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protein dna_rna ligands metals Protein-protein interface(s) links
Ribosome PDB id
1j5e
Jmol
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. *
DNA/RNA
Ligands
UNX ×188
Metals
_ZN ×2
* Residue conservation analysis
PDB id:
1j5e
Name: Ribosome
Title: Structure of the thermus thermophilus 30s ribosomal subunit
Structure: 16s ribosomal RNA. Chain: a. 30s ribosomal protein s2. Chain: b. 30s ribosomal protein s3. Chain: c. 30s ribosomal protein s4. Chain: d. 30s ribosomal protein s5.
Source: Thermus thermophilus. Organism_taxid: 274. Organism_taxid: 274
Biol. unit: 21mer (from PQS)
Resolution:
3.05Å     R-factor:   0.208     R-free:   0.252
Authors: B.T.Wimberly,D.E.Brodersen,W.M.Clemons Jr.,R.Morgan-Warren, A.P.Carter,C.Vonrhein,T.Hartsch,V.Ramakrishnan
Key ref:
B.T.Wimberly et al. (2000). Structure of the 30S ribosomal subunit. Nature, 407, 327-339. PubMed id: 11014182 DOI: 10.1038/35030006
Date:
08-Apr-02     Release date:   12-Apr-02    
Supersedes: 1fjf
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P80371  (RS2_THET8) -  30S ribosomal protein S2
Seq:
Struc: 		256 a.a.
234 a.a.
Protein chain
Pfam   ArchSchema ?
P80372  (RS3_THET8) -  30S ribosomal protein S3
Seq:
Struc: 		239 a.a.
206 a.a.
Protein chain
Pfam   ArchSchema ?
P80373  (RS4_THET8) -  30S ribosomal protein S4
Seq:
Struc: 		209 a.a.
208 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHQ5  (RS5_THET8) -  30S ribosomal protein S5
Seq:
Struc: 		162 a.a.
150 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SLP8  (RS6_THET8) -  30S ribosomal protein S6
Seq:
Struc: 		101 a.a.
101 a.a.
Protein chain
Pfam   ArchSchema ?
P17291  (RS7_THET8) -  30S ribosomal protein S7
Seq:
Struc: 		156 a.a.
155 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHQ2  (RS8_THET8) -  30S ribosomal protein S8
Seq:
Struc: 		138 a.a.
138 a.a.
Protein chain
Pfam   ArchSchema ?
P80374  (RS9_THET8) -  30S ribosomal protein S9
Seq:
Struc: 		128 a.a.
127 a.a.*
Protein chain
Pfam   ArchSchema ?
Q5SHN7  (RS10_THET8) -  30S ribosomal protein S10
Seq:
Struc: 		105 a.a.
98 a.a.
Protein chain
Pfam   ArchSchema ?
P80376  (RS11_THET8) -  30S ribosomal protein S11
Seq:
Struc: 		129 a.a.
119 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHN3  (RS12_THET8) -  30S ribosomal protein S12
Seq:
Struc: 		132 a.a.
124 a.a.
Protein chain
Pfam   ArchSchema ?
P80377  (RS13_THET8) -  30S ribosomal protein S13
Seq:
Struc: 		126 a.a.
125 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHQ1  (RS14Z_THET8) -  30S ribosomal protein S14 type Z
Seq:
Struc: 		61 a.a.
60 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SJ76  (RS15_THET8) -  30S ribosomal protein S15
Seq:
Struc: 		89 a.a.
88 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SJH3  (RS16_THET8) -  30S ribosomal protein S16
Seq:
Struc: 		88 a.a.
83 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHP7  (RS17_THET8) -  30S ribosomal protein S17
Seq:
Struc: 		105 a.a.
104 a.a.*
Protein chain
Pfam   ArchSchema ?
Q5SLQ0  (RS18_THET8) -  30S ribosomal protein S18
Seq:
Struc: 		88 a.a.
73 a.a.*
Protein chain
Pfam   ArchSchema ?
Q5SHP2  (RS19_THET8) -  30S ribosomal protein S19
Seq:
Struc: 		93 a.a.
80 a.a.
Protein chain
Pfam   ArchSchema ?
P80380  (RS20_THET8) -  30S ribosomal protein S20
Seq:
Struc: 		106 a.a.
99 a.a.*
Protein chain
Pfam   ArchSchema ?
Q5SIH3  (RSHX_THET8) -  30S ribosomal protein Thx
Seq:
Struc: 		27 a.a.
24 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 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     6 terms  

