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PDBsum entry 3d5a
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protein dna_rna metals Protein-protein interface(s) links
Ribosome PDB id
3d5a

 

 

 

 

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Contents
Protein chains
234 a.a. *
206 a.a. *
208 a.a. *
151 a.a. *
101 a.a. *
155 a.a. *
138 a.a. *
127 a.a. *
98 a.a. *
119 a.a. *
124 a.a. *
117 a.a. *
60 a.a. *
88 a.a. *
83 a.a. *
99 a.a. *
70 a.a. *
78 a.a. *
99 a.a. *
24 a.a. *
354 a.a. *
DNA/RNA
Metals
_ZN ×2
_MG ×381
* Residue conservation analysis
Obsolete entry
PDB id:
3d5a
Name: Ribosome
Title: Structural basis for translation termination on the 70s ribosome. This file contains the 30s subunit, release factor 1 (rf1), two tRNA, and mRNA molecules of one 70s ribosome. The entire crystal structure contains two 70s ribosomes as described in remark 400.
Structure: 16s rrna. Chain: a. P and e-site tRNA(fmet). Chain: z, y. mRNA. Chain: v. Engineered: yes. 30s ribosomal protein s2. Chain: b.
Source: Thermus thermophilus. Organism_taxid: 262724. Strain: hb27. Escherichia coli. Organism_taxid: 562. Synthetic: yes. Strain: hb27
Resolution:
3.21Å     R-factor:   0.292     R-free:   0.319
Authors: M.Laurberg,H.Asahara,A.Korostelev,J.Zhu,S.Trakhanov,H.F.Noller
Key ref:
M.Laurberg et al. (2008). Structural basis for translation termination on the 70S ribosome. Nature, 454, 852-857. PubMed id: 18596689 DOI: 10.1038/nature07115
Date:
16-May-08     Release date:   07-Oct-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P62662  (RS2_THET2) -  Small ribosomal subunit protein uS2 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		256 a.a.
234 a.a.
Protein chain
Pfam   ArchSchema ?
P62663  (RS3_THET2) -  Small ribosomal subunit protein uS3 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		239 a.a.
206 a.a.
Protein chain
Pfam   ArchSchema ?
P62664  (RS4_THET2) -  Small ribosomal subunit protein uS4 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		209 a.a.
208 a.a.
Protein chain
Pfam   ArchSchema ?
P62665  (RS5_THET2) -  Small ribosomal subunit protein uS5 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		162 a.a.
151 a.a.
Protein chain
Pfam   ArchSchema ?
P62666  (RS6_THET2) -  Small ribosomal subunit protein bS6 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		101 a.a.
101 a.a.
Protein chain
Pfam   ArchSchema ?
P62667  (RS7_THET2) -  Small ribosomal subunit protein uS7 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		156 a.a.
155 a.a.
Protein chain
Pfam   ArchSchema ?
P62668  (RS8_THET2) -  Small ribosomal subunit protein uS8 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		138 a.a.
138 a.a.
Protein chain
Pfam   ArchSchema ?
P62669  (RS9_THET2) -  Small ribosomal subunit protein uS9 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		128 a.a.
127 a.a.
Protein chain
Pfam   ArchSchema ?
P62653  (RS10_THET2) -  Small ribosomal subunit protein uS10 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		105 a.a.
98 a.a.
Protein chain
Pfam   ArchSchema ?
P62654  (RS11_THET2) -  Small ribosomal subunit protein uS11 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		129 a.a.
119 a.a.
Protein chain
Pfam   ArchSchema ?
P61941  (RS12_THET2) -  Small ribosomal subunit protein uS12 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		132 a.a.
124 a.a.
Protein chain
Pfam   ArchSchema ?
P62655  (RS13_THET2) -  Small ribosomal subunit protein uS13 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		126 a.a.
117 a.a.
Protein chain
Pfam   ArchSchema ?
P62656  (RS14Z_THET2) -  Small ribosomal subunit protein uS14 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		61 a.a.
60 a.a.
Protein chain
Pfam   ArchSchema ?
P62657  (RS15_THET2) -  Small ribosomal subunit protein uS15 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		89 a.a.
88 a.a.
Protein chain
Pfam   ArchSchema ?
P62238  (RS16_THET2) -  Small ribosomal subunit protein bS16 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		88 a.a.
83 a.a.
Protein chain
Pfam   ArchSchema ?
P62658  (RS17_THET2) -  Small ribosomal subunit protein uS17 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		105 a.a.
99 a.a.
Protein chain
Pfam   ArchSchema ?
P62659  (RS18_THET2) -  Small ribosomal subunit protein bS18 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		88 a.a.
70 a.a.
Protein chain
Pfam   ArchSchema ?
P62660  (RS19_THET2) -  Small ribosomal subunit protein uS19 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		93 a.a.
78 a.a.
Protein chain
Pfam   ArchSchema ?
P62661  (RS20_THET2) -  Small ribosomal subunit protein bS20 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		106 a.a.
99 a.a.
Protein chain
Pfam   ArchSchema ?
P62613  (RSHX_THET2) -  Small ribosomal subunit protein bTHX from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		27 a.a.
24 a.a.
Protein chain
Pfam   ArchSchema ?
Q72HB8  (RF1_THET2) -  Peptide chain release factor 1 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		354 a.a.
354 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
  C-G-C-G-G-G-G-U-G-G-A-G-C-A-G-C-C-U-G-G-U-A-G-C-U-C-G-U-C-G-G-G-C-U-C-A-U-A-A- 77 bases
  A-A-A-A-A-U-G-U-A-A-A-A 12 bases
  C-G-C-G-G-G-G-U-G-G-A-G-C-A-G-C-C-U-G-G-U-A-G-C-U-C-G-U-C-G-G-G-C-U-C-A-U-A-A- 77 bases

