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PDBsum entry 1kqs
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protein dna_rna ligands metals Protein-protein interface(s) links
Ribosome PDB id
1kqs

 

 

 

 

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JSmol PyMol  
Contents
Protein chains
237 a.a. *
337 a.a. *
246 a.a. *
140 a.a. *
172 a.a. *
119 a.a. *
29 a.a. *
156 a.a. *
142 a.a. *
132 a.a. *
145 a.a. *
194 a.a. *
186 a.a. *
115 a.a. *
143 a.a. *
95 a.a. *
150 a.a. *
81 a.a. *
119 a.a. *
53 a.a. *
65 a.a. *
154 a.a. *
82 a.a. *
142 a.a. *
73 a.a. *
56 a.a. *
46 a.a. *
92 a.a. *
DNA/RNA
Ligands
_DC-_DC
PPU-PHA-ACA-BTN
Metals
_CL ×22
_NA ×86
_MG ×117
_CD ×5
__K ×2
Waters ×7871
* Residue conservation analysis
PDB id:
1kqs
Name: Ribosome
Title: The haloarcula marismortui 50s complexed with a pretranslocational intermediate in protein synthesis
Structure: 23s rrna. Chain: 0. 5s rrna. Chain: 9. Cca. Chain: 3. Engineered: yes. Other_details: RNA analogue of 3' of deacylated-tRNA. Cc-pmn-pcb.
Source: Haloarcula marismortui. Organism_taxid: 2238. Synthetic: yes. Other_details: solid phase synthesis. Other_details: solid phase synthesis, followed by peptidyl transferase reaction.. Organism_taxid: 2238
Resolution:
3.10Å     R-factor:   0.173     R-free:   0.220
Authors: T.M.Schmeing,A.C.Seila,J.L.Hansen,B.Freeborn,J.K.Soukup,S.A.Scaringe, S.A.Strobel,P.B.Moore,T.A.Steitz
Key ref:
T.M.Schmeing et al. (2002). A pre-translocational intermediate in protein synthesis observed in crystals of enzymatically active 50S subunits. Nat Struct Biol, 9, 225-230. PubMed id: 11828326 DOI: 10.1038/nsb767
Date:
07-Jan-02     Release date:   22-Feb-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P20276  (RL2_HALMA) -  Large ribosomal subunit protein uL2 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		240 a.a.
237 a.a.*
Protein chain
Pfam   ArchSchema ?
P20279  (RL3_HALMA) -  Large ribosomal subunit protein uL3 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		338 a.a.
337 a.a.
Protein chain
Pfam   ArchSchema ?
P12735  (RL4_HALMA) -  Large ribosomal subunit protein uL4 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		246 a.a.
246 a.a.*
Protein chain
Pfam   ArchSchema ?
P14124  (RL5_HALMA) -  Large ribosomal subunit protein uL5 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		177 a.a.
140 a.a.
Protein chain
Pfam   ArchSchema ?
P14135  (RL6_HALMA) -  Large ribosomal subunit protein uL6 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		178 a.a.
172 a.a.
Protein chain
Pfam   ArchSchema ?
P12743  (RL7A_HALMA) -  Large ribosomal subunit protein eL8 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		120 a.a.
119 a.a.*
Protein chain
Pfam   ArchSchema ?
P15825  (RL10_HALMA) -  Large ribosomal subunit protein uL10 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		348 a.a.
29 a.a.*
Protein chain
Pfam   ArchSchema ?
P60617  (RL10E_HALMA) -  Large ribosomal subunit protein uL16 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		177 a.a.
156 a.a.*
Protein chain
Pfam   ArchSchema ?
P29198  (RL13_HALMA) -  Large ribosomal subunit protein uL13 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		145 a.a.
142 a.a.
Protein chain
Pfam   ArchSchema ?
P22450  (RL14_HALMA) -  Large ribosomal subunit protein uL14 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		132 a.a.
132 a.a.
Protein chain
Pfam   ArchSchema ?
P12737  (RL15_HALMA) -  Large ribosomal subunit protein uL15 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		165 a.a.
145 a.a.
