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PDBsum entry 1ekc

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protein dna_rna Protein-protein interface(s) links
Ribosome PDB id
1ekc
Jmol
Contents
Protein chains
98 a.a.
88 a.a.
50 a.a.
DNA/RNA
Superseded by: 1g1x
PDB id:
1ekc
Name: Ribosome
Title: Structure of ribosomal proteins s15, s6, s18, and 16s ribosomal RNA
Structure: 30s ribosomal protein s6. Chain: a, f. 30s ribosomal protein s15. Chain: b, g. 30s ribosomal protein s18. Chain: c, h. 16s ribosomal RNA. Chain: d, i. Fragment: residues 582-675.
Source: Thermus thermophilus. Bacteria. Synthetic: yes. Other_details: sequence from t. Thermophilus. Other_details: sequence from t. Thermophilus
Resolution:
2.60Å     R-factor:   0.266     R-free:   0.298
Authors: S.C.Agalarov,G.S.Prasad,P.M.Funke,C.D.Stout,J.R.Williamson
Key ref:
S.C.Agalarov et al. (2000). Structure of the S15,S6,S18-rRNA complex: assembly of the 30S ribosome central domain. Science, 288, 107-113. PubMed id: 10753109 DOI: 10.1126/science.288.5463.107
Date:
07-Mar-00     Release date:   17-Apr-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P23370  (RS6_THETH) -  30S ribosomal protein S6
Seq:
Struc:
101 a.a.
98 a.a.
Protein chains
Pfam   ArchSchema ?
P80378  (RS15_THETH) -  30S ribosomal protein S15
Seq:
Struc:
89 a.a.
88 a.a.*
Protein chains
No UniProt id for this chain
Struc: 50 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 

 
DOI no: 10.1126/science.288.5463.107 Science 288:107-113 (2000)
PubMed id: 10753109  
 
 
Structure of the S15,S6,S18-rRNA complex: assembly of the 30S ribosome central domain.
S.C.Agalarov, G.Sridhar Prasad, P.M.Funke, C.D.Stout, J.R.Williamson.
 
  ABSTRACT  
 
The crystal structure of a 70-kilodalton ribonucleoprotein complex from the central domain of the Thermus thermophilus 30S ribosomal subunit was solved at 2.6 angstrom resolution. The complex consists of a 104-nucleotide RNA fragment composed of two three-helix junctions that lie at the end of a central helix, and the ribosomal proteins S15, S6, and S18. S15 binds the ribosomal RNA early in the assembly of the 30S ribosomal subunit, stabilizing a conformational reorganization of the two three-helix junctions that creates the RNA fold necessary for subsequent binding of S6 and S18. The structure of the complex demonstrates the central role of S15-induced reorganization of central domain RNA for the subsequent steps of ribosome assembly.
 
  Selected figure(s)  
 
Figure 4.
Fig. 4. Details of S15-Tth T4 RNA interactions. Bases and side chains are rendered as thick sticks, riboses as thin sticks, groups involved in interactions are colored by atom. (A) S15 interactions with the helix 20, 21, 22 junction. Nucleotides U652, G654, G752, A753, and C754 in the junction are blue. The OH group of the highly conserved Tyr68 contacts G752 O3', while the side-chain ring packs tightly against C754. S15 residues in the 1- 2 loop make direct minor groove contacts in helix 22, including Asp20 to G750 O2'; Thr21 to G657 N2 and O2'; Gly22 backbone N and O to G750 O2' and N2, respectively; Thr24 to U751 O2'; and Gln27 to C656 O2 and O2' and to G750 N2. (B) S15 interactions with the helix 22 purine-rich loop. Residue His41 stacks under His45, forms a hydrogen bond with Asp48, and contacts C739 O2', while His45 contacts G668 N2. Residue Asp48 interacts with Ser51 and contacts G667 N2 and O2', while Ser51 makes contacts to U740 O2 and O2', and to G666 N2. (C) S15 interaction with the helix 23a GAAG tetraloop. Nucleotide A665 from helix 22 is in green, all bases in helix 23a are in pink. Residue His50 from 3 contacts A728 N6, A729 N6, and G730 O6, while conserved residue Arg53 stacks below the purine ring of A728. Figure created with InsightII.