 

 
DOI no: 10.1038/nature07115 Nature 454:852-857 (2008)
PubMed id: 18596689  
 
 
Structural basis for translation termination on the 70S ribosome.
M.Laurberg, H.Asahara, A.Korostelev, J.Zhu, S.Trakhanov, H.F.Noller.
 
  ABSTRACT  
 
At termination of protein synthesis, type I release factors promote hydrolysis of the peptidyl-transfer RNA linkage in response to recognition of a stop codon. Here we describe the crystal structure of the Thermus thermophilus 70S ribosome in complex with the release factor RF1, tRNA and a messenger RNA containing a UAA stop codon, at 3.2 A resolution. The stop codon is recognized in a pocket formed by conserved elements of RF1, including its PxT recognition motif, and 16S ribosomal RNA. The codon and the 30S subunit A site undergo an induced fit that results in stabilization of a conformation of RF1 that promotes its interaction with the peptidyl transferase centre. Unexpectedly, the main-chain amide group of Gln 230 in the universally conserved GGQ motif of the factor is positioned to contribute directly to peptidyl-tRNA hydrolysis.
 
  Selected figure(s)  
 
Figure 3.
Figure 3: Interactions of the GGQ region of RF1 in the PTC. a, Stereo view of [A]-weighted 3F[obs]–2F[calc] electron density for RF1 (yellow), P-site tRNA (orange) and 23S rRNA (grey) contoured at 1.7 . b, Position of Gln 230. c, Model for product stabilization by hydrogen bonding between the main-chain amide of Gln 230 and the 3'-OH of A76 of the P-site tRNA. d, Superposition of a peptidyl-transferase transition-state analogue (TSA, orange) complexed with the 50S subunit (grey)^25 on the structure of the termination complex (this work). The main-chain amide of Gln 230 is positioned to hydrogen bond with the oxyanion of the TSA. e, Model for transition-state stabilization. 		Figure 4.
Figure 4: Stereo view of the RF1 binding pocket for 23S rRNA nucleotide A2602. 23S rRNA is shown in grey, P-site tRNA in orange and RF1 in yellow.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2008, 454, 852-857) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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
21420300 B.P.Klaholz (2011).
Molecular recognition and catalysis in translation termination complexes.
  Trends Biochem Sci, 36, 282-292.  
21245352 J.Zhu, A.Korostelev, D.A.Costantino, J.P.Donohue, H.F.Noller, and J.S.Kieft (2011).
Crystal structures of complexes containing domains from two viral internal ribosome entry site (IRES) RNAs bound to the 70S ribosome.
  Proc Natl Acad Sci U S A, 108, 1839-1844.
PDB codes: 3pyn 3pyo 3pyq 3pyr 3pys 3pyt 3pyu 3pyv
21281690 K.Kipper, S.Sild, C.Hetényi, J.Remme, and A.Liiv (2011).
Pseudouridylation of 23S rRNA helix 69 promotes peptide release by release factor RF2 but not by release factor RF1.
  Biochimie, 93, 834-844.  
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.  
21804565 S.Kuhlenkoetter, W.Wintermeyer, and M.V.Rodnina (2011).
