PDBsum entry 2hgi

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protein dna_rna Protein-protein interface(s) links
Ribosome PDB id
Protein chains
234 a.a. *
206 a.a. *
208 a.a. *
150 a.a. *
101 a.a. *
155 a.a. *
138 a.a. *
127 a.a. *
98 a.a. *
119 a.a. *
124 a.a. *
125 a.a. *
60 a.a. *
88 a.a. *
83 a.a. *
104 a.a. *
73 a.a. *
80 a.a. *
99 a.a. *
24 a.a. *
* Residue conservation analysis
PDB id:
Name: Ribosome
Title: Crystal structure of the 70s thermus thermophilus ribosome s the 16s 3'-end mimicks mRNA e and p codons. This entry 2hgi 30s ribosomal subunit. The 50s ribosomal subunit can be fou entry 2hgj.
Structure: 16s rrna. Chain: a. tRNA fmet (unmodified bases). Chain: c. tRNA phe (unmodified bases). Chain: d. 30s ribosomal protein s2. Chain: e. 30s ribosomal protein s3.
Source: Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Escherichia coli. Organism_taxid: 562. Strain: hb8
Biol. unit: 23mer (from PQS)
5.00Å     R-factor:   0.263     R-free:   0.323
Authors: L.Jenner,G.Yusupova,B.Rees,D.Moras,M.Yusupov
Key ref:
G.Yusupova et al. (2006). Structural basis for messenger RNA movement on the ribosome. Nature, 444, 391-394. PubMed id: 17051149 DOI: 10.1038/nature05281
27-Jun-06     Release date:   07-Nov-06    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P80371  (RS2_THET8) -  30S ribosomal protein S2
256 a.a.
234 a.a.
Protein chain
Pfam   ArchSchema ?
P80372  (RS3_THET8) -  30S ribosomal protein S3
239 a.a.
206 a.a.
Protein chain
Pfam   ArchSchema ?
P80373  (RS4_THET8) -  30S ribosomal protein S4
209 a.a.
208 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHQ5  (RS5_THET8) -  30S ribosomal protein S5
162 a.a.
150 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SLP8  (RS6_THET8) -  30S ribosomal protein S6
101 a.a.
101 a.a.
Protein chain
Pfam   ArchSchema ?
P17291  (RS7_THET8) -  30S ribosomal protein S7
156 a.a.
155 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHQ2  (RS8_THET8) -  30S ribosomal protein S8
138 a.a.
138 a.a.
Protein chain
Pfam   ArchSchema ?
P80374  (RS9_THET8) -  30S ribosomal protein S9
128 a.a.
127 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHN7  (RS10_THET8) -  30S ribosomal protein S10
105 a.a.
98 a.a.
Protein chain
Pfam   ArchSchema ?
P80376  (RS11_THET8) -  30S ribosomal protein S11
129 a.a.
119 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHN3  (RS12_THET8) -  30S ribosomal protein S12
132 a.a.
124 a.a.
Protein chain
Pfam   ArchSchema ?
P80377  (RS13_THET8) -  30S ribosomal protein S13
126 a.a.
125 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHQ1  (RS14Z_THET8) -  30S ribosomal protein S14 type Z
61 a.a.
60 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SJ76  (RS15_THET8) -  30S ribosomal protein S15
89 a.a.
88 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SJH3  (RS16_THET8) -  30S ribosomal protein S16
88 a.a.
83 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHP7  (RS17_THET8) -  30S ribosomal protein S17
105 a.a.
104 a.a.*
Protein chain
Pfam   ArchSchema ?
Q5SLQ0  (RS18_THET8) -  30S ribosomal protein S18
88 a.a.
73 a.a.*
Protein chain
Pfam   ArchSchema ?
Q5SHP2  (RS19_THET8) -  30S ribosomal protein S19
93 a.a.
80 a.a.
Protein chain
Pfam   ArchSchema ?
P80380  (RS20_THET8) -  30S ribosomal protein S20
106 a.a.
