spacer
spacer

PDBsum entry 1vsa
Go to PDB code: 
protein dna_rna Protein-protein interface(s) links
Ribosome PDB id
1vsa

 

 

 

 

Loading ...

 
JSmol PyMol  
Contents
Protein chains
127 a.a. *
272 a.a. *
201 a.a. *
194 a.a. *
180 a.a. *
173 a.a. *
148 a.a. *
138 a.a. *
122 a.a. *
146 a.a. *
137 a.a. *
118 a.a. *
106 a.a. *
137 a.a. *
117 a.a. *
101 a.a. *
109 a.a. *
92 a.a. *
103 a.a. *
185 a.a. *
76 a.a. *
88 a.a. *
62 a.a. *
60 a.a. *
56 a.a. *
48 a.a. *
63 a.a. *
35 a.a. *
DNA/RNA
* Residue conservation analysis
Obsolete entry
PDB id:
1vsa
Name: Ribosome
Title: Crystal structure of a 70s ribosome-tRNA complex reveals functional interactions and rearrangements. This file, 1vsa, contains the 50s ribosome subunit. 30s ribosome subunit is in the file 2ow8
Structure: 23s large subunit ribosomal RNA. Chain: w. 5s large subunit ribosomal RNA. Chain: x. 50s ribosomal protein l1. Chain: a. 50s ribosomal protein l2. Chain: b. 50s ribosomal protein l3.
Source: Thermus thermophilus. Organism_taxid: 262724. Strain: hb27. Strain: hb27
Resolution:
3.71Å     R-factor:   0.349     R-free:   0.353
Authors: A.Korostelev,S.Trakhanov,M.Laurberg,H.F.Noller
Key ref:
A.Korostelev et al. (2006). Crystal structure of a 70S ribosome-tRNA complex reveals functional interactions and rearrangements. Cell, 126, 1065-1077. PubMed id: 16962654 DOI: 10.1016/j.cell.2006.08.032
Date:
15-Feb-07     Release date:   15-May-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q72GV9  (RL1_THET2) -  50S ribosomal protein L1 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		229 a.a.
127 a.a.
Protein chain
Pfam   ArchSchema ?
Q72I07  (RL2_THET2) -  50S ribosomal protein L2 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		276 a.a.
272 a.a.
Protein chain
Pfam   ArchSchema ?
Q72I04  (RL3_THET2) -  50S ribosomal protein L3 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		206 a.a.
201 a.a.
Protein chain
Pfam   ArchSchema ?
Q72I05  (RL4_THET2) -  50S ribosomal protein L4 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		205 a.a.
194 a.a.
Protein chain
Pfam   ArchSchema ?
Q72I16  (RL5_THET2) -  50S ribosomal protein L5 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		182 a.a.
180 a.a.
Protein chain
Pfam   ArchSchema ?
Q72I19  (RL6_THET2) -  50S ribosomal protein L6 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		180 a.a.
173 a.a.
Protein chain
Pfam   ArchSchema ?
Q72GV5  (RL9_THET2) -  50S ribosomal protein L9 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		148 a.a.
148 a.a.
Protein chain
Pfam   ArchSchema ?
Q72IN1  (RL13_THET2) -  50S ribosomal protein L13 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		140 a.a.
138 a.a.*
Protein chain
Pfam   ArchSchema ?
Q72I14  (RL14_THET2) -  50S ribosomal protein L14 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		122 a.a.
122 a.a.
Protein chain
Pfam   ArchSchema ?
Q72I23  (RL15_THET2) -  50S ribosomal protein L15 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		150 a.a.
146 a.a.
Protein chain
Pfam   ArchSchema ?
Q72I11  (RL16_THET2) -  50S ribosomal protein L16 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		141 a.a.
137 a.a.
Protein chain
Pfam   ArchSchema ?
Q72I33  (RL17_THET2) -  50S ribosomal protein L17 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		118 a.a.
118 a.a.
Protein chain
Pfam   ArchSchema ?
Q72I20  (RL18_THET2) -  50S ribosomal protein L18 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		112 a.a.
106 a.a.
Protein chain
Pfam   ArchSchema ?
Q72JU9  (RL19_THET2) -  50S ribosomal protein L19 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		146 a.a.
137 a.a.
Protein chain
Pfam   ArchSchema ?
Q72L76  (RL20_THET2) -  50S ribosomal protein L20 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		118 a.a.
117 a.a.
Protein chain
Pfam   ArchSchema ?
Q72HR2  (RL21_THET2) -  50S ribosomal protein L21 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		101 a.a.
101 a.a.
Protein chain
Pfam   ArchSchema ?
Q72I09  (RL22_THET2) -  50S ribosomal protein L22 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		113 a.a.
109 a.a.
Protein chain
Pfam   ArchSchema ?
Q72I06  (Q72I06_THET2) -  50S ribosomal protein L23 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		96 a.a.
92 a.a.
Protein chain
Pfam   ArchSchema ?
Q72I15  (RL24_THET2) -  50S ribosomal protein L24 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		110 a.a.
103 a.a.
Protein chain
Pfam   ArchSchema ?
Q72IA7  (RL25_THET2) -  50S ribosomal protein L25 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		206 a.a.
185 a.a.
Protein chain
Pfam   ArchSchema ?
Q72HR3  (RL27_THET2) -  50S ribosomal protein L27 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		85 a.a.
76 a.a.
Protein chain
Pfam   ArchSchema ?
Q72G84  (Q72G84_THET2) -  50S ribosomal protein L28 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		98 a.a.
88 a.a.
Protein chain
Pfam   ArchSchema ?
Q72I12  (RL29_THET2) -  50S ribosomal protein L29 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		72 a.a.
62 a.a.
Protein chain
Pfam   ArchSchema ?
Q72I22  (Q72I22_THET2) -  50S ribosomal protein L30 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		60 a.a.
60 a.a.
Protein chain
Pfam   ArchSchema ?
P62652  (RL32_THET2) -  50S ribosomal protein L32 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		60 a.a.
56 a.a.
Protein chain
Pfam   ArchSchema ?
P80340  (RL34_THET8) -  50S ribosomal protein L34 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		49 a.a.
48 a.a.
Protein chain
Pfam   ArchSchema ?
Q72L77  (RL35_THET2) -  50S ribosomal protein L35 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		65 a.a.
63 a.a.
Protein chain
Pfam   ArchSchema ?
Q72I28  (RL36_THET2) -  50S ribosomal protein L36 from Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
Seq:
Struc: 		37 a.a.
35 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chains
  G-G-U-C-A-A-G-A-U-G-G-U-A-A-G-G-G-C-C-C-A-C-G-G-U-G-G-A-U-G-C-C-U-C-G-G-C-A-C- ... 2889 bases
  U-C-C-C-C-C-G-U-G-C-C-C-A-U-A-G-C-G-G-C-G-U-G-G-A-A-C-C-A-C-C-C-G-U-U-C-C-C-A- 120 bases

