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PDBsum entry 1hr0
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protein dna_rna metals Protein-protein interface(s) links
Ribosome PDB id
1hr0

 

 

 

 

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Contents
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. *
71 a.a. *
DNA/RNA
Metals
_MG ×65
_ZN ×2
* Residue conservation analysis
PDB id:
1hr0
Name: Ribosome
Title: Crystal structure of initiation factor if1 bound to the 30s ribosomal subunit
Structure: 16s ribosomal RNA. Chain: a. Fragment of messenger RNA. Chain: x. 30s ribosomal protein s2. Chain: b. 30s ribosomal protein s3. Chain: c. 30s ribosomal protein s4.
Source: Thermus thermophilus. Organism_taxid: 274. Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: t7 expression system
Biol. unit: 24mer (from PQS)
Resolution:
3.20Å     R-factor:   0.218     R-free:   0.261
Authors: A.P.Carter,W.M.Clemons Jr.,D.E.Brodersen,R.J.Morgan-Warren, B.T.Wimberly,V.Ramakrishnan
Key ref:
A.P.Carter et al. (2001). Crystal structure of an initiation factor bound to the 30S ribosomal subunit. Science, 291, 498-501. PubMed id: 11228145 DOI: 10.1126/science.1057766
Date:
20-Dec-00     Release date:   24-Jan-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P80371  (RS2_THET8) -  Small ribosomal subunit protein uS2 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		256 a.a.
234 a.a.
Protein chain
Pfam   ArchSchema ?
P80372  (RS3_THET8) -  Small ribosomal subunit protein uS3 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		239 a.a.
206 a.a.
Protein chain
Pfam   ArchSchema ?
P80373  (RS4_THET8) -  Small ribosomal subunit protein uS4 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		209 a.a.
208 a.a.*
Protein chain
Pfam   ArchSchema ?
Q5SHQ5  (RS5_THET8) -  Small ribosomal subunit protein uS5 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		162 a.a.
150 a.a.
Protein chain
Q5SLP8  (RS6_THET8) -  Small ribosomal subunit protein bS6 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		101 a.a.
101 a.a.
Protein chain
Pfam   ArchSchema ?
P17291  (RS7_THET8) -  Small ribosomal subunit protein uS7 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		156 a.a.
155 a.a.
Protein chain
Pfam   ArchSchema ?
P0DOY9  (RS8_THET8) -  Small ribosomal subunit protein uS8 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		138 a.a.
138 a.a.
Protein chain
Pfam   ArchSchema ?
P80374  (RS9_THET8) -  Small ribosomal subunit protein uS9 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		128 a.a.
127 a.a.*
Protein chain
Pfam   ArchSchema ?
Q5SHN7  (RS10_THET8) -  Small ribosomal subunit protein uS10 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		105 a.a.
98 a.a.
Protein chain
Pfam   ArchSchema ?
P80376  (RS11_THET8) -  Small ribosomal subunit protein uS11 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		129 a.a.
119 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHN3  (RS12_THET8) -  Small ribosomal subunit protein uS12 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		132 a.a.
124 a.a.
Protein chain
Pfam   ArchSchema ?
P80377  (RS13_THET8) -  Small ribosomal subunit protein uS13 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		126 a.a.
125 a.a.
Protein chain
Pfam   ArchSchema ?
P0DOY6  (RS14Z_THET8) -  Small ribosomal subunit protein uS14 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		61 a.a.
60 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SJ76  (RS15_THET8) -  Small ribosomal subunit protein uS15 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		89 a.a.
88 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SJH3  (RS16_THET8) -  Small ribosomal subunit protein bS16 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		88 a.a.
83 a.a.
Protein chain
Pfam   ArchSchema ?
P0DOY7  (RS17_THET8) -  Small ribosomal subunit protein uS17 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		105 a.a.
104 a.a.*
Protein chain
Pfam   ArchSchema ?
Q5SLQ0  (RS18_THET8) -  Small ribosomal subunit protein bS18 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		88 a.a.
73 a.a.*
Protein chain
Pfam   ArchSchema ?
Q5SHP2  (RS19_THET8) -  Small ribosomal subunit protein uS19 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		93 a.a.
80 a.a.
Protein chain
Pfam   ArchSchema ?
P80380  (RS20_THET8) -  Small ribosomal subunit protein bS20 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		106 a.a.
99 a.a.*
Protein chain
Q5SIH3  (RSHX_THET8) -  Small ribosomal subunit protein bTHX from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		27 a.a.
24 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHR1  (IF1_THET8) -  Translation initiation factor IF-1 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
Seq:
Struc: 		72 a.a.
