank.
 
  ABSTRACT  
 
In translation, elongation factor Tu (EF-Tu) molecules deliver aminoacyl-tRNAs to the mRNA-programmed ribosome. The GTPase activity of EF-Tu is triggered by ribosome-induced conformational changes of the factor that play a pivotal role in the selection of the cognate aminoacyl-tRNAs. We present a 6.7-A cryo-electron microscopy map of the aminoacyl-tRNA.EF-Tu.GDP.kirromycin-bound Escherichia coli ribosome, together with an atomic model of the complex obtained through molecular dynamics flexible fitting. The model reveals the conformational changes in the conserved GTPase switch regions of EF-Tu that trigger hydrolysis of GTP, along with key interactions, including those between the sarcin-ricin loop and the P loop of EF-Tu, and between the effector loop of EF-Tu and a conserved region of the 16S rRNA. Our data suggest that GTP hydrolysis on EF-Tu is controlled through a hydrophobic gate mechanism.
 
  Selected figure(s)  
 
Figure 1.
Overview of EF-Tu structure bound to the ribosome. (A) Cryo-EM map of the 70S·fMet-tRNA^fMet·Phe-tRNA^Phe·EF-Tu·GDP·kir complex at a resolution of 6.7 Å shown in transparent surface. The atomic model obtained by molecular dynamics flexible fitting (MDFF) is shown in cartoon representation. (B) Atomic model of the ribosome-bound EF-Tu showing a domain orientation most similar to the closed, GTP-bound form. The switch regions are highlighted: switch I (Sw1) in blue, switch II (Sw2) in orange, and P-loop in green. The same coloring scheme is used in all figures. (C) Closeup of the GTPase domain of EF-Tu. The cryo-EM density map is displayed at a lower threshold to make the switch I density visible. Density thresholds are 2.6 σ (A), 2.2 σ (B), and 1.4 σ (C).
Figure 3.
Interaction (marked with an asterisk) between His-19 in the P loop of EF-Tu (green) and A2260 in the tetraloop of the SRL (cyan; tetraloop shown in blue). This interaction presumably establishes an anchor point holding one of the wings of the hydrophobic gate (compare Fig. 2) in place. (Inset) The ribosome is shown in the same orientation. The map is contoured at 2.5 σ. This figure is rotated 90° with respect to the view in Fig. 2.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22525755 M.Selmer, Y.G.Gao, A.Weixlbaumer, and V.Ramakrishnan (2012).
Ribosome engineering to promote new crystal forms.
  Acta Crystallogr D Biol Crystallogr, 68, 578-583.  
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
21256733 A.Petrov, G.Kornberg, S.O'Leary, A.Tsai, S.Uemura, and J.D.Puglisi (2011).
Dynamics of the translational machinery.
  Curr Opin Struct Biol, 21, 137-145.  
21857664 J.Fei, A.C.Richard, J.E.Bronson, and R.L.Gonzalez (2011).
Transfer RNA-mediated regulation of ribosome dynamics during protein synthesis.
  Nat Struct Mol Biol, 18, 1043-1051.  
21383139 J.Fu, J.B.Munro, S.C.Blanchard, and J.Frank (2011).
Cryoelectron microscopy structures of the ribosome complex in intermediate states during tRNA translocation.
  Proc Natl Acad Sci U S A, 108, 4817-4821.  
21138965 Q.Sun, A.Vila-Sanjurjo, and M.O'Connor (2011).
Mutations in the intersubunit bridge regions of 16S rRNA affect decoding and subunit-subunit interactions on the 70S ribosome.
  Nucleic Acids Res, 39, 3321-3330.  
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
  21365677 W.Li, L.G.Trabuco, K.Schulten, and J.Frank (2011).
Molecular dynamics of EF-G during translocation.
  Proteins, 79, 1478-1486.
PDB code: 3izp
21378755 X.Agirrezabala, E.Schreiner, L.G.Trabuco, J.Lei, R.F.Ortiz-Meoz, K.Schulten, R.Green, and J.Frank (2011).
Structural insights into cognate versus near-cognate discrimination during decoding.
  EMBO J, 30, 1497-1507.
PDB codes: 3izt 3izu 3izv 3izw
20888470 C.L.Lawson (2010).
Unified data resource for cryo-EM.
  Methods Enzymol, 483, 73-90.  
20038631 F.Weis, P.Bron, J.P.Rolland, D.Thomas, B.Felden, and R.Gillet (2010).
Accommodation of tmRNA-SmpB into stalled ribosomes: a cryo-EM study.
  RNA, 16, 299-306.  
20842102 I.Wohlgemuth, C.Pohl, and M.V.Rodnina (2010).
Optimization of speed and accuracy of decoding in translation.
  EMBO J, 29, 3701-3709.  
20192776 J.A.Dunkle, and J.H.Cate (2010).
Ribosome structure and dynamics during translocation and termination.
  Annu Rev Biophys, 39, 227-244.  
20235828 J.Frank, and R.L.Gonzalez (2010).
Structure and dynamics of a processive Brownian motor: the translating ribosome.
  Annu Rev Biochem, 79, 381-412.  
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