 

 
DOI no: 10.1016/j.cell.2006.08.032 Cell 126:1065-1077 (2006)
PubMed id: 16962654  
 
 
Crystal structure of a 70S ribosome-tRNA complex reveals functional interactions and rearrangements.
A.Korostelev, S.Trakhanov, M.Laurberg, H.F.Noller.
 
  ABSTRACT  
 
Our understanding of the mechanism of protein synthesis has undergone rapid progress in recent years as a result of low-resolution X-ray and cryo-EM structures of ribosome functional complexes and high-resolution structures of ribosomal subunits and vacant ribosomes. Here, we present the crystal structure of the Thermus thermophilus 70S ribosome containing a model mRNA and two tRNAs at 3.7 A resolution. Many structural details of the interactions between the ribosome, tRNA, and mRNA in the P and E sites and the ways in which tRNA structure is distorted by its interactions with the ribosome are seen. Differences between the conformations of vacant and tRNA-bound 70S ribosomes suggest an induced fit of the ribosome structure in response to tRNA binding, including significant changes in the peptidyl-transferase catalytic site.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. Interactions between the CCA Tail of tRNA and the 50S E Site 		Figure 5.
Figure 5. Distortion of tRNA Structure in the P and E Sites
 
  The above figures are reprinted by permission from Cell Press: Cell (2006, 126, 1065-1077) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21399643 D.N.Ermolenko, and H.F.Noller (2011).
mRNA translocation occurs during the second step of ribosomal intersubunit rotation.
  Nat Struct Mol Biol, 18, 457-462.  
21382609 I.Capek (2011).
Dispersions based on noble metal nanoparticles-DNA conjugates.
  Adv Colloid Interface Sci, 163, 123-143.  
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.  
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
21217697 S.Feng, H.Li, J.Zhao, K.Pervushin, K.Lowenhaupt, T.U.Schwartz, and P.Dröge (2011).
Alternate rRNA secondary structures as regulators of translation.
  Nat Struct Mol Biol, 18, 169-176.
PDB code: 2l54
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
20048003 A.K.Saini, J.S.Nanda, J.R.Lorsch, and A.G.Hinnebusch (2010).
Regulatory elements in eIF1A control the fidelity of start codon selection by modulating tRNA(i)(Met) binding to the ribosome.
  Genes Dev, 24, 97.  
20660012 A.Meskauskas, and J.D.Dinman (2010).
A molecular clamp ensures allosteric coordination of peptidyltransfer and ligand binding to the ribosomal A-site.
  Nucleic Acids Res, 38, 7800-7813.  
19962967 B.E.Christian, M.E.Haque, and L.L.Spremulli (2010).
The effect of spermine on the initiation of mitochondrial protein synthesis.
  Biochem Biophys Res Commun, 391, 942-946.  
20562856 C.E.Aitken, and J.D.Puglisi (2010).
Following the intersubunit conformation of the ribosome during translation in real time.
  Nat Struct Mol Biol, 17, 793-800.  
20457746 H.Asahara, and S.Chong (2010).
In vitro genetic reconstruction of bacterial transcription initiation by coupled synthesis and detection of RNA polymerase holoenzyme.
  Nucleic Acids Res, 38, e141.  
20192776 J.A.Dunkle, and J.H.Cate (2010).
Ribosome structure and dynamics during translocation and termination.
  Annu Rev Biophys, 39, 227-244.  
20018653 J.B.Munro, R.B.Altman, C.S.Tung, J.H.Cate, K.Y.Sanbonmatsu, and S.C.Blanchard (2010).
Spontaneous formation of the unlocked state of the ribosome is a multistep process.
  Proc Natl Acad Sci U S A, 107, 709-714.  
20033061 J.B.Munro, R.B.Altman, C.S.Tung, K.Y.Sanbonmatsu, and S.C.Blanchard (2010).