99 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SIH3  (RSHX_THET8) -  30S ribosomal protein Thx
27 a.a.
24 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   4 terms 
  Biological process     translation   1 term 
  Biochemical function     structural constituent of ribosome     8 terms  


DOI no: 10.1038/nature05281 Nature 444:391-394 (2006)
PubMed id: 17051149  
Structural basis for messenger RNA movement on the ribosome.
G.Yusupova, L.Jenner, B.Rees, D.Moras, M.Yusupov.
Translation initiation is a major determinant of the overall expression level of a gene. The translation of functionally active protein requires the messenger RNA to be positioned on the ribosome such that the start/initiation codon will be read first and in the correct frame. Little is known about the molecular basis for the interaction of mRNA with the ribosome at different states of translation. Recent crystal structures of the ribosomal subunits, the empty 70S ribosome and the 70S ribosome containing functional ligands have provided information about the general organization of the ribosome and its functional centres. Here we compare the X-ray structures of eight ribosome complexes modelling the translation initiation, post-initiation and elongation states. In the initiation and post-initiation complexes, the presence of the Shine-Dalgarno (SD) duplex causes strong anchoring of the 5'-end of mRNA onto the platform of the 30S subunit, with numerous interactions between mRNA and the ribosome. Conversely, the 5' end of the 'elongator' mRNA lacking SD interactions is flexible, suggesting a different exit path for mRNA during elongation. After the initiation of translation, but while an SD interaction is still present, mRNA moves in the 3'-->5' direction with simultaneous clockwise rotation and lengthening of the SD duplex, bringing it into contact with ribosomal protein S2.
  Selected figure(s)  
Figure 2.
Figure 2: Path of mRNA with a 5'-terminal extension through the ribosome. a, Interactions of (A)[33]SD(A)[4]AUG(A)[9] mRNA with protein S18 in the initiation complex. The globular density (grey, not modelled) may encompass the N-terminal part of protein S18 and about ten nucleotides of the poly(A) tail extension. b, Interactions of (U)[27]SD(U)[9]UUU(U)[10] mRNA with protein S2 in the post-initiation complex. c, Magnified fragment of the 30S subunit platform showing the environment of the SD duplex and the 5'-end extension of the post-initiation complex mRNA. A loop of the 5'-end extension of the mRNA enters a cavity in S2.
Figure 3.
Figure 3: mRNA path at the elongation step. a, Structure of the 3' end of 16S RNA (grey) in the ribosome complex without mRNA. b, SD nonanucleotide (red) in complex with the 70S ribosome and tRNA^fMet. The position of the SD duplex is similar to that seen in the post-initiation complex. c, Difference Fourier map between the ribosome complex containing elongator (U)[12]AUG(U)[9] mRNA and the SD nonanucleotide. d, e, Top views of the 70S ribosome complex in the post-initiation state with mRNA containing a 5'-terminal extension (d) and in the elongation state (e). f, Simplified diagram of mRNA motion on the ribosome.
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2006, 444, 391-394) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22622583 D.J.Ramrath, H.Yamamoto, K.Rother, D.Wittek, M.Pech, T.Mielke, J.Loerke, P.Scheerer, P.Ivanov, Y.Teraoka, O.Shpanchenko, K.H.Nierhaus, and C.M.Spahn (2012).
The complex of tmRNA-SmpB and EF-G on translocating ribosomes.
  Nature, 485, 526-529.
PDB codes: 3j18 3j19
22562136 P.Milón, C.Maracci, L.Filonava, C.O.Gualerzi, and M.V.Rodnina (2012).
Real-time assembly landscape of bacterial 30S translation initiation complex.
  Nat Struct Mol Biol, 19, 609-615.  
22664983 S.Melnikov, A.Ben-Shem, N.Garreau de Loubresse, L.Jenner, G.Yusupova, and M.Yusupov (2012).
One core, two shells: bacterial and eukaryotic ribosomes.