71 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 6 residue positions (black crosses)

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- ... 1507 bases
  C-U-U-U-C-U 6 bases

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

 

 
DOI no: 10.1126/science.1057766 Science 291:498-501 (2001)
PubMed id: 11228145  
 
 
Crystal structure of an initiation factor bound to the 30S ribosomal subunit.
A.P.Carter, W.M.Clemons, D.E.Brodersen, R.J.Morgan-Warren, T.Hartsch, B.T.Wimberly, V.Ramakrishnan.
 
  ABSTRACT  
 
Initiation of translation at the correct position on messenger RNA is essential for accurate protein synthesis. In prokaryotes, this process requires three initiation factors: IF1, IF2, and IF3. Here we report the crystal structure of a complex of IF1 and the 30S ribosomal subunit. Binding of IF1 occludes the ribosomal A site and flips out the functionally important bases A1492 and A1493 from helix 44 of 16S RNA, burying them in pockets in IF1. The binding of IF1 causes long-range changes in the conformation of H44 and leads to movement of the domains of 30S with respect to each other. The structure explains how localized changes at the ribosomal A site lead to global alterations in the conformation of the 30S subunit.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Stereo views of electron density maps of the 30S-IF1 complex, showing a sheet in IF1. (A) [A]-weighted 2mF[o] DF[c] maps from an initial refinement in which no model for IF1 was included. (B) The corresponding maps after refinement with IF1. 		Figure 2.
Fig. 2. Interaction of IF1 with the 30S subunit. (A) Close-up of the IF1 binding site, with IF1 in purple, helix 44 in cyan, the 530 loop in green, and protein S12 in orange. These colors are used throughout Figs. 2 and 3. (B) Overview showing the position of IF1 (purple) with respect to the 30S subunit (gray). H44, 530 loop, and S12 are colored as in (A). H, head; Bo, body; N, neck; Sh, shoulder; P, platform. (C) Overview of the 30S showing helix 44, S12, and the 530 loop as in (A), but with the A- P- and E-site tRNAs modeled as described in the text, in dark blue, orange, and yellow, respectively. Comparison with (B) shows that IF1 would block the binding of A-site tRNA. (D) Stereo pair showing A1492 and A1493 in H44 buried into protein pockets formed by IF1 and a combination of IF1 and S12.
 
  The above figures are reprinted by permission from the AAAs: Science (2001, 291, 498-501) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
21368145 A.S.Yassin, M.E.Haque, P.P.Datta, K.Elmore, N.K.Banavali, L.L.Spremulli, and R.K.Agrawal (2011).
Insertion domain within mammalian mitochondrial translation initiation factor 2 serves the role of eubacterial initiation factor 1.
  Proc Natl Acad Sci U S A, 108, 3918-3923.
PDB codes: 3izy 3izz
22002225 B.S.Shin, J.R.Kim, S.E.Walker, J.Dong, J.R.Lorsch, and T.E.Dever (2011).
Initiation factor eIF2γ promotes eIF2-GTP-Met-tRNAi(Met) ternary complex binding to the 40S ribosome.
  Nat Struct Mol Biol, 18, 1227-1234.  
  21418143 J.M.Belotserkovsky, G.I.Isak, and L.A.Isaksson (2011).
Suppression of a cold-sensitive mutant initiation factor 1 by alterations in the 23S rRNA maturation region.
  FEBS J, 278, 1745-1756.  
21205638 J.Rabl, M.Leibundgut, S.F.Ataide, A.Haag, and N.Ban (2011).
Crystal structure of the eukaryotic 40S ribosomal subunit in complex with initiation factor 1.
  Science, 331, 730-736.
PDB codes: 2xzm 2xzn
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.  
20487556 H.Hartman, and T.F.Smith (2010).
GTPases and the origin of the ribosome.
  Biol Direct, 5, 36.  
20603079 H.S.Zaher, and R.Green (2010).
Hyperaccurate and error-prone ribosomes exploit distinct mechanisms during tRNA selection.
  Mol Cell, 39, 110-120.  
20192776 J.A.Dunkle, and J.H.Cate (2010).
Ribosome structure and dynamics during translocation and termination.
  Annu Rev Biophys, 39, 227-244.  
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.  
20713520 M.A.Skabkin, O.V.Skabkina, V.Dhote, A.A.Komar, C.U.Hellen, and T.V.Pestova (2010).
Activities of Ligatin and MCT-1/DENR in eukaryotic translation initiation and ribosomal recycling.
  Genes Dev, 24, 1787-1801.  