20083494 J.Perla-Kajan, X.Lin, B.S.Cooperman, E.Goldman, H.Jakubowski, C.R.Knudsen, and W.Mandecki (2010).
Properties of Escherichia coli EF-Tu mutants designed for fluorescence resonance energy transfer from tRNA molecules.
  Protein Eng Des Sel, 23, 129-136.  
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.  
20215430 L.García-Ortega, E.Alvarez-García, J.G.Gavilanes, A.Martínez-del-Pozo, and S.Joseph (2010).
Cleavage of the sarcin-ricin loop of 23S rRNA differentially affects EF-G and EF-Tu binding.
  Nucleic Acids Res, 38, 4108-4119.  
19962317 M.V.Rodnina, and W.Wintermeyer (2010).
The ribosome goes Nobel.
  Trends Biochem Sci, 35, 1-5.  
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.  
20631791 N.Fischer, A.L.Konevega, W.Wintermeyer, M.V.Rodnina, and H.Stark (2010).
Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy.
  Nature, 466, 329-333.  
20427512 P.C.Whitford, P.Geggier, R.B.Altman, S.C.Blanchard, J.N.Onuchic, and K.Y.Sanbonmatsu (2010).
Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways.
  RNA, 16, 1196-1204.  
21119764 R.Giegé, and C.Sauter (2010).
Biocrystallography: past, present, future.
  HFSP J, 4, 109-121.  
21051640 R.M.Voorhees, T.M.Schmeing, A.C.Kelley, and V.Ramakrishnan (2010).
The mechanism for activation of GTP hydrolysis on the ribosome.
  Science, 330, 835-838.
PDB codes: 2xqd 2xqe
20699303 S.P.McClory, J.M.Leisring, D.Qin, and K.Fredrick (2010).
Missense suppressor mutations in 16S rRNA reveal the importance of helices h8 and h14 in aminoacyl-tRNA selection.
  RNA, 16, 1925-1934.  
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.  
19833922 A.Liljas (2009).
Biochemistry. Leaps in translational elongation.
  Science, 326, 677-678.  
19536129 C.Ticu, R.Nechifor, B.Nguyen, M.Desrosiers, and K.S.Wilson (2009).
Conformational changes in switch I of EF-G drive its directional cycling on and off the ribosome.
  EMBO J, 28, 2053-2065.  
  19929179 D.N.Wilson (2009).
The A-Z of bacterial translation inhibitors.
  Crit Rev Biochem Mol Biol, 44, 393-433.  
19836330 E.H.Lee, J.Hsin, M.Sotomayor, G.Comellas, and K.Schulten (2009).
Discovery through the computational microscope.
  Structure, 17, 1295-1306.  
20025794 J.Frank (2009).
Single-particle reconstruction of biological macromolecules in electron microscopy--30 years.
  Q Rev Biophys, 42, 139-158.  
19913480 J.Gumbart, L.G.Trabuco, E.Schreiner, E.Villa, and K.Schulten (2009).
Regulation of the protein-conducting channel by a bound ribosome.
  Structure, 17, 1453-1464.
PDB codes: 3kc4 3kcr
19580770 J.Hsin, J.Gumbart, L.G.Trabuco, E.Villa, P.Qian, C.N.Hunter, and K.Schulten (2009).
Protein-induced membrane curvature investigated through molecular dynamics flexible fitting.
  Biophys J, 97, 321-329.  
19398010 L.G.Trabuco, E.Villa, E.Schreiner, C.B.Harrison, and K.Schulten (2009).
Molecular dynamics flexible fitting: a practical guide to combine cryo-electron microscopy and X-ray crystallography.
  Methods, 49, 174-180.  
19595805 M.Simonović, and T.A.Steitz (2009).
A structural view on the mechanism of the ribosome-catalyzed peptide bond formation.
  Biochim Biophys Acta, 1789, 612-623.  
19164543 M.V.Rodnina (2009).
Visualizing the protein synthesis machinery: new focus on the translational GTPase elongation factor Tu.
  Proc Natl Acad Sci U S A, 106, 969-970.  
19295500 M.V.Rodnina (2009).
Long-range signalling in activation of the translational GTPase EF-Tu.
  EMBO J, 28, 619-620.  
19915542 P.R.Effraim, J.Wang, M.T.Englander, J.Avins, T.S.Leyh, R.L.Gonzalez, and V.W.Cornish (2009).
Natural amino acids do not require their native tRNAs for efficient selection by the ribosome.
  Nat Chem Biol, 5, 947-953.  
19604479 S.Lindert, R.Staritzbichler, N.Wötzel, M.Karakaş, P.L.Stewart, and J.Meiler (2009).
EM-fold: De novo folding of alpha-helical proteins guided by intermediate-resolution electron microscopy density maps.
  Structure, 17, 990.  
19833920 T.M.Schmeing, R.M.Voorhees, A.C.Kelley, Y.G.Gao, F.V.Murphy, J.R.Weir, and V.Ramakrishnan (2009).
The crystal structure of the ribosome bound to EF-Tu and aminoacyl-tRNA.
  Science, 326, 688-694.
PDB codes: 2wrn 2wro 2wrq 2wrr
19838167 T.M.Schmeing, and V.Ramakrishnan (2009).
What recent ribosome structures have revealed about the mechanism of translation.
  Nature, 461, 1234-1242.  
20025795 X.Agirrezabala, and J.Frank (2009).
Elongation in translation as a dynamic interaction among the ribosome, tRNA, and elongation factors EF-G and EF-Tu.
  Q Rev Biophys, 42, 159-200.  
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.