A fast dynamic mode of the EF-G-bound ribosome.
  EMBO J, 29, 770-781.  
19897649 J.Crandall, M.Rodriguez-Lopez, M.Pfeiffer, B.Mortensen, and A.Buskirk (2010).
rRNA mutations that inhibit transfer-messenger RNA activity on stalled ribosomes.
  J Bacteriol, 192, 553-559.  
20159470 J.F.Flanagan, O.Namy, I.Brierley, and R.J.Gilbert (2010).
Direct observation of distinct A/P hybrid-state tRNAs in translocating ribosomes.
  Structure, 18, 257-264.  
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.  
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
19946275 M.B.Feldman, D.S.Terry, R.B.Altman, and S.C.Blanchard (2010).
Aminoglycoside activity observed on single pre-translocation ribosome complexes.
  Nat Chem Biol, 6, 54-62.  
19962317 M.V.Rodnina, and W.Wintermeyer (2010).
The ribosome goes Nobel.
  Trends Biochem Sci, 35, 1-5.  
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.  
19914248 P.Khade, and S.Joseph (2010).
Functional interactions by transfer RNAs in the ribosome.
  FEBS Lett, 584, 420-426.  
20354152 P.Sharma, M.Chawla, S.Sharma, and A.Mitra (2010).
On the role of Hoogsteen:Hoogsteen interactions in RNA: ab initio investigations of structures and energies.
  RNA, 16, 942-957.  
20419210 S.De, K.Mahata, and M.Schmittel (2010).
Metal-coordination-driven dynamic heteroleptic architectures.
  Chem Soc Rev, 39, 1555-1575.  
19925799 S.E.Kolitz, and J.R.Lorsch (2010).
Eukaryotic initiator tRNA: finely tuned and ready for action.
  FEBS Lett, 584, 396-404.  
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.  
20151411 X.Ge, and B.Roux (2010).
Calculation of the standard binding free energy of sparsomycin to the ribosomal peptidyl-transferase P-site using molecular dynamics simulations with restraining potentials.
  J Mol Recognit, 23, 128-141.  
  20101632 Y.M.Hou (2010).
CCA addition to tRNA: implications for tRNA quality control.
  IUBMB Life, 62, 251-260.  
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.  
19416977 A.S.Spirin (2009).
The ribosome as a conveying thermal ratchet machine.
  J Biol Chem, 284, 21103-21119.  
19656820 A.Yonath (2009).
Large facilities and the evolving ribosome, the cellular machine for genetic-code translation.
  J R Soc Interface, 6, S575-S585.  
18621088 D.P.Giedroc, and P.V.Cornish (2009).
Frameshifting RNA pseudoknots: structure and mechanism.
  Virus Res, 139, 193-208.
PDB codes: 2rp0 2rp1
19154330 D.Qin, and K.Fredrick (2009).
Control of translation initiation involves a factor-induced rearrangement of helix 44 of 16S ribosomal RNA.
  Mol Microbiol, 71, 1239-1249.  
19400805 E.Purta, M.O'Connor, J.M.Bujnicki, and S.Douthwaite (2009).
YgdE is the 2'-O-ribose methyltransferase RlmM specific for nucleotide C2498 in bacterial 23S rRNA.
  Mol Microbiol, 72, 1147-1158.  
19089882 E.Zimmerman, and A.Yonath (2009).
Biological implications of the ribosome's stunning stereochemistry.
  Chembiochem, 10, 63-72.  
19696344 G.Blaha, R.E.Stanley, and T.A.Steitz (2009).
Formation of the first peptide bond: the structure of EF-P bound to the 70S ribosome.
  Science, 325, 966-970.
PDB codes: 3huw 3hux 3huy 3huz
19239893 H.S.Zaher, and R.Green (2009).
Fidelity at the molecular level: lessons from protein synthesis.
  Cell, 136, 746-762.  
19571367 I.Tinoco, and J.D.Wen (2009).
Simulation and analysis of single-ribosome translation.
  Phys Biol, 6, 25006.  
19647434 J.B.Munro, K.Y.Sanbonmatsu, C.M.Spahn, and S.C.Blanchard (2009).
Navigating the ribosome's metastable energy landscape.
  Trends Biochem Sci, 34, 390-400.  
19074194 J.Ederth, C.S.Mandava, S.Dasgupta, and S.Sanyal (2009).