  Nat Struct Mol Biol, 19, 560-567.  
21383132 G.D.Tocchini-Valentini, P.Fruscoloni, and G.P.Tocchini-Valentini (2011).
Evolution of introns in the archaeal world.
  Proc Natl Acad Sci U S A, 108, 4782-4787.  
21383139 J.Fu, J.B.Munro, S.C.Blanchard, and J.Frank (2011).
Cryoelectron microscopy structures of the ribosome complex in intermediate states during tRNA translocation.
  Proc Natl Acad Sci U S A, 108, 4817-4821.  
20034956 A.A.Malygin, and G.G.Karpova (2010).
Structural motifs of the bacterial ribosomal proteins S20, S18 and S16 that contact rRNA present in the eukaryotic ribosomal proteins S25, S26 and S27A, respectively.
  Nucleic Acids Res, 38, 2089-2098.  
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
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.  
19910312 A.Nishizawa, M.Nakayama, T.Uemura, Y.Fukuda, and S.Kimura (2010).
Ribosome-binding site interference caused by Shine-Dalgarno-like nucleotide sequences in Escherichia coli cells.
  J Biochem, 147, 433-443.  
20348441 D.Kurita, A.Muto, and H.Himeno (2010).
Role of the C-terminal tail of SmpB in the early stage of trans-translation.
  RNA, 16, 980-990.  
20953161 F.Weis, P.Bron, E.Giudice, J.P.Rolland, D.Thomas, B.Felden, and R.Gillet (2010).
tmRNA-SmpB: a journey to the centre of the bacterial ribosome.
  EMBO J, 29, 3810-3818.
PDB codes: 3iyq 3iyr
20038631 F.Weis, P.Bron, J.P.Rolland, D.Thomas, B.Felden, and R.Gillet (2010).
Accommodation of tmRNA-SmpB into stalled ribosomes: a cryo-EM study.
  RNA, 16, 299-306.  
20733057 J.O.Ortiz, F.Brandt, V.R.Matias, L.Sennels, J.Rappsilber, S.H.Scheres, M.Eibauer, F.U.Hartl, and W.Baumeister (2010).
Structure of hibernating ribosomes studied by cryoelectron tomography in vitro and in situ.
  J Cell Biol, 190, 613-621.  
20117091 K.Ito, S.Chiba, and K.Pogliano (2010).
Divergent stalling sequences sense and control cellular physiology.
  Biochem Biophys Res Commun, 393, 1-5.  
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
  20634982 L.Ponnala (2010).
A plausible role for the presence of internal shine-dalgarno sites.
  Bioinform Biol Insights, 4, 55-60.  
19965869 M.R.Sharma, A.Dönhöfer, C.Barat, V.Marquez, P.P.Datta, P.Fucini, D.N.Wilson, and R.K.Agrawal (2010).
PSRP1 is not a ribosomal protein, but a ribosome-binding factor that is recycled by the ribosome-recycling factor (RRF) and elongation factor G (EF-G).
  J Biol Chem, 285, 4006-4014.  
19925799 S.E.Kolitz, and J.R.Lorsch (2010).
Eukaryotic initiator tRNA: finely tuned and ready for action.
  FEBS Lett, 584, 396-404.  
19095617 A.Devaraj, S.Shoji, E.D.Holbrook, and K.Fredrick (2009).
A role for the 30S subunit E site in maintenance of the translational reading frame.
  RNA, 15, 255-265.  
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.  
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
19539793 C.U.Hellen (2009).
IRES-induced conformational changes in the ribosome and the mechanism of translation initiation by internal ribosomal entry.
  Biochim Biophys Acta, 1789, 558-570.  
19861425 D.Hasenöhrl, A.Fabbretti, P.Londei, C.O.Gualerzi, and U.Bläsi (2009).
Translation initiation complex formation in the crenarchaeon Sulfolobus solfataricus.
  RNA, 15, 2288-2298.  