20091748 M.Mihailovich, C.Militti, T.Gabaldón, and F.Gebauer (2010).
Eukaryotic cold shock domain proteins: highly versatile regulators of gene expression.
  Bioessays, 32, 109-118.  
21054500 W.S.Song, S.M.Ryou, H.M.Kim, C.O.Jeon, J.M.Kim, S.H.Han, S.W.Kim, J.P.Szatkiewicz, P.R.Cunningham, and K.Lee (2010).
Functional investigation of residue G791 of Escherichia coli 16S rRNA: implication of initiation factor 1 in the restoration of P-site function.
  FEMS Microbiol Lett, 313, 141-147.  
19493673 A.G.Myasnikov, A.Simonetti, S.Marzi, and B.P.Klaholz (2009).
Structure-function insights into prokaryotic and eukaryotic translation initiation.
  Curr Opin Struct Biol, 19, 300-309.  
19656820 A.Yonath (2009).
Large facilities and the evolving ribosome, the cellular machine for genetic-code translation.
  J R Soc Interface, 6, S575-S585.  
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.  
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.  
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.  
19702336 J.L.Miller, H.Cimen, H.Koc, and E.C.Koc (2009).
Phosphorylated proteins of the mammalian mitochondrial ribosome: implications in protein synthesis.
  J Proteome Res, 8, 4789-4798.  
18976658 M.G.Acker, B.S.Shin, J.S.Nanda, A.K.Saini, T.E.Dever, and J.R.Lorsch (2009).
Kinetic analysis of late steps of eukaryotic translation initiation.
  J Mol Biol, 385, 491-506.  
19595714 R.A.Marshall, C.E.Aitken, and J.D.Puglisi (2009).
GTP hydrolysis by IF2 guides progression of the ribosome into elongation.
  Mol Cell, 35, 37-47.  
19132006 S.Nonin-Lecomte, N.Germain-Amiot, R.Gillet, M.Hallier, L.Ponchon, F.Dardel, and B.Felden (2009).
Ribosome hijacking: a role for small protein B during trans-translation.
  EMBO Rep, 10, 160-165.  
19838167 T.M.Schmeing, and V.Ramakrishnan (2009).
What recent ribosome structures have revealed about the mechanism of translation.
  Nature, 461, 1234-1242.  
19561193 Y.Yu, A.Marintchev, V.G.Kolupaeva, A.Unbehaun, T.Veryasova, S.C.Lai, P.Hong, G.Wagner, C.U.Hellen, and T.V.Pestova (2009).
Position of eukaryotic translation initiation factor eIF1A on the 40S ribosomal subunit mapped by directed hydroxyl radical probing.
  Nucleic Acids Res, 37, 5167-5182.  
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
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.  
18497739 M.Y.Pavlov, A.Antoun, M.Lovmar, and M.Ehrenberg (2008).
Complementary roles of initiation factor 1 and ribosome recycling factor in 70S ribosome splitting.
  EMBO J, 27, 1706-1717.  
18243113 R.Gaur, D.Grasso, P.P.Datta, P.D.Krishna, G.Das, A.Spencer, R.K.Agrawal, L.Spremulli, and U.Varshney (2008).
A single mammalian mitochondrial translation initiation factor functionally replaces two bacterial factors.
  Mol Cell, 29, 180-190.  
18976282 S.Kapralou, A.Fabbretti, C.Garulli, R.Spurio, C.O.Gualerzi, A.E.Dahlberg, and C.L.Pon (2008).
Translation initiation factor IF1 of Bacillus stearothermophilus and Thermus thermophilus substitute for Escherichia coli IF1 in vivo and in vitro without a direct IF1-IF2 interaction.
  Mol Microbiol, 70, 1368-1377.  
18094123 S.de Breyne, Y.Yu, T.V.Pestova, and C.U.Hellen (2008).
Factor requirements for translation initiation on the Simian picornavirus internal ribosomal entry site.
  RNA, 14, 367-380.  
18223068 T.L.Campbell, and E.D.Brown (2008).
Genetic interaction screens with ordered overexpression and deletion clone sets implicate the Escherichia coli GTPase YjeQ in late ribosome biogenesis.
  J Bacteriol, 190, 2537-2545.  
17956730 A.V.Pisarev, C.U.Hellen, and T.V.Pestova (2007).
Recycling of eukaryotic posttermination ribosomal complexes.
  Cell, 131, 286-299.  
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.  
18072984 C.S.Fraser, and J.A.Doudna (2007).
Quantitative studies of ribosome conformational dynamics.
  Q Rev Biophys, 40, 163-189.  