A single-step method for purification of active His-tagged ribosomes from a genetically engineered Escherichia coli.
  Nucleic Acids Res, 37, e15.  
19717422 J.Fei, J.E.Bronson, J.M.Hofman, R.L.Srinivas, C.H.Wiggins, and R.L.Gonzalez (2009).
Allosteric collaboration between elongation factor G and the ribosomal L1 stalk directs tRNA movements during translation.
  Proc Natl Acad Sci U S A, 106, 15702-15707.  
19240142 J.Stombaugh, C.L.Zirbel, E.Westhof, and N.B.Leontis (2009).
Frequency and isostericity of RNA base pairs.
  Nucleic Acids Res, 37, 2294-2312.  
20018739 L.D.Cabrita, S.T.Hsu, H.Launay, C.M.Dobson, and J.Christodoulou (2009).
Probing ribosome-nascent chain complexes produced in vivo by NMR spectroscopy.
  Proc Natl Acad Sci U S A, 106, 22239-22244.  
19603183 M.O'Connor (2009).
Helix 69 in 23S rRNA modulates decoding by wild type and suppressor tRNAs.
  Mol Genet Genomics, 282, 371-380.  
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.  
19628400 N.D.Abeydeera, and C.S.Chow (2009).
Synthesis and characterization of modified nucleotides in the 970 hairpin loop of Escherichia coli 16S ribosomal RNA.
  Bioorg Med Chem, 17, 5887-5893.  
19222865 P.B.Moore (2009).
The ribosome returned.
  J Biol, 8, 8.  
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.  
19190181 P.V.Cornish, D.N.Ermolenko, D.W.Staple, L.Hoang, R.P.Hickerson, H.F.Noller, and T.Ha (2009).
Following movement of the L1 stalk between three functional states in single ribosomes.
  Proc Natl Acad Sci U S A, 106, 2571-2576.  
19294348 Q.Wu, L.Huang, and Y.Zhang (2009).
The structure and function of catalytic RNAs.
  Sci China C Life Sci, 52, 232-244.  
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
19825982 R.Moreno, S.Marzi, P.Romby, and F.Rojo (2009).
The Crc global regulator binds to an unpaired A-rich motif at the Pseudomonas putida alkS mRNA coding sequence and inhibits translation initiation.
  Nucleic Acids Res, 37, 7678-7690.  
19749755 S.Goto-Ito, T.Ito, M.Kuratani, Y.Bessho, and S.Yokoyama (2009).
Tertiary structure checkpoint at anticodon loop modification in tRNA functional maturation.
  Nat Struct Mol Biol, 16, 1109-1115.
PDB codes: 2zzm 2zzn
19696158 S.Kim, C.Liu, K.Halkidis, H.B.Gamper, and Y.M.Hou (2009).
Distinct kinetic determinants for the stepwise CCA addition to tRNA.
  RNA, 15, 1827-1836.  
19432457 S.P.Edmondson, J.Turri, K.Smith, A.Clark, and J.W.Shriver (2009).
Structure, stability, and flexibility of ribosomal protein L14e from Sulfolobus solfataricus.
  Biochemistry, 48, 5553-5562.  
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.  
19966413 T.J.McLellan, E.S.Marr, L.M.Wondrack, T.A.Subashi, P.A.Aeed, S.Han, Z.Xu, I.K.Wang, and B.A.Maguire (2009).
A systematic study of 50S ribosomal subunit purification enabling robust crystallization.
  Acta Crystallogr D Biol Crystallogr, 65, 1270-1282.  
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.  
19545171 X.Shi, K.Chiu, S.Ghosh, and S.Joseph (2009).
Bases in 16S rRNA important for subunit association, tRNA binding, and translocation.
  Biochemistry, 48, 6772-6782.  
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
18208838 A.B.Taylor, B.Meyer, B.Z.Leal, P.Kötter, V.Schirf, B.Demeler, P.J.Hart, K.D.Entian, and J.Wöhnert (2008).
The crystal structure of Nep1 reveals an extended SPOUT-class methyltransferase fold and a pre-organized SAM-binding site.
  Nucleic Acids Res, 36, 1542-1554.
PDB codes: 3bbd 3bbe 3bbh
19915655 A.Bashan, and A.Yonath (2008).
The linkage between ribosomal crystallography, metal ions, heteropolytungstates and functional flexibility.