Figure 5.
Fig. 5. Details of S6:S18-Tth T4 RNA interaction. Molecules are rendered and colored as in Fig. 4, with phosphate groups shown as spheres. S6 residues located near the NH[2]-terminus, in 2, and in 4 make electrostatic and hydrogen-bonding contacts to the Tth T4 RNA in the minor groove between helix 22 and helix 23b. These contacts include Arg2, Tyr4, and Lys92 to A737 and C738 phosphates, Arg87 to G673 phosphate and O3', Val90 carbonyl oxygen to C736 O2', and Asn73 to G670 N2 and A737 N3. The charged S18 residues Lys68, Lys71, and Arg72, from the COOH-terminal end of the helix, contact the phosphate groups of C735, C736, and A737 in helix 22 near the upper three-helix junction. Residue Arg64, which is located near the other end of the S18 helix, contacts the G664 phosphate located across the narrowed major groove of helix 22 near the interhelical A665:G724 base pair. Residues Lys71 and Arg74 also make four base-specific contacts to the single-stranded nucleotides C719, C720, and G721 in helix 23a. Figure created with InsightII.
 
  The above figures are reprinted by permission from the AAAs: Science (2000, 288, 107-113) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22337051 E.A.Dethoff, J.Chugh, A.M.Mustoe, and H.M.Al-Hashimi (2012).
Functional complexity and regulation through RNA dynamics.
  Nature, 482, 322-330.  
20207951 A.E.Bunner, A.H.Beck, and J.R.Williamson (2010).
Kinetic cooperativity in Escherichia coli 30S ribosomal subunit reconstitution reveals additional complexity in the assembly landscape.
  Proc Natl Acad Sci U S A, 107, 5417-5422.  
  19937661 A.Ohman, T.Oman, and M.Oliveberg (2010).
Solution structures and backbone dynamics of the ribosomal protein S6 and its permutant P(54-55).
  Protein Sci, 19, 183-189.
PDB codes: 2kjv 2kjw
19706509 A.C.Lamanna, and K.Karbstein (2009).
Nob1 binds the single-stranded cleavage site D at the 3'-end of 18S rRNA with its PIN domain.
  Proc Natl Acad Sci U S A, 106, 14259-14264.  
18368466 J.Siltberg-Liberles, and A.Martinez (2009).
Searching distant homologs of the regulatory ACT domain in phenylalanine hydroxylase.
  Amino Acids, 36, 235-249.  
19416066 M.T.Sykes, and J.R.Williamson (2009).
A complex assembly landscape for the 30S ribosomal subunit.
  Annu Rev Biophys, 38, 197-215.  
19343072 P.Ramaswamy, and S.A.Woodson (2009).
S16 throws a conformational switch during assembly of 30S 5' domain.
  Nat Struct Mol Biol, 16, 438-445.  
18452949 A.Shulman-Peleg, M.Shatsky, R.Nussinov, and H.J.Wolfson (2008).
Prediction of interacting single-stranded RNA bases by protein-binding patterns.
  J Mol Biol, 379, 299-316.  
19771145 A.Yan, Y.Wang, A.Kloczkowski, and R.L.Jernigan (2008).
Effects of protein subunits removal on the computed motions of partial 30S structures of the ribosome.
  J Chem Theory Comput, 4, 1757-1767.  
18155048 L.M.Dutca, and G.M.Culver (2008).
Assembly of the 5' and 3' minor domains of 16S ribosomal RNA as monitored by tethered probing from ribosomal protein S20.
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18573075 R.K.Montange, and R.T.Batey (2008).
Riboswitches: emerging themes in RNA structure and function.
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17981525 R.Russell (2008).
RNA misfolding and the action of chaperones.
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17523187 A.P.Heath, L.E.Kavraki, and C.Clementi (2007).
From coarse-grain to all-atom: toward multiscale analysis of protein landscapes.