Different substrate-dependent transition states in the active site of the ribosome.
  Nature, 476, 351-354.  
  21418110 Y.Chadani, K.Ono, K.Kutsukake, and T.Abo (2011).
Escherichia coli YaeJ protein mediates a novel ribosome-rescue pathway distinct from SsrA- and ArfA-mediated pathways.
  Mol Microbiol, 80, 772-785.  
21051357 Y.Handa, N.Inaho, and N.Nameki (2011).
YaeJ is a novel ribosome-associated protein in Escherichia coli that can hydrolyze peptidyl-tRNA on stalled ribosomes.
  Nucleic Acids Res, 39, 1739-1748.  
21109664 A.Ben-Shem, L.Jenner, G.Yusupova, and M.Yusupov (2010).
Crystal structure of the eukaryotic ribosome.
  Science, 330, 1203-1209.
PDB codes: 3o2z 3o30 3o58 3o5h
20588254 A.Korostelev, J.Zhu, H.Asahara, and H.F.Noller (2010).
Recognition of the amber UAG stop codon by release factor RF1.
  EMBO J, 29, 2577-2585.
PDB codes: 3mr8 3mrz 3ms0 3ms1
20359191 D.A.Hiller, M.Zhong, V.Singh, and S.A.Strobel (2010).
Transition states of uncatalyzed hydrolysis and aminolysis reactions of a ribosomal P-site substrate determined by kinetic isotope effects.
  Biochemistry, 49, 3868-3878.  
20584893 D.J.Young, C.D.Edgar, E.S.Poole, and W.P.Tate (2010).
The codon specificity of eubacterial release factors is determined by the sequence and size of the recognition loop.
  RNA, 16, 1623-1633.  
20421313 D.J.Young, C.D.Edgar, J.Murphy, J.Fredebohm, E.S.Poole, and W.P.Tate (2010).
Bioinformatic, structural, and functional analyses support release factor-like MTRF1 as a protein able to decode nonstandard stop codons beginning with adenine in vertebrate mitochondria.
  RNA, 16, 1146-1155.  
20421507 H.Jin, A.C.Kelley, D.Loakes, and V.Ramakrishnan (2010).
Structure of the 70S ribosome bound to release factor 2 and a substrate analog provides insights into catalysis of peptide release.
  Proc Natl Acad Sci U S A, 107, 8593-8598.
PDB codes: 2x9r 2x9s 2x9t 2x9u
20603079 H.S.Zaher, and R.Green (2010).
Hyperaccurate and error-prone ribosomes exploit distinct mechanisms during tRNA selection.
  Mol Cell, 39, 110-120.  
20507916 I.Besseová, K.Réblová, N.B.Leontis, and J.Sponer (2010).
Molecular dynamics simulations suggest that RNA three-way junctions can act as flexible RNA structural elements in the ribosome.
  Nucleic Acids Res, 38, 6247-6264.  
20192776 J.A.Dunkle, and J.H.Cate (2010).
Ribosome structure and dynamics during translocation and termination.
  Annu Rev Biophys, 39, 227-244.  
20512119 J.Sund, M.Andér, and J.Aqvist (2010).
Principles of stop-codon reading on the ribosome.
  Nature, 465, 947-950.  
20974926 K.Saito, K.Kobayashi, M.Wada, I.Kikuno, A.Takusagawa, M.Mochizuki, T.Uchiumi, R.Ishitani, O.Nureki, and K.Ito (2010).
Omnipotent role of archaeal elongation factor 1 alpha (EF1α in translational elongation and termination, and quality control of protein synthesis.
  Proc Natl Acad Sci U S A, 107, 19242-19247.
PDB code: 3agk
20400952 L.B.Jenner, N.Demeshkina, G.Yusupova, and M.Yusupov (2010).
Structural aspects of messenger RNA reading frame maintenance by the ribosome.