 

 
DOI no: 10.1038/35030006 Nature 407:327-339 (2000)
PubMed id: 11014182  
 
 
Structure of the 30S ribosomal subunit.
B.T.Wimberly, D.E.Brodersen, W.M.Clemons, R.J.Morgan-Warren, A.P.Carter, C.Vonrhein, T.Hartsch, V.Ramakrishnan.
 
  ABSTRACT  
 
Genetic information encoded in messenger RNA is translated into protein by the ribosome, which is a large nucleoprotein complex comprising two subunits, denoted 30S and 50S in bacteria. Here we report the crystal structure of the 30S subunit from Thermus thermophilus, refined to 3 A resolution. The final atomic model rationalizes over four decades of biochemical data on the ribosome, and provides a wealth of information about RNA and protein structure, protein-RNA interactions and ribosome assembly. It is also a structural basis for analysis of the functions of the 30S subunit, such as decoding, and for understanding the action of antibiotics. The structure will facilitate the interpretation in molecular terms of lower resolution structural data on several functional states of the ribosome from electron microscopy and crystallography.
 
  Selected figure(s)  
 
Figure 4.
Figure 4: Structure of the 5' domain of 16S RNA. a, Stereo view of the entire 5' domain, with an inset on the right showing its location in the 30S subunit. The upper (b), middle (c) and lower (d) subdomains are shown separately next to corresponding parts of the secondary structure diagrams. The colours in the secondary structure diagrams match those in the structure in this and Figs 5 and 6. 		Figure 6.
Figure 6: Structure of the 3' major and 3' minor domains of 16S RNA. a, Stereo view of the 3' major domain with inset showing its location in the 30S. b-d, The upper, middle and lower parts of the 3' major domain, with corresponding secondary structure diagrams. e, Stereo view of the 3' minor domain, with secondary structure diagram and inset showing its location in the 30S.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2000, 407, 327-339) copyright 2000.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21382373 C.W.Lee, L.Li, and D.P.Giedroc (2011).
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PDB codes: 2xzm 2xzn
21333656 J.Wang, and E.P.Nikonowicz (2011).
Solution structure of the K-turn and Specifier Loop domains from the Bacillus subtilis tyrS T-box leader RNA.
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21382498 K.Fujii, M.T.Young, and K.D.Harris (2011).
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21336521 M.Valle (2011).
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21240270 T.R.Blower, X.Y.Pei, F.L.Short, P.C.Fineran, D.P.Humphreys, B.F.Luisi, and G.P.Salmond (2011).
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PDB codes: 2xd0 2xdb
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Multitude of binding modes attainable by intrinsically disordered proteins: a portrait gallery of disorder-based complexes.
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  Science, 330, 1203-1209.
PDB codes: 3o2z 3o30 3o58 3o5h
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PDB code: 3iin
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PDB codes: 2kjv 2kjw
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PDB code: 3imq
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20552334 F.J.Sun, and G.Caetano-Anollés (2010).
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20122215 G.Ciriello, C.Gallina, and C.Guerra (2010).
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20494981 H.David-Eden, A.S.Mankin, and Y.Mandel-Gutfreund (2010).
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Multi-site-specific 16S rRNA methyltransferase RsmF from Thermus thermophilus.
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PDB codes: 3m6u 3m6v 3m6w 3m6x
20208344 H.Nanamiya, and F.Kawamura (2010).
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20603079 H.S.Zaher, and R.Green (2010).
Hyperaccurate and error-prone ribosomes exploit distinct mechanisms during tRNA selection.
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Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-A resolution.