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17376481 L.M.Dutc─â, I.Jagannathan, J.F.Grondek, and G.M.Culver (2007).
Temperature-dependent RNP conformational rearrangements: analysis of binary complexes of primary binding proteins with 16 S rRNA.
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17318679 P.C.Liao, B.H.Huang, and S.Huang (2007).
Microbial community composition of the Danshui river estuary of Northern Taiwan and the practicality of the phylogenetic method in microbial barcoding.
  Microb Ecol, 54, 497-507.  
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
17434535 T.S.Maity, and K.M.Weeks (2007).
A threefold RNA-protein interface in the signal recognition particle gates native complex assembly.
  J Mol Biol, 369, 512-524.  
16373494 A.Lescoute, and E.Westhof (2006).
Topology of three-way junctions in folded RNAs.
  RNA, 12, 83-93.  
16682557 M.Bubunenko, A.Korepanov, D.L.Court, I.Jagannathan, D.Dickinson, B.R.Chaudhuri, M.B.Garber, and G.M.Culver (2006).
30S ribosomal subunits can be assembled in vivo without primary binding ribosomal protein S15.
  RNA, 12, 1229-1239.  
16761081 M.Gutman, E.Nachliel, and R.Friedman (2006).
The dynamics of proton transfer between adjacent sites.
  Photochem Photobiol Sci, 5, 531-537.  
16707260 R.T.Batey (2006).
Structures of regulatory elements in mRNAs.
  Curr Opin Struct Biol, 16, 299-306.  
16043494 A.Mushegian (2005).
Protein content of minimal and ancestral ribosome.
  RNA, 11, 1400-1406.  
16245373 B.D.Gooch, M.Krishnamurthy, M.Shadid, and P.A.Beal (2005).
Binding of helix-threading peptides to E. coli 16S ribosomal RNA and inhibition of the S15-16S complex.
  Chembiochem, 6, 2247-2254.  
15853795 D.E.Brodersen, and P.Nissen (2005).
The social life of ribosomal proteins.
  FEBS J, 272, 2098-2108.  
16138302 H.M.Al-Hashimi (2005).
Dynamics-based amplification of RNA function and its characterization by using NMR spectroscopy.
  Chembiochem, 6, 1506-1519.  
15840820 M.Guillier, F.Allemand, M.Graffe, S.Raibaud, F.Dardel, M.Springer, and C.Chiaruttini (2005).
The N-terminal extension of Escherichia coli ribosomal protein L20 is important for ribosome assembly, but dispensable for translational feedback control.
  RNA, 11, 728-738.  
15894639 R.Friedman, E.Nachliel, and M.Gutman (2005).
Molecular dynamics of a protein surface: ion-residues interactions.
  Biophys J, 89, 768-781.  
15811917 S.Ghosh, and S.Joseph (2005).
Nonbridging phosphate oxygens in 16S rRNA important for 30S subunit assembly and association with the 50S ribosomal subunit.
  RNA, 11, 657-667.  
15389607 C.L.Smith, R.Afroz, G.J.Bassell, H.M.Furneaux, N.I.Perrone-Bizzozero, and R.W.Burry (2004).
GAP-43 mRNA in growth cones is associated with HuD and ribosomes.
  J Neurobiol, 61, 222-235.  
15148358 D.Klostermeier, P.Sears, C.H.Wong, D.P.Millar, and J.R.Williamson (2004).
A three-fluorophore FRET assay for high-throughput screening of small-molecule inhibitors of ribosome assembly.
  Nucleic Acids Res, 32, 2707-2715.  
15150413 I.A.Hubner, M.Oliveberg, and E.I.Shakhnovich (2004).
Simulation, experiment, and evolution: understanding nucleation in protein S6 folding.
  Proc Natl Acad Sci U S A, 101, 8354-8359.  
15189152 J.A.Doudna, and R.T.Batey (2004).
Structural insights into the signal recognition particle.
  Annu Rev Biochem, 73, 539-557.  