  Nat Struct Mol Biol, 17, 555-560.
PDB codes: 3i8f 3i8g 3i8h 3i8i 3i9b 3i9c 3i9d 3i9e
20631789 M.Ehrenberg (2010).
Protein synthesis: Translocation in slow motion.
  Nature, 466, 325-326.  
19962317 M.V.Rodnina, and W.Wintermeyer (2010).
The ribosome goes Nobel.
  Trends Biochem Sci, 35, 1-5.  
20154709 R.E.Stanley, G.Blaha, R.L.Grodzicki, M.D.Strickler, and T.A.Steitz (2010).
The structures of the anti-tuberculosis antibiotics viomycin and capreomycin bound to the 70S ribosome.
  Nat Struct Mol Biol, 17, 289-293.
PDB codes: 3knh 3kni 3knj 3knk 3knl 3knm 3knn 3kno
20186120 R.Richter, J.Rorbach, A.Pajak, P.M.Smith, H.J.Wessels, M.A.Huynen, J.A.Smeitink, R.N.Lightowlers, and Z.M.Chrzanowska-Lightowlers (2010).
A functional peptidyl-tRNA hydrolase, ICT1, has been recruited into the human mitochondrial ribosome.
  EMBO J, 29, 1116-1125.  
19965768 S.Kimura, and T.Suzuki (2010).
Fine-tuning of the ribosomal decoding center by conserved methyl-modifications in the Escherichia coli 16S rRNA.
  Nucleic Acids Res, 38, 1341-1352.  
20208546 S.L.He, and R.Green (2010).
Visualization of codon-dependent conformational rearrangements during translation termination.
  Nat Struct Mol Biol, 17, 465-470.  
19822758 A.Korostelev, M.Laurberg, and H.F.Noller (2009).
Multistart simulated annealing refinement of the crystal structure of the 70S ribosome.
  Proc Natl Acad Sci U S A, 106, 18195-18200.  
19656820 A.Yonath (2009).
Large facilities and the evolving ribosome, the cellular machine for genetic-code translation.
  J R Soc Interface, 6, S575-S585.  
19761774 B.D.Janssen, and C.S.Hayes (2009).
Kinetics of paused ribosome recycling in Escherichia coli.
  J Mol Biol, 394, 251-267.  
19874047 B.Hetrick, K.Lee, and S.Joseph (2009).
Kinetics of stop codon recognition by release factor 1.
  Biochemistry, 48, 11178-11184.  
20005802 C.Neubauer, Y.G.Gao, K.R.Andersen, C.M.Dunham, A.C.Kelley, J.Hentschel, K.Gerdes, V.Ramakrishnan, and D.E.Brodersen (2009).
The structural basis for mRNA recognition and cleavage by the ribosome-dependent endonuclease RelE.
  Cell, 139, 1084-1095.
PDB codes: 3kha 3kiq 3kir 3kis 3kit 3kiu 3kiw 3kix 3kiy
19019162 E.Diago-Navarro, L.Mora, R.H.Buckingham, R.Díaz-Orejas, and M.Lemonnier (2009).
Novel Escherichia coli RF1 mutants with decreased translation termination activity and increased sensitivity to the cytotoxic effect of the bacterial toxins Kid and RelE.
  Mol Microbiol, 71, 66-78.  
19156357 F.Cava, A.Hidalgo, and J.Berenguer (2009).
Thermus thermophilus as biological model.
  Extremophiles, 13, 213-231.  
19239893 H.S.Zaher, and R.Green (2009).
Fidelity at the molecular level: lessons from protein synthesis.
  Cell, 136, 746-762.  
19129838 K.Fredrick, and M.Ibba (2009).
Protein synthesis: Errors rectified in retrospect.
  Nature, 457, 157-158.  
19603183 M.O'Connor (2009).
Helix 69 in 23S rRNA modulates decoding by wild type and suppressor tRNAs.
  Mol Genet Genomics, 282, 371-380.  