17592040 D.L.Taliaferro, and P.J.Farabaugh (2007).
Testing constraints on rRNA bases that make nonsequence-specific contacts with the codon-anticodon complex in the ribosomal A site.
  RNA, 13, 1279-1286.  
17942743 D.Qin, N.M.Abdi, and K.Fredrick (2007).
Characterization of 16S rRNA mutations that decrease the fidelity of translation initiation.
  RNA, 13, 2348-2355.  
17238926 G.S.Allen, and J.Frank (2007).
Structural insights on the translation initiation complex: ghosts of a universal initiation complex.
  Mol Microbiol, 63, 941-950.  
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.  
17299130 K.Takada, C.Takemoto, M.Kawazoe, T.Konno, K.Hanawa-Suetsugu, S.Lee, M.Shirouzu, S.Yokoyama, A.Muto, and H.Himeno (2007).
In vitro trans-translation of Thermus thermophilus: ribosomal protein S1 is not required for the early stage of trans-translation.
  RNA, 13, 503-510.  
17434125 L.A.Passmore, T.M.Schmeing, D.Maag, D.J.Applefield, M.G.Acker, M.A.Algire, J.R.Lorsch, and V.Ramakrishnan (2007).
The eukaryotic translation initiation factors eIF1 and eIF1A induce an open conformation of the 40S ribosome.
  Mol Cell, 26, 41-50.  
17462025 M.Giangrossi, A.Brandi, A.M.Giuliodori, C.O.Gualerzi, and C.L.Pon (2007).
Cold-shock-induced de novo transcription and translation of infA and role of IF1 during cold adaptation.
  Mol Microbiol, 64, 807-821.  
17996707 P.P.Datta, D.N.Wilson, M.Kawazoe, N.K.Swami, T.Kaminishi, M.R.Sharma, T.M.Booth, C.Takemoto, P.Fucini, S.Yokoyama, and R.K.Agrawal (2007).
Structural aspects of RbfA action during small ribosomal subunit assembly.
  Mol Cell, 28, 434-445.
PDB codes: 2dyj 2r1c 2r1g
17283211 S.V.Steinberg, and Y.I.Boutorine (2007).
G-ribo: a new structural motif in ribosomal RNA.
  RNA, 13, 549-554.  
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
16682566 A.Raman, C.Guarraia, D.Taliaferro, G.Stahl, and P.J.Farabaugh (2006).
An mRNA sequence derived from a programmed frameshifting signal decreases codon discrimination during translation initiation.
  RNA, 12, 1154-1160.  
16510876 A.V.Pisarev, V.G.Kolupaeva, V.P.Pisareva, W.C.Merrick, C.U.Hellen, and T.V.Pestova (2006).
Specific functional interactions of nucleotides at key -3 and +4 positions flanking the initiation codon with components of the mammalian 48S translation initiation complex.
  Genes Dev, 20, 624-636.  
16421445 H.Kettenberger, and P.Cramer (2006).
Fluorescence detection of nucleic acids and proteins in multi-component crystals.
  Acta Crystallogr D Biol Crystallogr, 62, 146-150.  
17069639 J.J.Gillespie, J.S.Johnston, J.J.Cannone, and R.R.Gutell (2006).
Characteristics of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) rRNA genes of Apis mellifera (Insecta: Hymenoptera): structure, organization, and retrotransposable elements.
  Insect Mol Biol, 15, 657-686.  
16452297 J.Kondo, A.Urzhumtsev, and E.Westhof (2006).
Two conformational states in the crystal structure of the Homo sapiens cytoplasmic ribosomal decoding A site.
  Nucleic Acids Res, 34, 676-685.
PDB code: 2fqn
16538608 K.Réblová, F.Lankas, F.Rázga, M.V.Krasovska, J.Koca, and J.Sponer (2006).
Structure, dynamics, and elasticity of free 16s rRNA helix 44 studied by molecular dynamics simulations.
  Biopolymers, 82, 504-520.  
16565414 L.D.Kapp, S.E.Kolitz, and J.R.Lorsch (2006).
Yeast initiator tRNA identity elements cooperate to influence multiple steps of translation initiation.
  RNA, 12, 751-764.  
16391058 M.A.Díaz, R.K.Cooper, A.Cloeckaert, and R.J.Siebeling (2006).
Plasmid-mediated high-level gentamicin resistance among enteric bacteria isolated from pet turtles in Louisiana.
  Appl Environ Microbiol, 72, 306-312.  
16611927 M.Hallier, J.Desreac, and B.Felden (2006).
Small protein B interacts with the large and the small subunits of a stalled ribosome during trans-translation.