14730351 K.L.Holmes, and G.M.Culver (2004).
Mapping structural differences between 30S ribosomal subunit assembly intermediates.
  Nat Struct Mol Biol, 11, 179-186.  
15339800 K.Réblová, N.Spacková, J.Koca, N.B.Leontis, and J.Sponer (2004).
Long-residency hydration, cation binding, and dynamics of loop E/helix IV rRNA-L25 protein complex.
  Biophys J, 87, 3397-3412.  
15101974 N.Mathy, O.Pellegrini, A.Serganov, D.J.Patel, C.Ehresmann, and C.Portier (2004).
Specific recognition of rpsO mRNA and 16S rRNA by Escherichia coli ribosomal protein S15 relies on both mimicry and site differentiation.
  Mol Microbiol, 52, 661-675.  
15627386 S.V.Revtovich, A.D.Nikulin, and S.V.Nikonov (2004).
Role of N-terminal helix in interaction of ribosomal protein S15 with 16S rRNA.
  Biochemistry (Mosc), 69, 1319-1323.
PDB code: 1kuq
12682022 A.Serganov, A.Polonskaia, B.Ehresmann, C.Ehresmann, and D.J.Patel (2003).
Ribosomal protein S15 represses its own translation via adaptation of an rRNA-like fold within its mRNA.
  EMBO J, 22, 1898-1908.  
12595703 D.B.Hoggan, J.A.Chao, G.S.Prasad, C.D.Stout, and J.R.Williamson (2003).
Combinatorial crystallization of an RNA-protein complex.
  Acta Crystallogr D Biol Crystallogr, 59, 466-473.  
12853646 F.Beaurain, C.Di Primo, J.J.Toulmé, and M.Laguerre (2003).
Molecular dynamics reveals the stabilizing role of loop closing residues in kissing interactions: comparison between TAR-TAR* and TAR-aptamer.
  Nucleic Acids Res, 31, 4275-4284.  
12581310 G.Horiguchi, H.Kodama, and K.Iba (2003).
Mutations in a gene for plastid ribosomal protein S6-like protein reveal a novel developmental process required for the correct organization of lateral root meristem in Arabidopsis.
  Plant J, 33, 521-529.  
12548626 G.M.Culver (2003).
Assembly of the 30S ribosomal subunit.
  Biopolymers, 68, 234-249.  
12554857 J.R.Williamson (2003).
After the ribosome structures: how are the subunits assembled?
  RNA, 9, 165-167.  
12768202 M.Springer, and C.Portier (2003).
More than one way to skin a cat: translational autoregulation by ribosomal protein S15.
  Nat Struct Biol, 10, 420-422.  
12527771 W.Li, B.Ma, and B.A.Shapiro (2003).
Binding interactions between the core central domain of 16S rRNA and the ribosomal protein S15 determined by molecular dynamics simulations.
  Nucleic Acids Res, 31, 629-638.  
11929999 H.D.Kim, G.U.Nienhaus, T.Ha, J.W.Orr, J.R.Williamson, and S.Chu (2002).
Mg2+-dependent conformational change of RNA studied by fluorescence correlation and FRET on immobilized single molecules.
  Proc Natl Acad Sci U S A, 99, 4284-4289.  
11839490 H.J.Dyson, and P.E.Wright (2002).
Coupling of folding and binding for unstructured proteins.
  Curr Opin Struct Biol, 12, 54-60.  
12087167 I.Amarantos, I.K.Zarkadis, and D.L.Kalpaxis (2002).
The identification of spermine binding sites in 16S rRNA allows interpretation of the spermine effect on ribosomal 30S subunit functions.
  Nucleic Acids Res, 30, 2832-2843.  
12162888 J.Zhang (2002).
Analysis of information content for biological sequences.
  J Comput Biol, 9, 487-503.  
11839493 K.Wild, O.Weichenrieder, K.Strub, I.Sinning, and S.Cusack (2002).
Towards the structure of the mammalian signal recognition particle.
  Curr Opin Struct Biol, 12, 72-81.  