  J Mol Struct, 890, 289-294.  
18848900 A.Korostelev, D.N.Ermolenko, and H.F.Noller (2008).
Structural dynamics of the ribosome.
  Curr Opin Chem Biol, 12, 674-683.  
18824477 A.N.Petrov, A.Meskauskas, S.C.Roshwalb, and J.D.Dinman (2008).
Yeast ribosomal protein L10 helps coordinate tRNA movement through the large subunit.
  Nucleic Acids Res, 36, 6187-6198.  
18758445 A.Simonetti, S.Marzi, A.G.Myasnikov, A.Fabbretti, M.Yusupov, C.O.Gualerzi, and B.P.Klaholz (2008).
Structure of the 30S translation initiation complex.
  Nature, 455, 416-420.  
18842120 A.Tats, T.Tenson, and M.Remm (2008).
Preferred and avoided codon pairs in three domains of life.
  BMC Genomics, 9, 463.  
17998293 B.A.Maguire, L.M.Wondrack, L.G.Contillo, and Z.Xu (2008).
A novel chromatography system to isolate active ribosomes from pathogenic bacteria.
  RNA, 14, 188-195.  
18218711 B.Wu, A.Yee, Y.J.Huang, T.A.Ramelot, J.R.Cort, A.Semesi, J.W.Jung, W.Lee, G.T.Montelione, M.A.Kennedy, and C.H.Arrowsmith (2008).
The solution structure of ribosomal protein S17E from Methanobacterium thermoautotrophicum: a structural homolog of the FF domain.
  Protein Sci, 17, 583-588.
PDB code: 1rq6
19098107 C.Davidovich, A.Bashan, and A.Yonath (2008).
Structural basis for cross-resistance to ribosomal PTC antibiotics.
  Proc Natl Acad Sci U S A, 105, 20665-20670.  
18755841 C.M.Zhang, C.Liu, T.Christian, H.Gamper, J.Rozenski, D.Pan, J.B.Randolph, E.Wickstrom, B.S.Cooperman, and Y.M.Hou (2008).
Pyrrolo-C as a molecular probe for monitoring conformations of the tRNA 3' end.
  RNA, 14, 2245-2253.  
18683165 C.Voisset, J.Y.Thuret, D.Tribouillard-Tanvier, S.J.Saupe, and M.Blondel (2008).
Tools for the study of ribosome-borne protein folding activity.
  Biotechnol J, 3, 1033-1040.  
17981968 C.Wicker-Planquart, A.E.Foucher, M.Louwagie, R.A.Britton, and J.M.Jault (2008).
Interactions of an essential Bacillus subtilis GTPase, YsxC, with ribosomes.
  J Bacteriol, 190, 681-690.  
18448426 D.Pan, C.M.Zhang, S.Kirillov, Y.M.Hou, and B.S.Cooperman (2008).
Perturbation of the tRNA tertiary core differentially affects specific steps of the elongation cycle.
  J Biol Chem, 283, 18431-18440.  
18824514 D.Rodriguez-Correa, and A.E.Dahlberg (2008).
Kinetic and thermodynamic studies of peptidyltransferase in ribosomes from the extreme thermophile Thermus thermophilus.
  RNA, 14, 2314-2318.  
18755835 E.Purta, K.H.Kaminska, J.M.Kasprzak, J.M.Bujnicki, and S.Douthwaite (2008).
YbeA is the m3Psi methyltransferase RlmH that targets nucleotide 1915 in 23S rRNA.
  RNA, 14, 2234-2244.  
18288206 G.Das, D.K.Thotala, S.Kapoor, S.Karunanithi, S.S.Thakur, N.S.Singh, and U.Varshney (2008).
Role of 16S ribosomal RNA methylations in translation initiation in Escherichia coli.
  EMBO J, 27, 840-851.  
19089822 G.Emmerechts, L.Maes, P.Herdewijn, J.Anné, and J.Rozenski (2008).
Characterization of the posttranscriptional modifications in Legionella pneumophila small-subunit ribosomal RNA.
  Chem Biodivers, 5, 2640-2653.  
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.  
18844986 H.Grosjean, C.Gaspin, C.Marck, W.A.Decatur, and V.de Crécy-Lagard (2008).
RNomics and Modomics in the halophilic archaea Haloferax volcanii: identification of RNA modification genes.
  BMC Genomics, 9, 470.  
18936244 H.Ishida, and S.Hayward (2008).
Path of nascent polypeptide in exit tunnel revealed by molecular dynamics simulation of ribosome.
  Biophys J, 95, 5962-5973.  
18286627 J.B.Munro, A.Vaiana, K.Y.Sanbonmatsu, and S.C.Blanchard (2008).