  Nucleic Acids Res, 34, 1935-1943.  
16619019 N.Gao, and J.Frank (2006).
A library of RNA bridges.
  Nat Chem Biol, 2, 231-232.  
16600874 S.M.Studer, and S.Joseph (2006).
Unfolding of mRNA secondary structure by the bacterial translation initiation complex.
  Mol Cell, 22, 105-115.  
16284619 A.G.Myasnikov, S.Marzi, A.Simonetti, A.M.Giuliodori, C.O.Gualerzi, G.Yusupova, M.Yusupov, and B.P.Klaholz (2005).
Conformational transition of initiation factor 2 from the GTP- to GDP-bound state visualized on the ribosome.
  Nat Struct Mol Biol, 12, 1145-1149.  
15876367 A.R.Cukras, and R.Green (2005).
Multiple effects of S13 in modulating the strength of intersubunit interactions in the ribosome during translation.
  J Mol Biol, 349, 47-59.  
15755955 B.S.Laursen, H.P.Sørensen, K.K.Mortensen, and H.U.Sperling-Petersen (2005).
Initiation of protein synthesis in bacteria.
  Microbiol Mol Biol Rev, 69, 101-123.  
16193068 C.A.Fekete, D.J.Applefield, S.A.Blakely, N.Shirokikh, T.Pestova, J.R.Lorsch, and A.G.Hinnebusch (2005).
The eIF1A C-terminal domain promotes initiation complex assembly, scanning and AUG selection in vivo.
  EMBO J, 24, 3588-3601.  
16266719 D.L.Theobald, and D.S.Wuttke (2005).
Divergent evolution within protein superfolds inferred from profile-based phylogenetics.
  J Mol Biol, 354, 722-737.  
15616575 D.N.Wilson, F.Schluenzen, J.M.Harms, T.Yoshida, T.Ohkubo, R.Albrecht, J.Buerger, Y.Kobayashi, and P.Fucini (2005).
X-ray crystallography study on ribosome recycling: the mechanism of binding and action of RRF on the 50S ribosomal subunit.
  EMBO J, 24, 251-260.
PDB code: 1y69
16336118 D.N.Wilson, J.M.Harms, K.H.Nierhaus, F.Schlünzen, and P.Fucini (2005).
Species-specific antibiotic-ribosome interactions: implications for drug development.
  Biol Chem, 386, 1239-1252.  
15952884 J.M.Ogle, and V.Ramakrishnan (2005).
Structural insights into translational fidelity.
  Annu Rev Biochem, 74, 129-177.  
15630477 M.P.Robertson, H.Igel, R.Baertsch, D.Haussler, M.Ares, and W.G.Scott (2005).
The structure of a rigorously conserved RNA element within the SARS virus genome.
  PLoS Biol, 3, e5.
PDB code: 1xjr
15808741 P.Londei (2005).
Evolution of translational initiation: new insights from the archaea.
  FEMS Microbiol Rev, 29, 185-200.  
15963891 S.R.Holbrook (2005).
RNA structure: the long and the short of it.
  Curr Opin Struct Biol, 15, 302-308.  
15703437 V.G.Kolupaeva, A.Unbehaun, I.B.Lomakin, C.U.Hellen, and T.V.Pestova (2005).
Binding of eukaryotic initiation factor 3 to ribosomal 40S subunits and its role in ribosomal dissociation and anti-association.
  RNA, 11, 470-486.  
15601822 A.Unbehaun, S.I.Borukhov, C.U.Hellen, and T.V.Pestova (2004).
Release of initiation factors from 48S complexes during ribosomal subunit joining and the link between establishment of codon-anticodon base-pairing and hydrolysis of eIF2-bound GTP.
  Genes Dev, 18, 3078-3093.  
15502846 A.Vila-Sanjurjo, B.S.Schuwirth, C.W.Hau, and J.H.Cate (2004).
Structural basis for the control of translation initiation during stress.
  Nat Struct Mol Biol, 11, 1054-1059.
PDB codes: 1voq 1vor 1vos 1vou 1vov 1vow 1vox 1voy 1voz 1vp0
15315759 C.M.Spahn, E.Jan, A.Mulder, R.A.Grassucci, P.Sarnow, and J.Frank (2004).
Cryo-EM visualization of a viral internal ribosome entry site bound to human ribosomes: the IRES functions as an RNA-based translation factor.
  Cell, 118, 465-475.  
15466596 H.Himeno, K.Hanawa-Suetsugu, T.Kimura, K.Takagi, W.Sugiyama, S.Shirata, T.Mikami, F.Odagiri, Y.Osanai, D.Watanabe, S.Goto, L.Kalachnyuk, C.Ushida, and A.Muto (2004).