Protein chain
Pfam   ArchSchema ?
P60618  (RL15E_HALMA) -  Large ribosomal subunit protein eL15 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		196 a.a.
194 a.a.*
Protein chain
Pfam   ArchSchema ?
P14123  (RL18_HALMA) -  Large ribosomal subunit protein uL18 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		187 a.a.
186 a.a.
Protein chain
Pfam   ArchSchema ?
P12733  (RL18E_HALMA) -  Large ribosomal subunit protein eL18 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		116 a.a.
115 a.a.
Protein chain
Pfam   ArchSchema ?
P14119  (RL19E_HALMA) -  Large ribosomal subunit protein eL19 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		149 a.a.
143 a.a.*
Protein chain
Pfam   ArchSchema ?
P12734  (RL21_HALMA) -  Large ribosomal subunit protein eL21 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		96 a.a.
95 a.a.
Protein chain
Pfam   ArchSchema ?
P10970  (RL22_HALMA) -  Large ribosomal subunit protein uL22 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		155 a.a.
150 a.a.
Protein chain
Pfam   ArchSchema ?
P12732  (RL23_HALMA) -  Large ribosomal subunit protein uL23 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		85 a.a.
81 a.a.
Protein chain
Pfam   ArchSchema ?
P10972  (RL24_HALMA) -  Large ribosomal subunit protein uL24 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		120 a.a.
119 a.a.
Protein chain
Pfam   ArchSchema ?
P14116  (RL24E_HALMA) -  Large ribosomal subunit protein eL24 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		67 a.a.
53 a.a.
Protein chain
Pfam   ArchSchema ?
P10971  (RL29_HALMA) -  Large ribosomal subunit protein uL29 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		71 a.a.
65 a.a.
Protein chain
Pfam   ArchSchema ?
P14121  (RL30_HALMA) -  Large ribosomal subunit protein uL30 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		154 a.a.
154 a.a.
Protein chain
Pfam   ArchSchema ?
P18138  (RL31_HALMA) -  Large ribosomal subunit protein eL31 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		92 a.a.
82 a.a.
Protein chain
Pfam   ArchSchema ?
P12736  (RL32_HALMA) -  Large ribosomal subunit protein eL32 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		241 a.a.
142 a.a.
Protein chain
Pfam   ArchSchema ?
P60619  (RL37A_HALMA) -  Large ribosomal subunit protein eL43 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		92 a.a.
73 a.a.*
Protein chain
Pfam   ArchSchema ?
P32410  (RL37_HALMA) -  Large ribosomal subunit protein eL37 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		57 a.a.
56 a.a.
Protein chain
Pfam   ArchSchema ?
P22452  (RL39_HALMA) -  Large ribosomal subunit protein eL39 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		50 a.a.
46 a.a.*
Protein chain
Pfam   ArchSchema ?
P32411  (RL44E_HALMA) -  Large ribosomal subunit protein eL42 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		92 a.a.
92 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 185 residue positions (black crosses)

DNA/RNA chains
  U-A-U-G-C-C-A-G-C-U-G-G-U-G-G-A-U-U-G-C-U-C-G-G-C-U-C-A-G-G-C-G-C-U-G-A-U-G-A- ... 2754 bases
  U-U-A-G-G-C-G-G-C-C-A-C-A-G-C-G-G-U-G-G-G-G-U-U-G-C-C-U-C-C-C-G-U-A-C-C-C-A-U- 122 bases
  C-C-A 3 bases

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, 1, 2: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1038/nsb767 Nat Struct Biol 9:225-230 (2002)
PubMed id: 11828326  
 
 
A pre-translocational intermediate in protein synthesis observed in crystals of enzymatically active 50S subunits.
T.M.Schmeing, A.C.Seila, J.L.Hansen, B.Freeborn, J.K.Soukup, S.A.Scaringe, S.A.Strobel, P.B.Moore, T.A.Steitz.
