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PDBsum entry 2wrn
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protein dna_rna ligands metals Protein-protein interface(s) links
Ribosome PDB id
2wrn

 

 

 

 

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Contents
Protein chains
235 a.a. *
207 a.a. *
208 a.a. *
151 a.a. *
101 a.a. *
155 a.a. *
138 a.a. *
127 a.a. *
99 a.a. *
119 a.a. *
125 a.a. *
125 a.a. *
60 a.a. *
88 a.a. *
84 a.a. *
100 a.a. *
70 a.a. *
79 a.a. *
99 a.a. *
25 a.a. *
374 a.a. *
DNA/RNA
Ligands
PAR
GDP
KIR
Metals
_MG
_ZN ×4
* Residue conservation analysis
Obsolete entry
PDB id:
2wrn
Name: Ribosome
Title: The crystal structure of the 70s ribosome bound to ef-tu and tRNA (part 1 of 4).
Structure: 16s ribosomal RNA. Chain: a. Synonym: 16s rrna. Other_details: chain a (16s RNA) has e.Coli numbering, based on a structural alignment with the corresponding e.Coli structure in 2avy.. 30s ribosomal protein s2. Chain: b. 30s ribosomal protein s3.
Source: Thermus thermophilus. Organism_taxid: 300852. Strain: hb8 - mrc - msaw1. Atcc: 27634. Escherichia coli. Organism_taxid: 83333. Strain: k-12. Synthetic: yes. Atcc: 27634
Resolution:
3.60Å     R-factor:   0.280     R-free:   0.315
Authors: T.M.Schmeing,R.M.Voorhees,V.Ramakrishnan
Key ref:
T.M.Schmeing et al. (2009). The crystal structure of the ribosome bound to EF-Tu and aminoacyl-tRNA. Science, 326, 688-694. PubMed id: 19833920 DOI: 10.1126/science.1179700
Date:
01-Sep-09     Release date:   20-Oct-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P80371  (RS2_THET8) -  Small ribosomal subunit protein uS2 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		256 a.a.
235 a.a.
Protein chain
Pfam   ArchSchema ?
P80372  (RS3_THET8) -  Small ribosomal subunit protein uS3 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		239 a.a.
207 a.a.
Protein chain
Pfam   ArchSchema ?
P80373  (RS4_THET8) -  Small ribosomal subunit protein uS4 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		209 a.a.
208 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHQ5  (RS5_THET8) -  Small ribosomal subunit protein uS5 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		162 a.a.
151 a.a.
Protein chain
Q5SLP8  (RS6_THET8) -  Small ribosomal subunit protein bS6 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		101 a.a.
101 a.a.
Protein chain
Pfam   ArchSchema ?
P17291  (RS7_THET8) -  Small ribosomal subunit protein uS7 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		156 a.a.
155 a.a.
Protein chain
Q5SHQ2  (RS8_THET8) - 
Protein chain
Pfam   ArchSchema ?
P80374  (RS9_THET8) -  Small ribosomal subunit protein uS9 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		128 a.a.
127 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHN7  (RS10_THET8) -  Small ribosomal subunit protein uS10 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		105 a.a.
99 a.a.
Protein chain
Pfam   ArchSchema ?
P80376  (RS11_THET8) -  Small ribosomal subunit protein uS11 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		129 a.a.
119 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHN3  (RS12_THET8) -  Small ribosomal subunit protein uS12 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		132 a.a.
125 a.a.
Protein chain
Pfam   ArchSchema ?
P80377  (RS13_THET8) -  Small ribosomal subunit protein uS13 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		126 a.a.
125 a.a.
Protein chain
Q5SHQ1  (RS14Z_THET8) - 
Protein chain
Pfam   ArchSchema ?
Q5SJ76  (RS15_THET8) -  Small ribosomal subunit protein uS15 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		89 a.a.
88 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SJH3  (RS16_THET8) -  Small ribosomal subunit protein bS16 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		88 a.a.
84 a.a.
Protein chain
Q5SHP7  (RS17_THET8) - 
Protein chain
Pfam   ArchSchema ?
Q5SLQ0  (RS18_THET8) -  Small ribosomal subunit protein bS18 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		88 a.a.
70 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHP2  (RS19_THET8) -  Small ribosomal subunit protein uS19 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		93 a.a.
79 a.a.
Protein chain
Pfam   ArchSchema ?
P80380  (RS20_THET8) -  Small ribosomal subunit protein bS20 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		106 a.a.
99 a.a.
Protein chain
Q5SIH3  (RSHX_THET8) -  Small ribosomal subunit protein bTHX from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		27 a.a.
25 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHN6  (EFTU1_THET8) -  Elongation factor Tu-A from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		406 a.a.
374 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