12368899 M.Lindberg, J.Tångrot, and M.Oliveberg (2002).
Complete change of the protein folding transition state upon circular permutation.
  Nat Struct Biol, 9, 818-822.  
12374753 S.Nottrott, H.Urlaub, and R.Lührmann (2002).
Hierarchical, clustered protein interactions with U4/U6 snRNA: a biochemical role for U4/U6 proteins.
  EMBO J, 21, 5527-5538.  
12050674 T.Hainzl, S.Huang, and A.E.Sauer-Eriksson (2002).
Structure of the SRP19 RNA complex and implications for signal recognition particle assembly.
  Nature, 417, 767-771.
PDB code: 1lng
11839494 T.M.Hall (2002).
Poly(A) tail synthesis and regulation: recent structural insights.
  Curr Opin Struct Biol, 12, 82-88.  
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
11341947 A.Walles-Granberg, R.Schnell, L.A.Isaksson, and M.Rydén-Aulin (2001).
Ribosomes with large synthetic N-terminal extensions of protein S15 are active in vivo.
  Biochim Biophys Acta, 1544, 378-385.  
11406379 D.K.Treiber, and J.R.Williamson (2001).
Beyond kinetic traps in RNA folding.
  Curr Opin Struct Biol, 11, 309-314.  
11438677 H.Peled-Zehavi, J.A.Berglund, M.Rosbash, and A.D.Frankel (2001).
Recognition of RNA branch point sequences by the KH domain of splicing factor 1 (mammalian branch point binding protein) in a splicing factor complex.
  Mol Cell Biol, 21, 5232-5241.  
11389613 J.M.Diamond, D.H.Turner, and D.H.Mathews (2001).
Thermodynamics of three-way multibranch loops in RNA.
  Biochemistry, 40, 6971-6981.  
11891627 J.Sühnel (2001).
Beyond nucleic acid base pairs: from triads to heptads.
  Biopolymers, 61, 32-51.  
  11680843 J.Yin, C.H.Yang, and C.Zwieb (2001).
Assembly of the human signal recognition particle (SRP): overlap of regions required for binding of protein SRP54 and assembly control.
  RNA, 7, 1389-1396.  
12762060 M.I.Recht, and J.R.Williamson (2001).
Thermodynamics and kinetics of central domain assembly.
  Cold Spring Harb Symp Quant Biol, 66, 591-598.  
11160927 S.Jones, D.T.Daley, N.M.Luscombe, H.M.Berman, and J.M.Thornton (2001).
Protein-RNA interactions: a structural analysis.
  Nucleic Acids Res, 29, 943-954.  
11340059 W.Wang, O.Donini, C.M.Reyes, and P.A.Kollman (2001).
Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions.
  Annu Rev Biophys Biomol Struct, 30, 211-243.  
10851193 A.D.Frankel (2000).
Fitting peptides into the RNA world.
  Curr Opin Struct Biol, 10, 332-340.  
11123902 E.J.Jeong, G.S.Hwang, K.H.Kim, M.J.Kim, S.Kim, and K.S.Kim (2000).
Structural analysis of multifunctional peptide motifs in human bifunctional tRNA synthetase: identification of RNA-binding residues and functional implications for tandem repeats.
  Biochemistry, 39, 15775-15782.
PDB code: 1fyj
10944102 G.Martin, W.Keller, and S.Doublié (2000).
Crystal structure of mammalian poly(A) polymerase in complex with an analog of ATP.
  EMBO J, 19, 4193-4203.
PDB code: 1f5a
11080632 R.Brimacombe (2000).
The bacterial ribosome at atomic resolution.
  Structure, 8, R195-R200.  
11114159 X.Zheng, and P.C.Bevilacqua (2000).
Straightening of bulged RNA by the double-stranded RNA-binding domain from the protein kinase PKR.
  Proc Natl Acad Sci U S A, 97, 14162-14167.  
11295748 S.J.Schroeder, M.E.Burkard, and D.H.Turner (1999).
The energetics of small internal loops in RNA.
  Biopolymers, 52, 157-167.  
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.