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Base pairing constraints drive structural epistasis in ribosomal RNA sequences.
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A structural database for k-turn motifs in RNA.
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Structural rearrangements of the ribosome at the tRNA proofreading step.
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21079586 M.Bucci, C.Goodman, and T.L.Sheppard (2010).
A decade of chemical biology.
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Recurrent RNA motifs as probes for studying RNA-protein interactions in the ribosome.
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20056148 M.Rusu, and S.Birmanns (2010).
Evolutionary tabu search strategies for the simultaneous registration of multiple atomic structures in cryo-EM reconstructions.
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The ribosome goes Nobel.
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Diffraction cartography: applying microbeams to macromolecular crystallography sample evaluation and data collection.
  Acta Crystallogr D Biol Crystallogr, 66, 855-864.  
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Yeast 18 S rRNA is directly involved in the ribosomal response to stringent AUG selection during translation initiation.
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20185573 O.P.Barrett, and J.W.Chin (2010).
Evolved orthogonal ribosome purification for in vitro characterization.
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O-GlcNAc cycling enzymes associate with the translational machinery and modify core ribosomal proteins.
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The resurgence of acyclic nucleic acids.
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Mg2+ dependence of 70 S ribosomal protein flexibility revealed by hydrogen/deuterium exchange and mass spectrometry.
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A decade of user operation on the macromolecular crystallography MAD beamline ID14-4 at the ESRF.
  J Synchrotron Radiat, 16, 803-812.  
19424134 A.Bhattacharya (2009).
Protein structures: Structures of desire.
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19416977 A.S.Spirin (2009).
The ribosome as a conveying thermal ratchet machine.
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19553343 B.Llano-Sotelo, R.P.Hickerson, L.Lancaster, H.F.Noller, and A.S.Mankin (2009).
Fluorescently labeled ribosomes as a tool for analyzing antibiotic binding.
  RNA, 15, 1597-1604.  
19517026 B.Lu, X.Cheng, J.Huang, and J.A.McCammon (2009).
An Adaptive Fast Multipole Boundary Element Method for Poisson-Boltzmann Electrostatics.
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19279186 C.Hsiao, and L.D.Williams (2009).
A recurrent magnesium-binding motif provides a framework for the ribosomal peptidyl transferase center.
  Nucleic Acids Res, 37, 3134-3142.  
19528080 C.L.Zirbel, J.E.Sponer, J.Sponer, J.Stombaugh, and N.B.Leontis (2009).
Classification and energetics of the base-phosphate interactions in RNA.
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19445952 C.Laing, and T.Schlick (2009).
Analysis of four-way junctions in RNA structures.
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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
19604473 C.Oubridge, D.A.Krummel, A.K.Leung, J.Li, and K.Nagai (2009).
Interpreting a low resolution map of human U1 snRNP using anomalous scatterers.
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19278652 C.Tu, J.E.Tropea, B.P.Austin, D.L.Court, D.S.Waugh, and X.Ji (2009).
Structural basis for binding of RNA and cofactor by a KsgA methyltransferase.
  Structure, 17, 374-385.
PDB codes: 3ftc 3ftd 3fte 3ftf
20004159 C.W.Carter (2009).
E pluribus tres: the 2009 nobel prize in chemistry.
  Structure, 17, 1558-1561.  
19190093 D.L.Bellur, and S.A.Woodson (2009).
A minimized rRNA-binding site for ribosomal protein S4 and its implications for 30S assembly.
  Nucleic Acids Res, 37, 1886-1896.  
19213046 D.M.Hamburg, M.J.Suh, and P.A.Limbach (2009).
Limited proteolysis analysis of the ribosome is affected by subunit association.