18621088 D.P.Giedroc, and P.V.Cornish (2009).
Frameshifting RNA pseudoknots: structure and mechanism.
  Virus Res, 139, 193-208.
PDB codes: 2rp0 2rp1
19861420 E.Y.Bugaeva, S.Surkov, A.V.Golovin, L.G.Ofverstedt, U.Skoglund, L.A.Isaksson, A.A.Bogdanov, O.V.Shpanchenko, and O.A.Dontsova (2009).
Structural features of the tmRNA-ribosome interaction.
  RNA, 15, 2312-2320.  
19089882 E.Zimmerman, and A.Yonath (2009).
Biological implications of the ribosome's stunning stereochemistry.
  Chembiochem, 10, 63-72.  
19167328 F.Brandt, S.A.Etchells, J.O.Ortiz, A.H.Elcock, F.U.Hartl, and W.Baumeister (2009).
The native 3D organization of bacterial polysomes.
  Cell, 136, 261-271.  
19469554 G.Y.Soung, J.L.Miller, H.Koc, and E.C.Koc (2009).
Comprehensive analysis of phosphorylated proteins of Escherichia coli ribosomes.
  J Proteome Res, 8, 3390-3402.  
19625386 M.H.Mazauric, J.L.Leroy, K.Visscher, S.Yoshizawa, and D.Fourmy (2009).
Footprinting analysis of BWYV pseudoknot-ribosome complexes.
  RNA, 15, 1775-1786.  
19497863 M.R.Sharma, T.M.Booth, L.Simpson, D.A.Maslov, and R.K.Agrawal (2009).
Structure of a mitochondrial ribosome with minimal RNA.
  Proc Natl Acad Sci U S A, 106, 9637-9642.
PDB codes: 3iy8 3iy9
19239892 N.Sonenberg, and A.G.Hinnebusch (2009).
Regulation of translation initiation in eukaryotes: mechanisms and biological targets.
  Cell, 136, 731-745.  
19686666 O.Kurkcuoglu, O.T.Turgut, S.Cansu, R.L.Jernigan, and P.Doruker (2009).
Focused functional dynamics of supramolecules by use of a mixed-resolution elastic network model.
  Biophys J, 97, 1178-1187.  
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.  
19779460 S.Chiba, A.Lamsa, and K.Pogliano (2009).
A ribosome-nascent chain sensor of membrane protein biogenesis in Bacillus subtilis.
  EMBO J, 28, 3461-3475.  
  19173642 S.Shoji, S.E.Walker, and K.Fredrick (2009).
Ribosomal translocation: one step closer to the molecular mechanism.
  ACS Chem Biol, 4, 93.  
18848900 A.Korostelev, D.N.Ermolenko, and H.F.Noller (2008).
Structural dynamics of the ribosome.
  Curr Opin Chem Biol, 12, 674-683.  
18832371 A.Meskauskas, and J.D.Dinman (2008).
Ribosomal protein L3 functions as a 'rocker switch' to aid in coordinating of large subunit-associated functions in eukaryotes and Archaea.
  Nucleic Acids Res, 36, 6175-6186.  
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.  
18464793 A.V.Pisarev, V.G.Kolupaeva, M.M.Yusupov, C.U.Hellen, and T.V.Pestova (2008).
Ribosomal position and contacts of mRNA in eukaryotic translation initiation complexes.
  EMBO J, 27, 1609-1621.  
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.  
18648071 L.V.Aseev, A.A.Levandovskaya, L.S.Tchufistova, N.V.Scaptsova, and I.V.Boni (2008).
A new regulatory circuit in ribosomal protein operons: S2-mediated control of the rpsB-tsf expression in vivo.
  RNA, 14, 1882-1894.  
18658239 N.E.Shirokikh, and A.S.Spirin (2008).
Poly(A) leader of eukaryotic mRNA bypasses the dependence of translation on initiation factors.
  Proc Natl Acad Sci U S A, 105, 10738-10743.  