 
  ABSTRACT  
 
The large ribosomal subunit catalyzes peptide bond formation during protein synthesis. Its peptidyl transferase activity has often been studied using a 'fragment assay' that depends on high concentrations of methanol or ethanol. Here we describe a version of this assay that does not require alcohol and use it to show, both crystallographically and biochemically, that crystals of the large ribosomal subunits from Haloarcula marismortui are enzymatically active. Addition of these crystals to solutions containing substrates results in formation of products, which ceases when crystals are removed. When substrates are diffused into large subunit crystals, the subsequent structure shows that products have formed. The CC-puromycin-peptide product is found bound to the A-site and the deacylated CCA is bound to the P-site, with its 3prime prime or minute OH near N3 A2486 (Escherichia coli A2451). Thus, this structure represents a state that occurs after peptide bond formation but before the hybrid state of protein synthesis.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Schematic of the modified fragment assay. The substrates are shown on the left. CCA-phenylalanine-caproic acid-biotin (CCA-pcb) and C-puromycin (C-pmn) undergo a ribosome-dependent reaction in which a peptide bond is formed between the -amino group of C-pmn and the carbonyl ester of the phenylalanine moiety of CCA-pcb, yielding the two products: C-puromycin-phenylalanine-caproic acid-biotin (C-pmn-pcb) and a deacylated CCA. 		Figure 4.
Figure 4. Structure of the new fragment reaction products bound to the ribosome. a, A space-filling representation of the 50S particle (RNA in white and protein in yellow) in complex with products, with the three tRNAs as they were observed^25 binding to the Thermus thermophilus 70S ribosome superimposed for reference. The subunit has been split through the tunnel, and the front half was removed to reveal the tunnel and the peptidyl transferase site (boxed). The orientation is the crown view, with the L1 protein to the left and the L7−L12 stalk to the right. b, A close-up view of the active site shows that the peptidyl-product (CC-Pmn-pcb) (green) binds the A-loop (yellow), whereas the deacylated product (CCA) (violet) base pairs to the P-loop (blue). The N3 of A2486 (A2451) (light blue) is in proximity to the 3' OH of the deacylated product, and the base of U2620 (U2585) (red) has moved near to the newly formed peptidyl ester link and the 3' OH of dimethyl A76.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2002, 9, 225-230) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
19929179 D.N.Wilson (2009).
The A-Z of bacterial translation inhibitors.
  Crit Rev Biochem Mol Biol, 44, 393-433.  
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.  
19479032 P.V.Baranov, M.Venin, and G.Provan (2009).
Codon size reduction as the origin of the triplet genetic code.
  PLoS One, 4, e5708.  
  19173642 S.Shoji, S.E.Walker, and K.Fredrick (2009).
Ribosomal translocation: one step closer to the molecular mechanism.
  ACS Chem Biol, 4, 93.  
19129224 T.Dale, R.P.Fahlman, M.Olejniczak, and O.C.Uhlenbeck (2009).
Specificity of the ribosomal A site for aminoacyl-tRNAs.
  Nucleic Acids Res, 37, 1202-1210.  
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.  
18482701 D.A.Kingery, E.Pfund, R.M.Voorhees, K.Okuda, I.Wohlgemuth, D.E.Kitchen, M.V.Rodnina, and S.A.Strobel (2008).
An uncharged amine in the transition state of the ribosomal peptidyl transfer reaction.
  Chem Biol, 15, 493-500.  
18455733 G.Blaha, G.Gürel, S.J.Schroeder, P.B.Moore, and T.A.Steitz (2008).
Mutations outside the anisomycin-binding site can make ribosomes drug-resistant.
  J Mol Biol, 379, 505-519.
PDB codes: 3cc2 3cc4 3cc7 3cce 3ccj 3ccl 3ccm 3ccq 3ccr 3ccs 3ccu 3ccv 3cd6
18625614 H.David-Eden, and Y.Mandel-Gutfreund (2008).
Revealing unique properties of the ribosome using a network based analysis.
  Nucleic Acids Res, 36, 4641-4652.  
18430893 J.C.Cochrane, and S.A.Strobel (2008).
Riboswitch effectors as protein enzyme cofactors.
  RNA, 14, 993.  
18187576 M.Simonović, and T.A.Steitz (2008).
Cross-crystal averaging reveals that the structure of the peptidyl-transferase center is the same in the 70S ribosome and the 50S subunit.
