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PDBsum entry 1qa6

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protein dna_rna metals links
Ribosome PDB id
1qa6
Jmol
Contents
Protein chains
67 a.a. *
DNA/RNA
Metals
_OS ×4
_MG ×4
* Residue conservation analysis
PDB id:
1qa6
Name: Ribosome
Title: Crystal structure of a conserved ribosomal protein-RNA complex
Structure: 58 nucleotide ribosomal RNA domain. Chain: c, d. Fragment: nts 1051-1108 from e. Coli 23s rrna. Engineered: yes. Mutation: yes. Ribosomal protein l11. Chain: a, b. Fragment: c-terminal domain of ribosomal protein l11. Engineered: yes
Source: Synthetic: yes. Other_details: RNA synthesized by in vitro transcription using t7 RNA polymerase. Geobacillus stearothermophilus. Organism_taxid: 1422. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Monomer (from PDB file)
Resolution:
2.80Å     R-factor:   0.240     R-free:   0.321
Authors: G.L.Conn,D.E.Draper,E.E.Lattman,A.G.Gittis
Key ref:
G.L.Conn et al. (1999). Crystal structure of a conserved ribosomal protein-RNA complex. Science, 284, 1171-1174. PubMed id: 10325228 DOI: 10.1126/science.284.5417.1171
Date:
15-Apr-99     Release date:   25-May-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P56210  (RL11_GEOSE) -  50S ribosomal protein L11 (Fragment)
Seq:
Struc:
133 a.a.
67 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

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

 

 
DOI no: 10.1126/science.284.5417.1171 Science 284:1171-1174 (1999)
PubMed id: 10325228  
 
 
Crystal structure of a conserved ribosomal protein-RNA complex.
G.L.Conn, D.E.Draper, E.E.Lattman, A.G.Gittis.
 
  ABSTRACT  
 
The structure of a highly conserved complex between a 58-nucleotide domain of large subunit ribosomal RNA and the RNA-binding domain of ribosomal protein L11 has been solved at 2.8 angstrom resolution. It reveals a precisely folded RNA structure that is stabilized by extensive tertiary contacts and contains an unusually large core of stacked bases. A bulge loop base from one hairpin of the RNA is intercalated into the distorted major groove of another helix; the protein locks this tertiary interaction into place by binding to the intercalated base from the minor groove side. This direct interaction with a key ribosomal RNA tertiary interaction suggests that part of the role of L11 is to stabilize an unusual RNA fold within the ribosome.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Stereo view of the stack of three base triples. Shown is a 2F[o ]F[c] electron density map contoured at 1.0 , calculated with the nine nucleotides in both RNA molecules omitted from the model (11% of the atoms in the asymmetric unit).
 
  The above figure is reprinted by permission from the AAAs: Science (1999, 284, 1171-1174) copyright 1999.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21133351 B.Liu, J.M.Diamond, D.H.Mathews, and D.H.Turner (2011).
Fluorescence competition and optical melting measurements of RNA three-way multibranch loops provide a revised model for thermodynamic parameters.
  Biochemistry, 50, 640-653.  
21549313 C.Chen, B.Stevens, J.Kaur, D.Cabral, H.Liu, Y.Wang, H.Zhang, G.Rosenblum, Z.Smilansky, Y.E.Goldman, and B.S.Cooperman (2011).
Single-molecule fluorescence measurements of ribosomal translocation dynamics.
  Mol Cell, 42, 367-377.  
20876687 C.Geary, A.Chworos, and L.Jaeger (2011).
Promoting RNA helical stacking via A-minor junctions.
  Nucleic Acids Res, 39, 1066-1080.  
19369248 M.S.Dunstan, P.C.Hang, N.V.Zelinskaya, J.F.Honek, and G.L.Conn (2009).
Structure of the thiostrepton resistance methyltransferase.S-adenosyl-L-methionine complex and its interaction with ribosomal RNA.
  J Biol Chem, 284, 17013-17020.
PDB code: 3gyq
19741022 M.de la Peña, D.Dufour, and J.Gallego (2009).
Three-way RNA junctions with remote tertiary contacts: a recurrent and highly versatile fold.
  RNA, 15, 1949-1964.  
19720737 W.Huang, J.Kim, S.Jha, and F.Aboul-ela (2009).
A mechanism for S-adenosyl methionine assisted formation of a riboswitch conformation: a small molecule with a strong arm.
  Nucleic Acids Res, 37, 6528-6539.  
17981525 R.Russell (2008).
RNA misfolding and the action of chaperones.