18772887 N.M.Wills, M.O'Connor, C.C.Nelson, C.C.Rettberg, W.M.Huang, R.F.Gesteland, and J.F.Atkins (2008).
Translational bypassing without peptidyl-tRNA anticodon scanning of coding gap mRNA.
  EMBO J, 27, 2533-2544.  
19029596 O.Kurkcuoglu, P.Doruker, T.Z.Sen, A.Kloczkowski, and R.L.Jernigan (2008).
The ribosome structure controls and directs mRNA entry, translocation and exit dynamics.
  Phys Biol, 5, 046005.  
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
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.  
18421289 S.C.Blanchard (2008).
Breaking the barriers of translation.
  Nat Chem Biol, 4, 275-276.  
18614050 S.Ledoux, and O.C.Uhlenbeck (2008).
Different aa-tRNAs are selected uniformly on the ribosome.
  Mol Cell, 31, 114-123.  
18953726 S.Marzi, P.Fechter, C.Chevalier, P.Romby, and T.Geissmann (2008).
RNA switches regulate initiation of translation in bacteria.
  Biol Chem, 389, 585-598.  
18667704 V.Di Giacco, V.Márquez, Y.Qin, M.Pech, F.J.Triana-Alonso, D.N.Wilson, and K.H.Nierhaus (2008).
Shine-Dalgarno interaction prevents incorporation of noncognate amino acids at the codon following the AUG.
  Proc Natl Acad Sci U S A, 105, 10715-10720.  
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
17868695 C.Grigoriadou, S.Marzi, D.Pan, C.O.Gualerzi, and B.S.Cooperman (2007).
The translational fidelity function of IF3 during transition from the 30 S initiation complex to the 70 S initiation complex.
  J Mol Biol, 373, 551-561.  
17881742 C.Guarraia, L.Norris, A.Raman, and P.J.Farabaugh (2007).
Saturation mutagenesis of a +1 programmed frameshift-inducing mRNA sequence derived from a yeast retrotransposon.
  RNA, 13, 1940-1947.  
18072984 C.S.Fraser, and J.A.Doudna (2007).
Quantitative studies of ribosome conformational dynamics.
  Q Rev Biophys, 40, 163-189.  
17889642 D.Boehringer, and N.Ban (2007).
Trapping the ribosome to control gene expression.
  Cell, 130, 983-985.  
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.  
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.  
18042701 M.R.Sharma, D.N.Wilson, P.P.Datta, C.Barat, F.Schluenzen, P.Fucini, and R.K.Agrawal (2007).
Cryo-EM study of the spinach chloroplast ribosome reveals the structural and functional roles of plastid-specific ribosomal proteins.
  Proc Natl Acad Sci U S A, 104, 19315-19320.
PDB codes: 3bbn 3bbo
17889647 S.Marzi, A.G.Myasnikov, A.Serganov, C.Ehresmann, P.Romby, M.Yusupov, and B.P.Klaholz (2007).
Structured mRNAs regulate translation initiation by binding to the platform of the ribosome.
  Cell, 130, 1019-1031.
PDB code: 2vaz
17355865 T.Kaminishi, D.N.Wilson, C.Takemoto, J.M.Harms, M.Kawazoe, F.Schluenzen, K.Hanawa-Suetsugu, M.Shirouzu, P.Fucini, and S.Yokoyama (2007).
A snapshot of the 30S ribosomal subunit capturing mRNA via the Shine-Dalgarno interaction.
  Structure, 15, 289-297.
PDB code: 2e5l
17574829 V.Berk, and J.H.Cate (2007).
Insights into protein biosynthesis from structures of bacterial ribosomes.
  Curr Opin Struct Biol, 17, 302-309.  
17973990 V.Vimberg, A.Tats, M.Remm, and T.Tenson (2007).
Translation initiation region sequence preferences in Escherichia coli.
  BMC Mol Biol, 8, 100.  
17173023 W.C.Merrick (2007).
Are we there yet?
  Nat Chem Biol, 3, 19-20.  
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.