  Proc Natl Acad Sci U S A, 105, 500-505.  
18951087 X.Agirrezabala, J.Lei, J.L.Brunelle, R.F.Ortiz-Meoz, R.Green, and J.Frank (2008).
Visualization of the hybrid state of tRNA binding promoted by spontaneous ratcheting of the ribosome.
  Mol Cell, 32, 190-197.  
17693476 H.D.Kim, J.D.Puglisi, and S.Chu (2007).
Fluctuations of transfer RNAs between classical and hybrid states.
  Biophys J, 93, 3575-3582.  
17169991 H.R.Jonker, S.Ilin, S.K.Grimm, J.Wöhnert, and H.Schwalbe (2007).
L11 domain rearrangement upon binding to RNA and thiostrepton studied by NMR spectroscopy.
  Nucleic Acids Res, 35, 441-454.
PDB codes: 2jq7 2nyo
17499045 K.L.Leach, S.M.Swaney, J.R.Colca, W.G.McDonald, J.R.Blinn, L.M.Thomasco, R.C.Gadwood, D.Shinabarger, L.Xiong, and A.S.Mankin (2007).
The site of action of oxazolidinone antibiotics in living bacteria and in human mitochondria.
  Mol Cell, 26, 393-402.  
17293420 L.R.Cruz-Vera, A.New, C.Squires, and C.Yanofsky (2007).
Ribosomal features essential for tna operon induction: tryptophan binding at the peptidyl transferase center.
  J Bacteriol, 189, 3140-3146.  
17660192 M.Amort, B.Wotzel, K.Bakowska-Zywicka, M.D.Erlacher, R.Micura, and N.Polacek (2007).
An intact ribose moiety at A2602 of 23S rRNA is key to trigger peptidyl-tRNA hydrolysis during translation termination.
  Nucleic Acids Res, 35, 5130-5140.  
17570820 M.Beringer, and M.V.Rodnina (2007).
Importance of tRNA interactions with 23S rRNA for peptide bond formation on the ribosome: studies with substrate analogs.
  Biol Chem, 388, 687-691.  
17499039 M.Beringer, and M.V.Rodnina (2007).
The ribosomal peptidyl transferase.
  Mol Cell, 26, 311-321.  
17157507 M.V.Rodnina, M.Beringer, and W.Wintermeyer (2007).
How ribosomes make peptide bonds.
  Trends Biochem Sci, 32, 20-26.  
16962654 A.Korostelev, S.Trakhanov, M.Laurberg, and H.F.Noller (2006).
Crystal structure of a 70S ribosome-tRNA complex reveals functional interactions and rearrangements.
  Cell, 126, 1065-1077.
PDB codes: 1vsa 2ow8
16522645 A.Mokdad, M.V.Krasovska, J.Sponer, and N.B.Leontis (2006).
Structural and evolutionary classification of G/U wobble basepairs in the ribosome.
  Nucleic Acids Res, 34, 1326-1341.  
16990543 D.J.Klein, and A.R.Ferré-D'Amaré (2006).
Structural basis of glmS ribozyme activation by glucosamine-6-phosphate.
  Science, 313, 1752-1756.
PDB codes: 2gcs 2gcv 2h0s 2h0w 2h0x 2h0z 2ho6 2ho7
16799464 I.Wohlgemuth, M.Beringer, and M.V.Rodnina (2006).
Rapid peptide bond formation on isolated 50S ribosomal subunits.
  EMBO Rep, 7, 699-703.  
16373492 J.L.Brunelle, E.M.Youngman, D.Sharma, and R.Green (2006).
The interaction between C75 of tRNA and the A loop of the ribosome stimulates peptidyl transferase activity.
  RNA, 12, 33-39.  
16959973 M.Selmer, C.M.Dunham, F.V.Murphy, A.Weixlbaumer, S.Petry, A.C.Kelley, J.R.Weir, and V.Ramakrishnan (2006).
Structure of the 70S ribosome complexed with mRNA and tRNA.
  Science, 313, 1935-1942.