  Front Biosci, 13, 1.  
17940088 A.García-Marcos, A.Morreale, E.Guarinos, E.Briones, M.Remacha, A.R.Ortiz, and J.P.Ballesta (2007).
In vivo assembling of bacterial ribosomal protein L11 into yeast ribosomes makes the particles sensitive to the prokaryotic specific antibiotic thiostrepton.
  Nucleic Acids Res, 35, 7109-7117.  
17868692 C.Grigoriadou, S.Marzi, S.Kirillov, C.O.Gualerzi, and B.S.Cooperman (2007).
A quantitative kinetic scheme for 70 S translation initiation complex formation.
  J Mol Biol, 373, 562-572.  
17555763 D.Lambert, and D.E.Draper (2007).
Effects of osmolytes on RNA secondary and tertiary structure stabilities and RNA-Mg2+ interactions.
  J Mol Biol, 370, 993.  
17292917 D.Lee, J.D.Walsh, P.Yu, M.A.Markus, T.Choli-Papadopoulou, C.D.Schwieters, S.Krueger, D.E.Draper, and Y.X.Wang (2007).
The structure of free L11 and functional dynamics of L11 in free, L11-rRNA(58 nt) binary and L11-rRNA(58 nt)-thiostrepton ternary complexes.
  J Mol Biol, 367, 1007-1022.
PDB codes: 2e34 2e35 2e36 2h8w
17464398 F.E.Alemdaroglu, and A.Herrmann (2007).
DNA meets synthetic polymers--highly versatile hybrid materials.
  Org Biomol Chem, 5, 1311-1320.  
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
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.  
17507661 R.Tyagi, and D.H.Mathews (2007).
Predicting helical coaxial stacking in RNA multibranch loops.
  RNA, 13, 939-951.  
16373494 A.Lescoute, and E.Westhof (2006).
Topology of three-way junctions in folded RNAs.
  RNA, 12, 83-93.  
16753066 B.Vester, L.H.Hansen, L.B.Lundberg, B.R.Babu, M.D.Sørensen, J.Wengel, and S.Douthwaite (2006).
Locked nucleoside analogues expand the potential of DNAzymes to cleave structured RNA targets.
  BMC Mol Biol, 7, 19.  
16716074 C.Maeder, G.L.Conn, and D.E.Draper (2006).
Optimization of a ribosomal structural domain by natural selection.
  Biochemistry, 45, 6635-6643.  
16966612 D.Grilley, A.M.Soto, and D.E.Draper (2006).
Mg2+-RNA interaction free energies and their relationship to the folding of RNA tertiary structures.
  Proc Natl Acad Sci U S A, 103, 14003-14008.  
17053098 D.Shcherbakov, M.Dontsova, M.Tribus, M.Garber, and W.Piendl (2006).
Stability of the 'L12 stalk' in ribosomes from mesophilic and (hyper)thermophilic Archaea and Bacteria.
  Nucleic Acids Res, 34, 5800-5814.  
16556224 H.Sato, K.Ito, and Y.Nakamura (2006).
Ribosomal protein L11 mutations in two functional domains equally affect release factors 1 and 2 activity.
  Mol Microbiol, 60, 108-120.  
17055412 N.Foloppe, N.Matassova, and F.Aboul-Ela (2006).
Towards the discovery of drug-like RNA ligands?
  Drug Discov Today, 11, 1019-1027.  
17139090 S.Tishchenko, E.Nikonova, A.Nikulin, N.Nevskaya, S.Volchkov, W.Piendl, M.Garber, and S.Nikonov (2006).
Structure of the ribosomal protein L1-mRNA complex at 2.1 A resolution: common features of crystal packing of L1-RNA complexes.
  Acta Crystallogr D Biol Crystallogr, 62, 1545-1554.
PDB code: 2hw8
16682558 W.Li, J.Sengupta, B.K.Rath, and J.Frank (2006).
Functional conformations of the L11-ribosomal RNA complex revealed by correlative analysis of cryo-EM and molecular dynamics simulations.
  RNA, 12, 1240-1253.
PDB code: 2gkz
16257826 D.N.Wilson, and K.H.Nierhaus (2005).
Ribosomal proteins in the spotlight.
  Crit Rev Biochem Mol Biol, 40, 243-267.  
15897324 M.A.Xaplanteri, A.D.Petropoulos, G.P.Dinos, and D.L.Kalpaxis (2005).
Localization of spermine binding sites in 23S rRNA by photoaffinity labeling: parsing the spermine contribution to ribosomal 50S subunit functions.