DNA/RNA chains
  U-G-G-A-G-A-G-U-U-U-G-A-U-C-C-U-G-G-C-U-C-A-G-G-G-U-G-A-A-C-G-C-U-G-G-C-G-G-C- ... 1504 bases
  G-C-C-C-G-G-A-U-A-G-C-U-C-A-G-U-C-G-G-U-A-G-A-G-C-A-G-G-G-G-A-U-U-G-A-A-A-A-U- 76 bases
  G-C-C-C-G-G-A-U-A-G-C-U-C-A-G-U-C-G-G-U-A-G-A-G-C-A-G-G-G-G-A-U-U-G-A-A-A-A-U- 76 bases
  A-A-U-G-U-U-C-A-C-C-A-A-A 13 bases
  G-C-U-G-A-U-A-U-A-G-C-U-C-A-G-H2U-H2U-G-G-H2U-A-G-A-G-C-G-C-A-C-C-C-U-U-G-G-U- 77 bases

 

 
DOI no: 10.1126/science.1179700 Science 326:688-694 (2009)
PubMed id: 19833920  
 
 
The crystal structure of the ribosome bound to EF-Tu and aminoacyl-tRNA.
T.M.Schmeing, R.M.Voorhees, A.C.Kelley, Y.G.Gao, F.V.Murphy, J.R.Weir, V.Ramakrishnan.
 
  ABSTRACT  
 
The ribosome selects a correct transfer RNA (tRNA) for each amino acid added to the polypeptide chain, as directed by messenger RNA. Aminoacyl-tRNA is delivered to the ribosome by elongation factor Tu (EF-Tu), which hydrolyzes guanosine triphosphate (GTP) and releases tRNA in response to codon recognition. The signaling pathway that leads to GTP hydrolysis upon codon recognition is critical to accurate decoding. Here we present the crystal structure of the ribosome complexed with EF-Tu and aminoacyl-tRNA, refined to 3.6 angstrom resolution. The structure reveals details of the tRNA distortion that allows aminoacyl-tRNA to interact simultaneously with the decoding center of the 30S subunit and EF-Tu at the factor binding site. A series of conformational changes in EF-Tu and aminoacyl-tRNA suggests a communication pathway between the decoding center and the guanosine triphosphatase center of EF-Tu.
 
  Selected figure(s)  
 
Figure 1.
View larger version (89K): [in this window] [in a new window] Fig. 1. Structure of EF-Tu and aminoacyl-tRNA bound to the ribosome. (A) Representative electron density from an unbiased difference Fourier map displayed at 1.3 , with the refined model of EF-Tu (red) and Thr-tRNA^Thr (purple). (B) Overall view of the complex, with EF-Tu and tRNAs depicted as surfaces, and rRNA and protein as cartoons. PTC, peptidyl transferase center; DC, decoding center. (C) Contacts between TC and the ribosome, with interacting residues shown as spheres. 		Figure 4.
View larger version (77K): [in this window] [in a new window] Fig. 4. Schematic representation of the decoding pathway. (A) The L7/L12 stalk recruits TC to a ribosome with deacylated tRNA in the E site and peptidyl-tRNA in the P site. The black frame represents the enlarged area depicted in (B) to (E). (B) The tRNA samples codon-to-anticodon pairing until a match (C) is sensed, by decoding center nucleotides 530, 1492, and 1493 (1). Codon recognition triggers domain closure of the 30S subunit (2), bringing the shoulder domain into contact with EF-Tu and shifting the β loop at 230 to 237 of domain 2 (3). This changes the conformation of the acceptor end of the tRNA (4), disrupting its contacts with switch I, which becomes disordered (5), opening the hydrophobic gate to allow His^84 to catalyze GTP hydrolysis. (D) GTP hydrolysis and P[i] release cause domain rearrangement of EF-Tu, leading to its release from the ribosome and (E and F) accommodation of aminoacyl-tRNA.
 