PDB codes: 2j00 2j01 2j02 2j03
17032763 N.S.Sato, N.Hirabayashi, I.Agmon, A.Yonath, and T.Suzuki (2006).
Comprehensive genetic selection revealed essential bases in the peptidyl-transferase center.
  Proc Natl Acad Sci U S A, 103, 15386-15391.  
16888324 S.Mansouri, E.Nourollahzadeh, and K.A.Hudak (2006).
Pokeweed antiviral protein depurinates the sarcin/ricin loop of the rRNA prior to binding of aminoacyl-tRNA to the ribosomal A-site.
  RNA, 12, 1683-1692.  
16553874 T.Tenson, and A.Mankin (2006).
Antibiotics and the ribosome.
  Mol Microbiol, 59, 1664-1677.  
16537400 W.H.McClain (2006).
Surprising contribution to aminoacylation and translation of non-Watson-Crick pairs in tRNA.
  Proc Natl Acad Sci U S A, 103, 4570-4575.  
16285924 B.A.Maguire, A.D.Beniaminov, H.Ramu, A.S.Mankin, and R.A.Zimmermann (2005).
A protein component at the heart of an RNA machine: the importance of protein l27 for the function of the bacterial ribosome.
  Mol Cell, 20, 427-435.  
16164408 I.Agmon, A.Bashan, R.Zarivach, and A.Yonath (2005).
Symmetry at the active site of the ribosome: structural and functional implications.
  Biol Chem, 386, 833-844.  
15870731 J.A.Doudna, and J.R.Lorsch (2005).
Ribozyme catalysis: not different, just worse.
  Nat Struct Mol Biol, 12, 395-402.  
15922593 J.Nilsson, and P.Nissen (2005).
Elongation factors on the ribosome.
  Curr Opin Struct Biol, 15, 349-354.  
16249344 K.Y.Sanbonmatsu, S.Joseph, and C.S.Tung (2005).
Simulating movement of tRNA into the ribosome during decoding.
  Proc Natl Acad Sci U S A, 102, 15854-15859.  
16061180 L.R.Cruz-Vera, S.Rajagopal, C.Squires, and C.Yanofsky (2005).
Features of ribosome-peptidyl-tRNA interactions essential for tryptophan induction of tna operon expression.
  Mol Cell, 19, 333-343.  
16177132 N.M.Abdi, and K.Fredrick (2005).
Contribution of 16S rRNA nucleotides forming the 30S subunit A and P sites to translation in Escherichia coli.
  RNA, 11, 1624-1632.  
16257828 N.Polacek, and A.S.Mankin (2005).
The ribosomal peptidyl transferase center: structure, function, evolution, inhibition.
  Crit Rev Biochem Mol Biol, 40, 285-311.  
16116099 S.Trobro, and J.Aqvist (2005).
Mechanism of peptide bond synthesis on the ribosome.
  Proc Natl Acad Sci U S A, 102, 12395-12400.  
16244128 T.Dale, and O.C.Uhlenbeck (2005).
Binding of misacylated tRNAs to the ribosomal A site.
  RNA, 11, 1610-1615.  
16285925 T.M.Schmeing, K.S.Huang, D.E.Kitchen, S.A.Strobel, and T.A.Steitz (2005).
Structural insights into the roles of water and the 2' hydroxyl of the P site tRNA in the peptidyl transferase reaction.
  Mol Cell, 20, 437-448.
PDB codes: 1vq4 1vq5 1vq8 1vq9 1vqk 1vql 1vqm 1vqo 1vqp
15141076 A.Sievers, M.Beringer, M.V.Rodnina, and R.Wolfenden (2004).
The ribosome as an entropy trap.
  Proc Natl Acad Sci U S A, 101, 7897-7901.  
15487937 A.Yonath, and A.Bashan (2004).
Ribosomal crystallography: initiation, peptide bond formation, and amino acid polymerization are hampered by antibiotics.
  Annu Rev Microbiol, 58, 233-251.  
15454463 C.S.Tung, and K.Y.Sanbonmatsu (2004).
Atomic model of the Thermus thermophilus 70S ribosome developed in silico.