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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.  
19485416 G.Chen, S.D.Kennedy, and D.H.Turner (2009).
A CA(+) pair adjacent to a sheared GA or AA pair stabilizes size-symmetric RNA internal loops.
  Biochemistry, 48, 5738-5752.  
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.  
19285505 H.Demirci, R.Belardinelli, E.Seri, S.T.Gregory, C.Gualerzi, A.E.Dahlberg, and G.Jogl (2009).
Structural rearrangements in the active site of the Thermus thermophilus 16S rRNA methyltransferase KsgA in a binary complex with 5'-methylthioadenosine.
  J Mol Biol, 388, 271-282.
PDB codes: 3fut 3fuu 3fuv 3fuw 3fux
19168615 H.M.Kim, S.M.Ryou, W.S.Song, S.H.Sim, C.J.Cha, S.H.Han, N.C.Ha, J.H.Kim, J.Bae, P.R.Cunningham, and K.Lee (2009).
Genetic analysis of the invariant residue G791 in Escherichia coli 16S rRNA implicates RelA in ribosome function.
  J Bacteriol, 191, 2042-2050.  
19239893 H.S.Zaher, and R.Green (2009).
Fidelity at the molecular level: lessons from protein synthesis.
  Cell, 136, 746-762.  
19386726 H.Vallabhaneni, and P.J.Farabaugh (2009).
Accuracy modulating mutations of the ribosomal protein S4-S5 interface do not necessarily destabilize the rps4-rps5 protein-protein interaction.
  RNA, 15, 1100-1109.  
19840948 J.Batisse, C.Batisse, A.Budd, B.Böttcher, and E.Hurt (2009).
Purification of nuclear poly(A)-binding protein Nab2 reveals association with the yeast transcriptome and a messenger ribonucleoprotein core structure.
  J Biol Chem, 284, 34911-34917.  
19778425 J.E.Jacob, B.Vanholme, T.Van Leeuwen, and G.Gheysen (2009).
A unique genetic code change in the mitochondrial genome of the parasitic nematode Radopholus similis.
  BMC Res Notes, 2, 192.  
19258537 J.F.Atkins, and G.R.Björk (2009).
A gripping tale of ribosomal frameshifting: extragenic suppressors of frameshift mutations spotlight P-site realignment.
  Microbiol Mol Biol Rev, 73, 178-210.  
20025794 J.Frank (2009).
Single-particle reconstruction of biological macromolecules in electron microscopy--30 years.
  Q Rev Biophys, 42, 139-158.  
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.  
19140156 J.Mo, G.C.Todd, and K.Håkansson (2009).
Characterization of nucleic acid higher order structure by gas-phase H/D exchange in a quadrupole-FT-ICR mass spectrometer.
  Biopolymers, 91, 256-264.  
20005796 J.R.Williamson, V.Ramakrishnan, T.Steitz, and A.Yonath (2009).
The ribosome at atomic resolution.
  Cell, 139, 1041-1043.  
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.  
19376708 K.Connolly, and G.Culver (2009).
Deconstructing ribosome construction.
  Trends Biochem Sci, 34, 256-263.  
19109441 K.E.Deigan, T.W.Li, D.H.Mathews, and K.M.Weeks (2009).
Accurate SHAPE-directed RNA structure determination.
  Proc Natl Acad Sci U S A, 106, 97.  
19783814 K.T.Schroeder, and D.M.Lilley (2009).
Ion-induced folding of a kink turn that departs from the conventional sequence.
  Nucleic Acids Res, 37, 7281-7289.  
19509311 M.E.Christiansen, and B.M.Znosko (2009).
Thermodynamic characterization of tandem mismatches found in naturally occurring RNA.
  Nucleic Acids Res, 37, 4696-4706.  
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
19903202 M.Sakamoto, S.Noguchi, S.Kawashima, Y.Okada, T.Enomoto, M.Seki, and M.Horikoshi (2009).
Global analysis of mutual interaction surfaces of nucleosomes with comprehensive point mutants.
  Genes Cells, 14, 1271-1330.  
19589804 M.Savic, J.Lovric, T.I.Tomic, B.Vasiljevic, and G.L.Conn (2009).
Determination of the target nucleosides for members of two families of 16S rRNA methyltransferases that confer resistance to partially overlapping groups of aminoglycoside antibiotics.
  Nucleic Acids Res, 37, 5420-5431.  
  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.  
19416066 M.T.Sykes, and J.R.Williamson (2009).
A complex assembly landscape for the 30S ribosomal subunit.
  Annu Rev Biophys, 38, 197-215.  
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.  
19222865 P.B.Moore (2009).
The ribosome returned.
  J Biol, 8, 8.  
19385727 P.Babitzke, C.S.Baker, and T.Romeo (2009).
Regulation of translation initiation by RNA binding proteins.
  Annu Rev Microbiol, 63, 27-44.