A new view of protein synthesis: mapping the free energy landscape of the ribosome using single-molecule FRET.
  Biopolymers, 89, 565-577.  
18327250 J.D.Wen, L.Lancaster, C.Hodges, A.C.Zeri, S.H.Yoshimura, H.F.Noller, C.Bustamante, and I.Tinoco (2008).
Following translation by single ribosomes one codon at a time.
  Nature, 452, 598-603.  
18708582 J.Dong, J.S.Nanda, H.Rahman, M.R.Pruitt, B.S.Shin, C.M.Wong, J.R.Lorsch, and A.G.Hinnebusch (2008).
Genetic identification of yeast 18S rRNA residues required for efficient recruitment of initiator tRNA(Met) and AUG selection.
  Genes Dev, 22, 2242-2255.  
18471980 J.Fei, P.Kosuri, D.D.MacDougall, and R.L.Gonzalez (2008).
Coupling of ribosomal L1 stalk and tRNA dynamics during translation elongation.
  Mol Cell, 30, 348-359.  
18755834 L.Lancaster, N.J.Lambert, E.J.Maklan, L.H.Horan, and H.F.Noller (2008).
The sarcin-ricin loop of 23S rRNA is essential for assembly of the functional core of the 50S ribosomal subunit.
  RNA, 14, 1999-2012.  
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.  
18653533 P.Barraud, E.Schmitt, Y.Mechulam, F.Dardel, and C.Tisné (2008).
A unique conformation of the anticodon stem-loop is associated with the capacity of tRNAfMet to initiate protein synthesis.
  Nucleic Acids Res, 36, 4894-4901.
PDB codes: 3cw5 3cw6
17937599 P.C.Bevilacqua, and J.M.Blose (2008).
Structures, kinetics, thermodynamics, and biological functions of RNA hairpins.
  Annu Rev Phys Chem, 59, 79.  
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
18946046 P.M.Petrone, C.D.Snow, D.Lucent, and V.S.Pande (2008).
Side-chain recognition and gating in the ribosome exit tunnel.
  Proc Natl Acad Sci U S A, 105, 16549-16554.  
18538656 P.V.Cornish, D.N.Ermolenko, H.F.Noller, and T.Ha (2008).
Spontaneous intersubunit rotation in single ribosomes.
  Mol Cell, 30, 578-588.  
18344525 P.Y.Liao, P.Gupta, A.N.Petrov, J.D.Dinman, and K.H.Lee (2008).
A new kinetic model reveals the synergistic effect of E-, P- and A-sites on +1 ribosomal frameshifting.
  Nucleic Acids Res, 36, 2619-2629.  
18518820 R.A.Marshall, C.E.Aitken, M.Dorywalska, and J.D.Puglisi (2008).
Translation at the single-molecule level.
  Annu Rev Biochem, 77, 177-203.  
18824686 R.A.Marshall, M.Dorywalska, and J.D.Puglisi (2008).
Irreversible chemical steps control intersubunit dynamics during translation.
  Proc Natl Acad Sci U S A, 105, 15364-15369.  
18836497 R.Giegé (2008).
Toward a more complete view of tRNA biology.
  Nat Struct Mol Biol, 15, 1007-1014.  
18591673 S.E.Walker, S.Shoji, D.Pan, B.S.Cooperman, and K.Fredrick (2008).
Role of hybrid tRNA-binding states in ribosomal translocation.
  Proc Natl Acad Sci U S A, 105, 9192-9197.  
18462671 S.J.Moran, J.F.Flanagan, O.Namy, D.I.Stuart, I.Brierley, and R.J.Gilbert (2008).
The mechanics of translocation: a molecular "spring-and-ratchet" system.
  Structure, 16, 664-672.  
18292779 T.A.Steitz (2008).
A structural understanding of the dynamic ribosome machine.
  Nat Rev Mol Cell Biol, 9, 242-253.  
18432622 T.J.Giese, and D.M.York (2008).
Extension of adaptive tree code and fast multipole methods to high angular momentum particle charge densities.
  J Comput Chem, 29, 1895-1904.  
18252772 T.Miyoshi, and T.Uchiumi (2008).
Functional interaction between bases C1049 in domain II and G2751 in domain VI of 23S rRNA in Escherichia coli ribosomes.
  Nucleic Acids Res, 36, 1783-1791.  
18456707 T.Yokoyama, and T.Suzuki (2008).
Ribosomal RNAs are tolerant toward genetic insertions: evolutionary origin of the expansion segments.
  Nucleic Acids Res, 36, 3539-3551.  
18094470 Y.Xiong (2008).