  Biophys J, 87, 2714-2722.
PDB codes: 1twt 1twv
15317974 D.J.Klein, P.B.Moore, and T.A.Steitz (2004).
The contribution of metal ions to the structural stability of the large ribosomal subunit.
  RNA, 10, 1366-1379.  
14681589 D.Sharma, D.R.Southworth, and R.Green (2004).
EF-G-independent reactivity of a pre-translocation-state ribosome complex with the aminoacyl tRNA substrate puromycin supports an intermediate (hybrid) state of tRNA binding.
  RNA, 10, 102-113.  
15554968 F.Schlünzen, E.Pyetan, P.Fucini, A.Yonath, and J.M.Harms (2004).
Inhibition of peptide bond formation by pleuromutilins: the structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with tiamulin.
  Mol Microbiol, 54, 1287-1294.
PDB code: 1xbp
15475967 J.S.Weinger, K.M.Parnell, S.Dorner, R.Green, and S.A.Strobel (2004).
Substrate-assisted catalysis of peptide bond formation by the ribosome.
  Nat Struct Mol Biol, 11, 1101-1106.  
15385552 M.Lovmar, T.Tenson, and M.Ehrenberg (2004).
Kinetics of macrolide action: the josamycin and erythromycin cases.
  J Biol Chem, 279, 53506-53515.  
15121895 P.S.Klosterman, D.K.Hendrix, M.Tamura, S.R.Holbrook, and S.E.Brenner (2004).
Three-dimensional motifs from the SCOR, structural classification of RNA database: extruded strands, base triples, tetraloops and U-turns.
  Nucleic Acids Res, 32, 2342-2352.  
15317937 S.C.Blanchard, H.D.Kim, R.L.Gonzalez, J.D.Puglisi, and S.Chu (2004).
tRNA dynamics on the ribosome during translation.
  Proc Natl Acad Sci U S A, 101, 12893-12898.  
12535524 A.Bashan, I.Agmon, R.Zarivach, F.Schluenzen, J.Harms, R.Berisio, H.Bartels, F.Franceschi, T.Auerbach, H.A.Hansen, E.Kossoy, M.Kessler, and A.Yonath (2003).
Structural basis of the ribosomal machinery for peptide bond formation, translocation, and nascent chain progression.
  Mol Cell, 11, 91.
PDB codes: 1njm 1njn 1njo 1njp
12925991 A.Bashan, R.Zarivach, F.Schluenzen, I.Agmon, J.Harms, T.Auerbach, D.Baram, R.Berisio, H.Bartels, H.A.Hansen, P.Fucini, D.Wilson, M.Peretz, M.Kessler, and A.Yonath (2003).
Ribosomal crystallography: peptide bond formation and its inhibition.
  Biopolymers, 70, 19-41.  
14523918 A.Yonath (2003).
Structural insight into functional aspects of ribosomal RNA targeting.
  Chembiochem, 4, 1008-1017.  
12907716 C.M.Duarte, L.M.Wadley, and A.M.Pyle (2003).
RNA structure comparison, motif search and discovery using a reduced representation of RNA conformational space.
  Nucleic Acids Res, 31, 4755-4761.  
12458201 D.J.Scarlett, K.K.McCaughan, D.N.Wilson, and W.P.Tate (2003).
Mapping functionally important motifs SPF and GGQ of the decoding release factor RF2 to the Escherichia coli ribosome by hydroxyl radical footprinting. Implications for macromolecular mimicry and structural changes in RF2.
  J Biol Chem, 278, 15095-15104.  
12932345 D.R.Southworth, and R.Green (2003).
Ribosomal translocation: sparsomycin pushes the button.
  Curr Biol, 13, R652-R654.  
12554858 E.P.Plant, K.L.Jacobs, J.W.Harger, A.Meskauskas, J.L.Jacobs, J.L.Baxter, A.N.Petrov, and J.D.Dinman (2003).
The 9-A solution: how mRNA pseudoknots promote efficient programmed -1 ribosomal frameshifting.
  RNA, 9, 168-174.  