A novel GTPase activated by the small subunit of ribosome.
  Nucleic Acids Res, 32, 5303-5309.  
15375145 J.Hager, B.L.Staker, and U.Jakob (2004).
Substrate binding analysis of the 23S rRNA methyltransferase RrmJ.
  J Bacteriol, 186, 6634-6642.  
15534366 J.Thompson, and A.E.Dahlberg (2004).
Testing the conservation of the translational machinery over evolution in diverse environments: assaying Thermus thermophilus ribosomes and initiation factors in a coupled transcription-translation system from Escherichia coli.
  Nucleic Acids Res, 32, 5954-5961.  
15189156 L.D.Kapp, and J.R.Lorsch (2004).
The molecular mechanics of eukaryotic translation.
  Annu Rev Biochem, 73, 657-704.  
14761973 L.Yatime, E.Schmitt, S.Blanquet, and Y.Mechulam (2004).
Functional molecular mapping of archaeal translation initiation factor 2.
  J Biol Chem, 279, 15984-15993.  
14691946 M.D.Disney, J.L.Childs, and D.H.Turner (2004).
New approaches to targeting RNA with oligonucleotides: inhibition of group I intron self-splicing.
  Biopolymers, 73, 151-161.  
15178758 R.K.Agrawal, M.R.Sharma, M.C.Kiel, G.Hirokawa, T.M.Booth, C.M.Spahn, R.A.Grassucci, A.Kaji, and J.Frank (2004).
Visualization of ribosome-recycling factor on the Escherichia coli 70S ribosome: functional implications.
  Proc Natl Acad Sci U S A, 101, 8900-8905.
PDB codes: 1t1m 1t1o
14670970 T.Udagawa, Y.Shimizu, and T.Ueda (2004).
Evidence for the translation initiation of leaderless mRNAs by the intact 70 S ribosome without its dissociation into subunits in eubacteria.
  J Biol Chem, 279, 8539-8546.  
15332113 T.V.Pestova, I.B.Lomakin, and C.U.Hellen (2004).
Position of the CrPV IRES on the 40S subunit and factor dependence of IRES/80S ribosome assembly.
  EMBO Rep, 5, 906-913.  
14728680 V.Croitoru, M.Bucheli-Witschel, P.Hägg, F.Abdulkarim, and L.A.Isaksson (2004).
Generation and characterization of functional mutants in the translation initiation factor IF1 of Escherichia coli.
  Eur J Biochem, 271, 534-544.  
15337844 Z.Druzina, and B.S.Cooperman (2004).
Photolabile anticodon stem-loop analogs of tRNAPhe as probes of ribosomal structure and structural fluctuation at the decoding center.
  RNA, 10, 1550-1562.  
12569173 A.Marintchev, V.G.Kolupaeva, T.V.Pestova, and G.Wagner (2003).
Mapping the binding interface between human eukaryotic initiation factors 1A and 5B: a new interaction between old partners.
  Proc Natl Acad Sci U S A, 100, 1535-1540.  
12853578 A.Vila-Sanjurjo, W.K.Ridgeway, V.Seymaner, W.Zhang, S.Santoso, K.Yu, and J.H.Cate (2003).
X-ray crystal structures of the WT and a hyper-accurate ribosome from Escherichia coli.
  Proc Natl Acad Sci U S A, 100, 8682-8687.
PDB codes: 1pns 1pnu 1pnx 1pny
12598368 D.L.Theobald, R.M.Mitton-Fry, and D.S.Wuttke (2003).
Nucleic acid recognition by OB-fold proteins.
  Annu Rev Biophys Biomol Struct, 32, 115-133.  
12514125 D.S.Olsen, E.M.Savner, A.Mathew, F.Zhang, T.Krishnamoorthy, L.Phan, and A.G.Hinnebusch (2003).
Domains of eIF1A that mediate binding to eIF2, eIF3 and eIF5B and promote ternary complex recruitment in vivo.
  EMBO J, 22, 193-204.  
12937172 F.Robert, and L.Brakier-Gingras (2003).
A functional interaction between ribosomal proteins S7 and S11 within the bacterial ribosome.
  J Biol Chem, 278, 44913-44920.  
12878726 F.Tama, M.Valle, J.Frank, and C.L.Brooks (2003).
Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy.
  Proc Natl Acad Sci U S A, 100, 9319-9323.  
12548626 G.M.Culver (2003).
Assembly of the 30S ribosomal subunit.
  Biopolymers, 68, 234-249.  