From electron microscopy to X-ray crystallography: molecular-replacement case studies.
  Acta Crystallogr D Biol Crystallogr, 64, 76-82.  
17897673 A.Korostelev, and H.F.Noller (2007).
Analysis of structural dynamics in the ribosome by TLS crystallographic refinement.
  J Mol Biol, 373, 1058-1070.  
17764954 A.Korostelev, and H.F.Noller (2007).
The ribosome in focus: new structures bring new insights.
  Trends Biochem Sci, 32, 434-441.  
17940016 A.Korostelev, S.Trakhanov, H.Asahara, M.Laurberg, L.Lancaster, and H.F.Noller (2007).
Interactions and dynamics of the Shine Dalgarno helix in the 70S ribosome.
  Proc Natl Acad Sci U S A, 104, 16840-16843.
PDB codes: 1vsp 2qnh
17660830 A.Weixlbaumer, S.Petry, C.M.Dunham, M.Selmer, A.C.Kelley, and V.Ramakrishnan (2007).
Crystal structure of the ribosome recycling factor bound to the ribosome.
  Nat Struct Mol Biol, 14, 733-737.
PDB codes: 2v46 2v47 2v48 2v49
17532253 B.Felden (2007).
RNA structure: experimental analysis.
  Curr Opin Microbiol, 10, 286-291.  
17360517 C.Davidovich, A.Bashan, T.Auerbach-Nevo, R.D.Yaggie, R.R.Gontarek, and A.Yonath (2007).
Induced-fit tightens pleuromutilins binding to ribosomes and remote interactions enable their selectivity.
  Proc Natl Acad Sci U S A, 104, 4291-4296.
PDB codes: 2ogm 2ogn 2ogo
18072984 C.S.Fraser, and J.A.Doudna (2007).
Quantitative studies of ribosome conformational dynamics.
  Q Rev Biophys, 40, 163-189.  
17515906 D.N.Ermolenko, P.C.Spiegel, Z.K.Majumdar, R.P.Hickerson, R.M.Clegg, and H.F.Noller (2007).
The antibiotic viomycin traps the ribosome in an intermediate state of translocation.
  Nat Struct Mol Biol, 14, 493-497.  
17553840 F.Rázga, J.Koca, A.Mokdad, and J.Sponer (2007).
Elastic properties of ribosomal RNA building blocks: molecular dynamics of the GTPase-associated center rRNA.
  Nucleic Acids Res, 35, 4007-4017.  
17872509 G.N.Basturea, and M.P.Deutscher (2007).
Substrate specificity and properties of the Escherichia coli 16S rRNA methyltransferase, RsmE.
  RNA, 13, 1969-1976.  
18047667 G.R.Moura, J.P.Lousado, M.Pinheiro, L.Carreto, R.M.Silva, J.L.Oliveira, and M.A.Santos (2007).
Codon-triplet context unveils unique features of the Candida albicans protein coding genome.
  BMC Genomics, 8, 444.  
17580114 H.Li (2007).
Complexes of tRNA and maturation enzymes: shaping up for translation.
  Curr Opin Struct Biol, 17, 293-301.  
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
17317624 J.B.Munro, R.B.Altman, N.O'Connor, and S.C.Blanchard (2007).
Identification of two distinct hybrid state intermediates on the ribosome.
  Mol Cell, 25, 505-517.  
18003906 J.Frank, H.Gao, J.Sengupta, N.Gao, and D.J.Taylor (2007).
The process of mRNA-tRNA translocation.
  Proc Natl Acad Sci U S A, 104, 19671-19678.  
18047298 J.M.Blose, M.L.Manni, K.A.Klapec, Y.Stranger-Jones, A.C.Zyra, V.Sim, C.A.Griffith, J.D.Long, and M.J.Serra (2007).
Non-nearest-neighbor dependence of the stability for RNA bulge loops based on the complete set of group I single-nucleotide bulge loops.
  Biochemistry, 46, 15123-15135.  
17553838 K.Kitahara, A.Kajiura, N.S.Sato, and T.Suzuki (2007).
Functional genetic selection of Helix 66 in Escherichia coli 23S rRNA identified the eukaryotic-binding sequence for ribosomal protein L2.
  Nucleic Acids Res, 35, 4018-4029.  
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.  
17592474 K.Wang, H.Neumann, S.Y.Peak-Chew, and J.W.Chin (2007).
Evolved orthogonal ribosomes enhance the efficiency of synthetic genetic code expansion.
  Nat Biotechnol, 25, 770-777.  
17360328 L.H.Horan, and H.F.Noller (2007).