12787020 I.Agmon, T.Auerbach, D.Baram, H.Bartels, A.Bashan, R.Berisio, P.Fucini, H.A.Hansen, J.Harms, M.Kessler, M.Peretz, F.Schluenzen, A.Yonath, and R.Zarivach (2003).
On peptide bond formation, translocation, nascent protein progression and the regulatory properties of ribosomes. Derived on 20 October 2002 at the 28th FEBS Meeting in Istanbul.
  Eur J Biochem, 270, 2543-2556.  
12433929 J.Dresios, P.Panopoulos, K.Suzuki, and D.Synetos (2003).
A dispensable yeast ribosomal protein optimizes peptidyltransferase activity and affects translocation.
  J Biol Chem, 278, 3314-3322.  
12750524 K.Fredrick, and H.F.Noller (2003).
Catalysis of ribosomal translocation by sparsomycin.
  Science, 300, 1159-1162.  
12869702 M.Beringer, S.Adio, W.Wintermeyer, and M.Rodnina (2003).
The G2447A mutation does not affect ionization of a ribosomal group taking part in peptide bond formation.
  RNA, 9, 919-922.  
12831884 M.V.Rodnina, and W.Wintermeyer (2003).
Peptide bond formation on the ribosome: structure and mechanism.
  Curr Opin Struct Biol, 13, 334-340.  
12859903 M.Valle, A.Zavialov, J.Sengupta, U.Rawat, M.Ehrenberg, and J.Frank (2003).
Locking and unlocking of ribosomal motions.
  Cell, 114, 123-134.
PDB codes: 1pn6 1pn7 1pn8
12554855 P.B.Moore, and T.A.Steitz (2003).
After the ribosome structures: how does peptidyl transferase work?
  RNA, 9, 155-159.  
14527328 P.B.Moore, and T.A.Steitz (2003).
The structural basis of large ribosomal subunit function.
  Annu Rev Biochem, 72, 813-850.  
14602912 S.Dorner, C.Panuschka, W.Schmid, and A.Barta (2003).
Mononucleotide derivatives as ribosomal P-site substrates reveal an important contribution of the 2'-OH to activity.
  Nucleic Acids Res, 31, 6536-6542.  
12554856 S.Joseph (2003).
After the ribosome structure: how does translocation work?
  RNA, 9, 160-164.  
12932729 T.A.Steitz, and P.B.Moore (2003).
RNA, the first macromolecular catalyst: the ribosome is a ribozyme.
  Trends Biochem Sci, 28, 411-418.  
14561884 T.M.Schmeing, P.B.Moore, and T.A.Steitz (2003).
Structures of deacylated tRNA mimics bound to the E site of the large ribosomal subunit.
  RNA, 9, 1345-1352.
PDB codes: 1qvf 1qvg
12364595 I.Tozik, Q.Huang, C.Zwieb, and J.Eichler (2002).
Reconstitution of the signal recognition particle of the halophilic archaeon Haloferax volcanii.
  Nucleic Acids Res, 30, 4166-4175.  
12185246 J.L.Hansen, T.M.Schmeing, P.B.Moore, and T.A.Steitz (2002).
Structural insights into peptide bond formation.
  Proc Natl Acad Sci U S A, 99, 11670-11675.
PDB codes: 1m90 1q7y 1q81 1q82 1q86
12185248 K.M.Parnell, A.C.Seila, and S.A.Strobel (2002).
Evidence against stabilization of the transition state oxyanion by a pKa-perturbed RNA base in the peptidyl transferase center.
  Proc Natl Acad Sci U S A, 99, 11658-11663.  
12209000 M.C.Ganoza, M.C.Kiel, and H.Aoki (2002).
Evolutionary conservation of reactions in translation.
  Microbiol Mol Biol Rev, 66, 460.  
12403820 S.I.Chamberlin, E.J.Merino, and K.M.Weeks (2002).
Catalysis of amide synthesis by RNA phosphodiester and hydroxyl groups.
  Proc Natl Acad Sci U S A, 99, 14688-14693.  
12114023 W.A.Decatur, and M.J.Fournier (2002).
rRNA modifications and ribosome function.
  Trends Biochem Sci, 27, 344-351.  
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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