14600024 I.B.Lomakin, V.G.Kolupaeva, A.Marintchev, G.Wagner, and T.V.Pestova (2003).
Position of eukaryotic initiation factor eIF1 on the 40S ribosomal subunit determined by directed hydroxyl radical probing.
  Genes Dev, 17, 2786-2797.  
12548625 J.Frank (2003).
Electron microscopy of functional ribosome complexes.
  Biopolymers, 68, 223-233.  
12651896 L.Valásek, A.A.Mathew, B.S.Shin, K.H.Nielsen, B.Szamecz, and A.G.Hinnebusch (2003).
The yeast eIF3 subunits TIF32/a, NIP1/c, and eIF5 make critical connections with the 40S ribosome in vivo.
  Genes Dev, 17, 786-799.  
12581660 N.Sonenberg, and T.E.Dever (2003).
Eukaryotic translation initiation factors and regulators.
  Curr Opin Struct Biol, 13, 56-63.  
12869707 S.Marzi, W.Knight, L.Brandi, E.Caserta, N.Soboleva, W.E.Hill, C.O.Gualerzi, and J.S.Lodmell (2003).
Ribosomal localization of translation initiation factor IF2.
  RNA, 9, 958-969.  
11988470 A.Yonath (2002).
The search and its outcome: high-resolution structures of ribosomal particles from mesophilic, thermophilic, and halophilic bacteria at various functional states.
  Annu Rev Biophys Biomol Struct, 31, 257-273.  
12244297 C.S.Tung, S.Joseph, and K.Y.Sanbonmatsu (2002).
All-atom homology model of the Escherichia coli 30S ribosomal subunit.
  Nat Struct Biol, 9, 750-755.
PDB code: 1m5g
12095986 E.C.Koc, and L.L.Spremulli (2002).
Identification of mammalian mitochondrial translational initiation factor 3 and examination of its role in initiation complex formation with natural mRNAs.
  J Biol Chem, 277, 35541-35549.  
12166646 G.A.Otto, P.J.Lukavsky, A.M.Lancaster, P.Sarnow, and J.D.Puglisi (2002).
Ribosomal proteins mediate the hepatitis C virus IRES-HeLa 40S interaction.
  RNA, 8, 913-923.  
11927568 G.Dong, J.Nowakowski, and D.W.Hoffman (2002).
Structure of small protein B: the protein component of the tmRNA-SmpB system for ribosome rescue.
  EMBO J, 21, 1845-1854.
PDB code: 1k8h
12169671 J.L.Childs, M.D.Disney, and D.H.Turner (2002).
Oligonucleotide directed misfolding of RNA inhibits Candida albicans group I intron splicing.
  Proc Natl Acad Sci U S A, 99, 11091-11096.  
11867615 M.A.Schäfer, A.O.Tastan, S.Patzke, G.Blaha, C.M.Spahn, D.N.Wilson, and K.H.Nierhaus (2002).
Codon-anticodon interaction at the P site is a prerequisite for tRNA interaction with the small ribosomal subunit.
  J Biol Chem, 277, 19095-19105.  
12171653 M.H.Weber, and M.A.Marahiel (2002).
Coping with the cold: the cold shock response in the Gram-positive soil bacterium Bacillus subtilis.
  Philos Trans R Soc Lond B Biol Sci, 357, 895-907.  
12093756 M.Valle, J.Sengupta, N.K.Swami, R.A.Grassucci, N.Burkhardt, K.H.Nierhaus, R.K.Agrawal, and J.Frank (2002).
Cryo-EM reveals an active role for aminoacyl-tRNA in the accommodation process.
  EMBO J, 21, 3557-3567.
PDB codes: 1ls2 1lu3
12426363 S.M.O'Donnell, and G.R.Janssen (2002).
Leaderless mRNAs bind 70S ribosomes more strongly than 30S ribosomal subunits in Escherichia coli.
  J Bacteriol, 184, 6730-6733.  
11909526 V.Ramakrishnan (2002).
Ribosome structure and the mechanism of translation.
  Cell, 108, 557-572.  
11839295 X.Cheng, and R.M.Blumenthal (2002).
Cytosines do it, thymines do it, even pseudouridines do it--base flipping by an enzyme that acts on RNA.
  Structure, 10, 127-129.  
11953318 Y.Yang, N.Declerck, X.Manival, S.Aymerich, and M.Kochoyan (2002).
Solution structure of the LicT-RNA antitermination complex: CAT clamping RAT.
  EMBO J, 21, 1987-1997.