  Nucleic Acids Res, 33, 2792-2805.  
15849690 Q.Han, Q.Zhao, S.Fish, K.B.Simonsen, D.Vourloumis, J.M.Froelich, D.Wall, and T.Hermann (2005).
Molecular recognition by glycoside pseudo base pairs and triples in an apramycin-RNA complex.
  Angew Chem Int Ed Engl, 44, 2694-2700.
PDB code: 1yrj
16094695 S.Ilin, A.Hoskins, O.Ohlenschläger, H.R.Jonker, H.Schwalbe, and J.Wöhnert (2005).
Domain reorientation and induced fit upon RNA binding: solution structure and dynamics of ribosomal protein L11 from Thermotoga maritima.
  Chembiochem, 6, 1611-1618.
PDB code: 2k3f
15853794 Y.Chen, and G.Varani (2005).
Protein families and RNA recognition.
  FEBS J, 272, 2088-2097.  
15199170 D.M.Cameron, J.Thompson, S.T.Gregory, P.E.March, and A.E.Dahlberg (2004).
Thiostrepton-resistant mutants of Thermus thermophilus.
  Nucleic Acids Res, 32, 3220-3227.  
15100432 M.B.Sagar, L.Lucast, and J.A.Doudna (2004).
Conserved but nonessential interaction of SRP RNA with translation factor EF-G.
  RNA, 10, 772-778.  
12511961 B.P.Klaholz, T.Pape, A.V.Zavialov, A.G.Myasnikov, E.V.Orlova, B.Vestergaard, M.Ehrenberg, and M.van Heel (2003).
Structure of the Escherichia coli ribosomal termination complex with release factor 2.
  Nature, 421, 90-94.
PDB code: 1ml5
12756325 C.D.Cilley, and J.R.Williamson (2003).
Structural mimicry in the phage phi21 N peptide-boxB RNA complex.
  RNA, 9, 663-676.
PDB code: 1nyb
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.  
12888505 D.R.Banatao, R.B.Altman, and T.E.Klein (2003).
Microenvironment analysis and identification of magnesium binding sites in RNA.
  Nucleic Acids Res, 31, 4450-4460.  
12527787 J.Fan, M.N.Schnare, and R.W.Lee (2003).
Characterization of fragmented mitochondrial ribosomal RNAs of the colorless green alga Polytomella parva.
  Nucleic Acids Res, 31, 769-778.  
14580192 J.W.Noah, and A.M.Lambowitz (2003).
Effects of maturase binding and Mg2+ concentration on group II intron RNA folding investigated by UV cross-linking.
  Biochemistry, 42, 12466-12480.  
12925990 T.Hermann (2003).
Chemical and functional diversity of small molecule ligands for RNA.
  Biopolymers, 70, 4.  
12717727 V.K.Misra, R.Shiman, and D.E.Draper (2003).
A thermodynamic framework for the magnesium-dependent folding of RNA.
  Biopolymers, 69, 118-136.  
12379845 H.Stark, M.V.Rodnina, H.J.Wieden, F.Zemlin, W.Wintermeyer, and M.van Heel (2002).
Ribosome interactions of aminoacyl-tRNA and elongation factor Tu in the codon-recognition complex.
  Nat Struct Biol, 9, 849-854.
PDB code: 1mj1
12177293 N.B.Leontis, J.Stombaugh, and E.Westhof (2002).
The non-Watson-Crick base pairs and their associated isostericity matrices.
  Nucleic Acids Res, 30, 3497-3531.  
12358430 U.Nagaswamy, and G.E.Fox (2002).
Frequent occurrence of the T-loop RNA folding motif in ribosomal RNAs.
  RNA, 8, 1112-1119.  
11807083 W.Xu, F.T.Pagel, and E.J.Murgola (2002).
Mutations in the GTPase center of Escherichia coli 23S rRNA indicate release factor 2-interactive sites.
  J Bacteriol, 184, 1200-1203.  
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
11320328 C.S.Bond, M.P.Shaw, M.S.Alphey, and W.N.Hunter (2001).
Structure of the macrocycle thiostrepton solved using the anomalous dispersion contribution of sulfur.
  Acta Crystallogr D Biol Crystallogr, 57, 755-758.
PDB code: 1e9w
11441810 E.A.Doherty, and J.A.Doudna (2001).
Ribozyme structures and mechanisms.
  Annu Rev Biophys Biomol Struct, 30, 457-475.  