19339279 M.Prestele, F.Vogel, A.S.Reichert, J.M.Herrmann, and M.Ott (2009).
Mrpl36 Is Important for Generation of Assembly Competent Proteins during Mitochondrial Translation.
  Mol Biol Cell, 20, 2615-2625.  
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.  
19222865 P.B.Moore (2009).
The ribosome returned.
  J Biol, 8, 8.  
19240333 R.F.Fischetti, S.Xu, D.W.Yoder, M.Becker, V.Nagarajan, R.Sanishvili, M.C.Hilgart, S.Stepanov, O.Makarov, and J.L.Smith (2009).
Mini-beam collimator enables microcrystallography experiments on standard beamlines.
  J Synchrotron Radiat, 16, 217-225.  
19363482 R.M.Voorhees, A.Weixlbaumer, D.Loakes, A.C.Kelley, and V.Ramakrishnan (2009).
Insights into substrate stabilization from snapshots of the peptidyl transferase center of the intact 70S ribosome.
  Nat Struct Mol Biol, 16, 528-533.
PDB codes: 2wdg 2wdh 2wdi 2wdj 2wdk 2wdl 2wdm 2wdn
19597483 S.H.Sternberg, J.Fei, N.Prywes, K.A.McGrath, and R.L.Gonzalez (2009).
Translation factors direct intrinsic ribosome dynamics during translation termination and ribosome recycling.
  Nat Struct Mol Biol, 16, 861-868.  
19838167 T.M.Schmeing, and V.Ramakrishnan (2009).
What recent ribosome structures have revealed about the mechanism of translation.
  Nature, 461, 1234-1242.  
19696352 W.Zhang, J.A.Dunkle, and J.H.Cate (2009).
Structures of the ribosome in intermediate states of ratcheting.
  Science, 325, 1014-1017.
PDB codes: 3i1m 3i1n 3i1o 3i1p 3i1q 3i1r 3i1s 3i1t 3i1z 3i20 3i21 3i22
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.  
19417105 Z.Cheng, K.Saito, A.V.Pisarev, M.Wada, V.P.Pisareva, T.V.Pestova, M.Gajda, A.Round, C.Kong, M.Lim, Y.Nakamura, D.I.Svergun, K.Ito, and H.Song (2009).
Structural insights into eRF3 and stop codon recognition by eRF1.
  Genes Dev, 23, 1106-1118.
PDB codes: 3e1y 3e20
18848900 A.Korostelev, D.N.Ermolenko, and H.F.Noller (2008).
Structural dynamics of the ribosome.
  Curr Opin Chem Biol, 12, 674-683.  
19064930 A.Korostelev, H.Asahara, L.Lancaster, M.Laurberg, A.Hirschi, J.Zhu, S.Trakhanov, W.G.Scott, and H.F.Noller (2008).
Crystal structure of a translation termination complex formed with release factor RF2.
  Proc Natl Acad Sci U S A, 105, 19684-19689.
PDB codes: 3f1e 3f1f 3f1g 3f1h
18988853 A.Weixlbaumer, H.Jin, C.Neubauer, R.M.Voorhees, S.Petry, A.C.Kelley, and V.Ramakrishnan (2008).
Insights into translational termination from the structure of RF2 bound to the ribosome.
  Science, 322, 953-956.
PDB codes: 2jl5 2jl6 2jl7 2jl8 2wh1 2wh2 2wh3 2wh4
19436497 E.H.Egelman (2008).
Problems in fitting high resolution structures into electron microscopic reconstructions.
  HFSP J, 2, 324-331.  
18818369 M.Simonović, and T.A.Steitz (2008).
Peptidyl-CCA deacylation on the ribosome promoted by induced fit and the O3'-hydroxyl group of A76 of the unacylated A-site tRNA.
  RNA, 14, 2372-2378.
PDB codes: 3cma 3cme
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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