Intersubunit movement is required for ribosomal translocation.
  Proc Natl Acad Sci U S A, 104, 4881-4885.  
17721443 L.Jenner, B.Rees, M.Yusupov, and G.Yusupova (2007).
Messenger RNA conformations in the ribosomal E site revealed by X-ray crystallography.
  EMBO Rep, 8, 846-850.  
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.  
17379816 M.E.Saks, and J.S.Conery (2007).
Anticodon-dependent conservation of bacterial tRNA gene sequences.
  RNA, 13, 651-660.  
17704133 M.Léger, D.Dulude, S.V.Steinberg, and L.Brakier-Gingras (2007).
The three transfer RNAs occupying the A, P and E sites on the ribosome are involved in viral programmed -1 ribosomal frameshift.
  Nucleic Acids Res, 35, 5581-5592.  
17937767 M.Leppik, L.Peil, K.Kipper, A.Liiv, and J.Remme (2007).
Substrate specificity of the pseudouridine synthase RluD in Escherichia coli.
  FEBS J, 274, 5759-5766.  
17828421 M.O'Connor (2007).
Selection for intragenic suppressors of lethal 23S rRNA mutations in Escherichia coli identifies residues important for ribosome assembly and function.
  Mol Genet Genomics, 278, 677-687.  
17157507 M.V.Rodnina, M.Beringer, and W.Wintermeyer (2007).
How ribosomes make peptide bonds.
  Trends Biochem Sci, 32, 20-26.  
17872507 P.P.Vaidyanathan, M.P.Deutscher, and A.Malhotra (2007).
RluD, a highly conserved pseudouridine synthase, modifies 50S subunits more specifically and efficiently than free 23S rRNA.
  RNA, 13, 1868-1876.  
17255199 R.Guymon, S.C.Pomerantz, J.N.Ison, P.F.Crain, and J.A.McCloskey (2007).
Post-transcriptional modifications in the small subunit ribosomal RNA from Thermotoga maritima, including presence of a novel modified cytidine.
  RNA, 13, 396-403.  
17660285 R.Leipuviene, and G.R.Björk (2007).
Alterations in the two globular domains or in the connecting alpha-helix of bacterial ribosomal protein L9 induces +1 frameshifts.
  J Bacteriol, 189, 7024-7031.  
17666711 R.Przybilski, and C.Hammann (2007).
The tolerance to exchanges of the Watson Crick base pair in the hammerhead ribozyme core is determined by surrounding elements.
  RNA, 13, 1625-1630.  
17321546 S.J.Schroeder, G.Blaha, J.Tirado-Rives, T.A.Steitz, and P.B.Moore (2007).
The structures of antibiotics bound to the E site region of the 50 S ribosomal subunit of Haloarcula marismortui: 13-deoxytedanolide and girodazole.
  J Mol Biol, 367, 1471-1479.
PDB codes: 2otj 2otl
17238915 S.Okamoto, A.Tamaru, C.Nakajima, K.Nishimura, Y.Tanaka, S.Tokuyama, Y.Suzuki, and K.Ochi (2007).
Loss of a conserved 7-methylguanosine modification in 16S rRNA confers low-level streptomycin resistance in bacteria.
  Mol Microbiol, 63, 1096-1106.  
17283211 S.V.Steinberg, and Y.I.Boutorine (2007).
G-ribo: a new structural motif in ribosomal RNA.
  RNA, 13, 549-554.  
17507660 S.V.Steinberg, and Y.I.Boutorine (2007).
G-ribo motif favors the formation of pseudoknots in ribosomal RNA.
  RNA, 13, 1036-1042.  
17652134 T.Betteridge, H.Liu, H.Gamper, S.Kirillov, B.S.Cooperman, and Y.M.Hou (2007).
Fluorescent labeling of tRNAs for dynamics experiments.
  RNA, 13, 1594-1601.  
17574829 V.Berk, and J.H.Cate (2007).
Insights into protein biosynthesis from structures of bacterial ribosomes.
  Curr Opin Struct Biol, 17, 302-309.  
17572081 W.G.Scott (2007).
Ribozymes.
  Curr Opin Struct Biol, 17, 280-286.  
17925437 W.Li, and J.Frank (2007).
Transfer RNA in the hybrid P/E state: correlating molecular dynamics simulations with cryo-EM data.
  Proc Natl Acad Sci U S A, 104, 16540-16545.  
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.

 

spacer
spacer