PDB code: 1l1c
12762007 A.Bashan, I.Agmon, R.Zarivach, F.Schluenzen, J.Harms, M.Pioletti, H.Bartels, M.Gluehmann, H.Hansen, T.Auerbach, F.Franceschi, and A.Yonath (2001).
High-resolution structures of ribosomal subunits: initiation, inhibition, and conformational variability.
  Cold Spring Harb Symp Quant Biol, 66, 43-56.  
11738593 A.Roll-Mecak, B.S.Shin, T.E.Dever, and S.K.Burley (2001).
Engaging the ribosome: universal IFs of translation.
  Trends Biochem Sci, 26, 705-709.  
11290319 B.A.Maguire, and R.A.Zimmermann (2001).
The ribosome in focus.
  Cell, 104, 813-816.  
11701127 C.M.Spahn, R.Beckmann, N.Eswar, P.A.Penczek, A.Sali, G.Blobel, and J.Frank (2001).
Structure of the 80S ribosome from Saccharomyces cerevisiae--tRNA-ribosome and subunit-subunit interactions.
  Cell, 107, 373-386.
PDB codes: 1k5x 1k5y
12762039 C.O.Gualerzi, L.Brandi, E.Caserta, C.Garofalo, M.Lammi, A.La Teana, D.Petrelli, R.Spurio, J.Tomsic, and C.L.Pon (2001).
Initiation factors in the early events of mRNA translation in bacteria.
  Cold Spring Harb Symp Quant Biol, 66, 363-376.  
12762005 D.E.Brodersen, A.P.Carter, W.M.Clemons, R.J.Morgan-Warren, F.V.Murphy, J.M.Ogle, M.J.Tarry, B.T.Wimberly, and V.Ramakrishnan (2001).
Atomic structures of the 30S subunit and its complexes with ligands and antibiotics.
  Cold Spring Harb Symp Quant Biol, 66, 17-32.  
11500382 D.Petrelli, A.LaTeana, C.Garofalo, R.Spurio, C.L.Pon, and C.O.Gualerzi (2001).
Translation initiation factor IF3: two domains, five functions, one mechanism?
  EMBO J, 20, 4560-4569.  
11566123 G.M.Culver (2001).
Meanderings of the mRNA through the ribosome.
  Structure, 9, 751-758.  
12762045 G.R.Andersen, and J.Nyborg (2001).
Structural studies of eukaryotic elongation factors.
  Cold Spring Harb Symp Quant Biol, 66, 425-437.  
12762008 H.F.Noller, M.M.Yusupov, G.Z.Yusupova, A.Baucom, K.Lieberman, L.Lancaster, A.Dallas, K.Fredrick, T.N.Earnest, and J.H.Cate (2001).
Structure of the ribosome at 5.5 A resolution and its interactions with functional ligands.
  Cold Spring Harb Symp Quant Biol, 66, 57-66.  
12762009 J.Frank, and R.K.Agrawal (2001).
Ratchet-like movements between the two ribosomal subunits: their implications in elongation factor recognition and tRNA translocation.
  Cold Spring Harb Symp Quant Biol, 66, 67-75.  
11717297 M.H.Weber, C.L.Beckering, and M.A.Marahiel (2001).
Complementation of cold shock proteins by translation initiation factor IF1 in vivo.
  J Bacteriol, 183, 7381-7386.  
11741540 S.Soelaiman, K.Jakes, N.Wu, C.Li, and M.Shoham (2001).
Crystal structure of colicin E3: implications for cell entry and ribosome inactivation.
  Mol Cell, 8, 1053-1062.
PDB code: 1jch
12762012 S.T.Gregory, M.A.Bayfield, M.O'Connor, J.Thompson, and A.E.Dahlberg (2001).
Probing ribosome structure and function by mutagenesis.
  Cold Spring Harb Symp Quant Biol, 66, 101-108.  
12762041 T.V.Pestova, and C.U.Hellen (2001).
Functions of eukaryotic factors in initiation of translation.
  Cold Spring Harb Symp Quant Biol, 66, 389-396.  
11297922 V.Ramakrishnan, and P.B.Moore (2001).
Atomic structures at last: the ribosome in 2000.
  Curr Opin Struct Biol, 11, 144-154.  
11714910 W.Li, and D.W.Hoffman (2001).
Structure and dynamics of translation initiation factor aIF-1A from the archaeon Methanococcus jannaschii determined by NMR spectroscopy.
  Protein Sci, 10, 2426-2438.
PDB code: 1jt8
11557810 X.Cheng, and R.J.Roberts (2001).
AdoMet-dependent methylation, DNA methyltransferases and base flipping.
  Nucleic Acids Res, 29, 3784-3795.  
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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