  The above figures are reprinted by permission from the AAAs: Science (2009, 326, 688-694) copyright 2009.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22245970 D.Takeshita, and K.Tomita (2012).
Molecular basis for RNA polymerization by Qβ replicase.
  Nat Struct Mol Biol, 19, 229-237.
PDB codes: 3avt 3avu 3avv 3avw 3avx 3avy
22337051 E.A.Dethoff, J.Chugh, A.M.Mustoe, and H.M.Al-Hashimi (2012).
Functional complexity and regulation through RNA dynamics.
  Nature, 482, 322-330.  
22902368 L.Wang, A.Pulk, M.R.Wasserman, M.B.Feldman, R.B.Altman, J.H.Doudna Cate, and S.C.Blanchard (2012).
Allosteric control of the ribosome by small-molecule antibiotics.
  Nat Struct Mol Biol, 19, 957-963.
PDB codes: 4gaq 4gar 4gas 4gau
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.  
23072885 M.Graille, and B.Séraphin (2012).
Surveillance pathways rescuing eukaryotic ribosomes lost in translation.
  Nat Rev Mol Cell Biol, 13, 727-735.  
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.  
22437501 N.Demeshkina, L.Jenner, E.Westhof, M.Yusupov, and G.Yusupova (2012).
A new understanding of the decoding principle on the ribosome.
  Nature, 484, 256-259.
PDB codes: 3tve 3tvf 3tvg 3tvh 3uyd 3uye 3uyf 3uyg 3uz1 3uz2 3uz3 3uz4 3uz6 3uz7 3uz8 3uz9 3uzf 3uzg 3uzh 3uzi 3uzk 3uzl 3uzm 3uzn
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.  
21368145 A.S.Yassin, M.E.Haque, P.P.Datta, K.Elmore, N.K.Banavali, L.L.Spremulli, and R.K.Agrawal (2011).
Insertion domain within mammalian mitochondrial translation initiation factor 2 serves the role of eubacterial initiation factor 1.
  Proc Natl Acad Sci U S A, 108, 3918-3923.
PDB codes: 3izy 3izz
22002225 B.S.Shin, J.R.Kim, S.E.Walker, J.Dong, J.R.Lorsch, and T.E.Dever (2011).
Initiation factor eIF2γ promotes eIF2-GTP-Met-tRNAi(Met) ternary complex binding to the 40S ribosome.
  Nat Struct Mol Biol, 18, 1227-1234.  
21549313 C.Chen, B.Stevens, J.Kaur, D.Cabral, H.Liu, Y.Wang, H.Zhang, G.Rosenblum, Z.Smilansky, Y.E.Goldman, and B.S.Cooperman (2011).
Single-molecule fluorescence measurements of ribosomal translocation dynamics.
  Mol Cell, 42, 367-377.  
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.  
21402928 J.M.Schrader, S.J.Chapman, and O.C.Uhlenbeck (2011).
Tuning the affinity of aminoacyl-tRNA to elongation factor Tu for optimal decoding.
  Proc Natl Acad Sci U S A, 108, 5215-5220.  
21152913 K.Kulczycka, M.Długosz, and J.Trylska (2011).
Molecular dynamics of ribosomal elongation factors G and Tu.
  Eur Biophys J, 40, 289-303.  
21169502 M.Johansson, K.W.Ieong, S.Trobro, P.Strazewski, J.Åqvist, M.Y.Pavlov, and M.Ehrenberg (2011).
pH-sensitivity of the ribosomal peptidyl transfer reaction dependent on the identity of the A-site aminoacyl-tRNA.
  Proc Natl Acad Sci U S A, 108, 79-84.  
21151095 M.Y.Pavlov, A.Zorzet, D.I.Andersson, and M.Ehrenberg (2011).
Activation of initiation factor 2 by ligands and mutations for rapid docking of ribosomal subunits.
  EMBO J, 30, 289-301.  
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
21378964 T.M.Schmeing, R.M.Voorhees, A.C.Kelley, and V.Ramakrishnan (2011).
How mutations in tRNA distant from the anticodon affect the fidelity of decoding.
  Nat Struct Mol Biol, 18, 432-436.
PDB codes: 2y0u 2y0v 2y0w 2y0x 2y0y 2y0z 2y10 2y11 2y12 2y13 2y14 2y15 2y16 2y17 2y18 2y19
  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
20798060 D.Takeshita, and K.Tomita (2010).
Assembly of Q{beta} viral RNA polymerase with host translational elongation factors EF-Tu and -Ts.
  Proc Natl Acad Sci U S A, 107, 15733-15738.
PDB codes: 3agp 3agq
20603079 H.S.Zaher, and R.Green (2010).
Hyperaccurate and error-prone ribosomes exploit distinct mechanisms during tRNA selection.
  Mol Cell, 39, 110-120.  
20842102 I.Wohlgemuth, C.Pohl, and M.V.Rodnina (2010).
Optimization of speed and accuracy of decoding in translation.
  EMBO J, 29, 3701-3709.  
20033956 I.Zündorf, and T.Dingermann (2010).
[In Process Citation]
  Pharm Unserer Zeit, 39, 8-9.  
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.  
20876129 K.Kobayashi, I.Kikuno, K.Kuroha, K.Saito, K.Ito, R.Ishitani, T.Inada, and O.Nureki (2010).
Structural basis for mRNA surveillance by archaeal Pelota and GTP-bound EF1α complex.
  Proc Natl Acad Sci U S A, 107, 17575-17579.
PDB codes: 3agj 3wxm
20890290 L.Chen, D.Muhlrad, V.Hauryliuk, Z.Cheng, M.K.Lim, V.Shyp, R.Parker, and H.Song (2010).
Structure of the Dom34-Hbs1 complex and implications for no-go decay.
  Nat Struct Mol Biol, 17, 1233-1240.
PDB code: 3mca
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.  
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.  
20360392 M.A.Preston, and E.M.Phizicky (2010).
The requirement for the highly conserved G-1 residue of Saccharomyces cerevisiae tRNAHis can be circumvented by overexpression of tRNAHis and its synthetase.
  RNA, 16, 1068-1077.  
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.  
21079633 N.M.Reynolds, B.A.Lazazzera, and M.Ibba (2010).
Cellular mechanisms that control mistranslation.
  Nat Rev Microbiol, 8, 849-856.  
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.  
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
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.  
20623998 S.Palioura, J.Herkel, M.Simonović, A.W.Lohse, and D.Söll (2010).
Human SepSecS or SLA/LP: selenocysteine formation and autoimmune hepatitis.
  Biol Chem, 391, 771-776.  
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.  
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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