11406375 F.Major, and R.Griffey (2001).
Computational methods for RNA structure determination.
  Curr Opin Struct Biol, 11, 282-286.  
11891627 J.Sühnel (2001).
Beyond nucleic acid base pairs: from triads to heptads.
  Biopolymers, 61, 32-51.  
11497427 J.Thompson, W.E.Tapprich, C.Munger, and A.E.Dahlberg (2001).
Staphylococcus aureus domain V functions in Escherichia coli ribosomes provided a conserved interaction with domain IV is restored.
  RNA, 7, 1076-1083.  
11453067 V.I.Lim, and J.F.Curran (2001).
Analysis of codon:anticodon interactions within the ribosome provides new insights into codon reading and the genetic code structure.
  RNA, 7, 942-957.  
11675490 V.K.Misra, and D.E.Draper (2001).
A thermodynamic framework for Mg2+ binding to RNA.
  Proc Natl Acad Sci U S A, 98, 12456-12461.  
11673421 X.Yang, and E.E.Ishiguro (2001).
Involvement of the N terminus of ribosomal protein L11 in regulation of the RelA protein of Escherichia coli.
  J Bacteriol, 183, 6532-6537.  
10679466 A.A.Antson (2000).
Single-stranded-RNA binding proteins.
  Curr Opin Struct Biol, 10, 87-94.  
10851193 A.D.Frankel (2000).
Fitting peptides into the RNA world.
  Curr Opin Struct Biol, 10, 332-340.  
11018283 A.L.Arkov, D.V.Freistroffer, M.Y.Pavlov, M.Ehrenberg, and E.J.Murgola (2000).
Mutations in conserved regions of ribosomal RNAs decrease the productive association of peptide-chain release factors with the ribosome during translation termination.
  Biochimie, 82, 671-682.  
11071938 C.Briones, and J.P.Ballesta (2000).
Conformational changes induced in the Saccharomyces cerevisiae GTPase-associated rRNA by ribosomal stalk components and a translocation inhibitor.
  Nucleic Acids Res, 28, 4497-4505.  
10882080 D.Niessing, W.Driever, F.Sprenger, H.Taubert, H.Jäckle, and R.Rivera-Pomar (2000).
Homeodomain position 54 specifies transcriptional versus translational control by Bicoid.
  Mol Cell, 5, 395-401.  
10966470 E.A.Doherty, and J.A.Doudna (2000).
Ribozyme structures and mechanisms.
  Annu Rev Biochem, 69, 597-615.  
10745012 E.Westhof, and V.Fritsch (2000).
RNA folding: beyond Watson-Crick pairs.
  Structure, 8, R55-R65.  
10721991 I.S.Gabashvili, R.K.Agrawal, C.M.Spahn, R.A.Grassucci, D.I.Svergun, J.Frank, and P.Penczek (2000).
Solution structure of the E. coli 70S ribosome at 11.5 A resolution.
  Cell, 100, 537-549.
PDB code: 1eg0
10734197 L.B.Blyn, L.M.Risen, R.H.Griffey, and D.E.Draper (2000).
The RNA-binding domain of ribosomal protein L11 recognizes an rRNA tertiary structure stabilized by both thiostrepton and magnesium ion.
  Nucleic Acids Res, 28, 1778-1784.  
10801497 L.Jovine, T.Hainzl, C.Oubridge, W.G.Scott, J.Li, T.K.Sixma, A.Wonacott, T.Skarzynski, and K.Nagai (2000).
Crystal structure of the ffh and EF-G binding sites in the conserved domain IV of Escherichia coli 4.5S RNA.
  Structure, 8, 527-540.
PDB code: 1duh
10637222 M.C.Wahl, G.P.Bourenkov, H.D.Bartunik, and R.Huber (2000).
Flexibility, conformational diversity and two dimerization modes in complexes of ribosomal protein L12.
  EMBO J, 19, 174-186.
PDB codes: 1dd3 1dd4
10696113 M.Lu, and T.A.Steitz (2000).
Structure of Escherichia coli ribosomal protein L25 complexed with a 5S rRNA fragment at 1.8-A resolution.
  Proc Natl Acad Sci U S A, 97, 2023-2028.
PDB code: 1dfu
10937867 M.Sprinzl, S.Brock, Y.Huang, P.Milovnik, M.Nanninga, M.Nesper-Brock, H.Rütthard, and K.Szkaradkiewicz (2000).
Regulation of GTPases in the bacterial translation machinery.
  Biol Chem, 381, 367-375.  
10698923 M.Worbs, R.Huber, and M.C.Wahl (2000).
Crystal structure of ribosomal protein L4 shows RNA-binding sites for ribosome incorporation and feedback control of the S10 operon.
  EMBO J, 19, 807-818.
PDB code: 1dmg
11004163 N.S.Chernyaeva, and E.J.Murgola (2000).
Covariance of complementary rRNA loop nucleotides does not necessarily represent functional pseudoknot formation in vivo.
  J Bacteriol, 182, 5671-5675.  
10896472 P.B.Rupert, and A.R.Ferré-D'amaré (2000).
SRPrises in RNA-protein recognition.
  Structure, 8, R99-104.  
11080632 R.Brimacombe (2000).
The bacterial ribosome at atomic resolution.
  Structure, 8, R195-R200.  
11073218 R.Klinck, E.Westhof, S.Walker, M.Afshar, A.Collier, and F.Aboul-Ela (2000).
A potential RNA drug target in the hepatitis C virus internal ribosomal entry site.
  RNA, 6, 1423-1431.
PDB code: 1fqz
11114498 S.Chandra Sanyal, and A.Liljas (2000).
The end of the beginning: structural studies of ribosomal proteins.
  Curr Opin Struct Biol, 10, 633-636.  
10924119 S.J.Schroeder, and D.H.Turner (2000).
Factors affecting the thermodynamic stability of small asymmetric internal loops in RNA.
  Biochemistry, 39, 9257-9274.  
10745015 T.Hermann, and D.J.Patel (2000).
RNA bulges as architectural and recognition motifs.
  Structure, 8, R47-R54.  
10781065 U.Stelzl, C.M.Spahn, and K.H.Nierhaus (2000).
Selecting rRNA binding sites for the ribosomal proteins L4 and L6 from randomly fragmented rRNA: application of a method called SERF.
  Proc Natl Acad Sci U S A, 97, 4597-4602.  
11087388 V.L.Murthy, and G.D.Rose (2000).
Is counterion delocalization responsible for collapse in RNA folding?
  Biochemistry, 39, 14365-14370.  
10969026 W.Wriggers, R.K.Agrawal, D.L.Drew, A.McCammon, and J.Frank (2000).
Domain motions of EF-G bound to the 70S ribosome: insights from a hand-shaking between multi-resolution structures.
  Biophys J, 79, 1670-1678.  
10660288 Y.Muto, C.Oubridge, and K.Nagai (2000).
RNA-binding proteins: TRAPping RNA bases.
  Curr Biol, 10, R19-R21.  
  10444595 C.A.Collins, and C.Guthrie (1999).
Allele-specific genetic interactions between Prp8 and RNA active site residues suggest a function for Prp8 at the catalytic core of the spliceosome.
  Genes Dev, 13, 1970-1982.  
10600730 D.G.McCafferty, P.Cudic, M.K.Yu, D.C.Behenna, and R.Kruger (1999).
Synergy and duality in peptide antibiotic mechanisms.
  Curr Opin Chem Biol, 3, 672-680.  
10647177 F.Jiang, A.Gorin, W.Hu, A.Majumdar, S.Baskerville, W.Xu, A.Ellington, and D.J.Patel (1999).
Anchoring an extended HTLV-1 Rex peptide within an RNA major groove containing junctional base triples.
  Structure, 7, 1461-1472.
PDB codes: 1c4j 1exy
10600721 F.Walter, Q.Vicens, and E.Westhof (1999).
Aminoglycoside-RNA interactions.
  Curr Opin Chem Biol, 3, 694-704.  
10562563 M.Stoldt, J.Wöhnert, O.Ohlenschläger, M.Görlach, and L.R.Brown (1999).
The NMR structure of the 5S rRNA E-domain-protein L25 complex shows preformed and induced recognition.
  EMBO J, 18, 6508-6521.
PDB code: 1d6k
10449736 M.V.Rodnina, A.Savelsbergh, N.B.Matassova, V.I.Katunin, Y.P.Semenkov, and W.Wintermeyer (1999).
Thiostrepton inhibits the turnover but not the GTPase of elongation factor G on the ribosome.
  Proc Natl Acad Sci U S A, 96, 9586-9590.  
10580471 P.Babin, M.Dolan, P.Wollenzien, and R.R.Gutell (1999).
Identity and geometry of a base triple in 16S rRNA determined by comparative sequence analysis and molecular modeling.
  RNA, 5, 1430-1439.  
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 code is shown on the right.