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

 

 

 

 

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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. *
DNA/RNA
Ligands
PAR
Metals
_MG ×107
_ZN ×2
* Residue conservation analysis
PDB id:
1xnq
Name: Ribosome
Title: Structure of an inosine-adenine wobble base pair complex in the context of the decoding center
Structure: 16s ribosomal RNA. Chain: a. Anticodon tRNA. Chain: x. Engineered: yes. mRNA. Chain: w. Engineered: yes. Ribosomal protein s2.
Source: Thermus thermophilus. Organism_taxid: 274. Synthetic: yes. Organism_taxid: 274
Biol. unit: 23mer (from PQS)
Resolution:
3.05Å     R-factor:   0.228     R-free:   0.270
Authors: F.V.Murphy,V.Ramakrishnan
Key ref:
F.V.Murphy and V.Ramakrishnan (2004). Structure of a purine-purine wobble base pair in the decoding center of the ribosome. Nat Struct Mol Biol, 11, 1251-1252. PubMed id: 15558050 DOI: 10.1038/nsmb866
Date:
05-Oct-04     Release date:   14-Dec-04    
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
Pfam   ArchSchema ?
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
Pfam   ArchSchema ?
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.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 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
  G-G-C-U-I-C-G-A-A-C-C 11 bases
  C-G-A-A 4 bases

 

 
DOI no: 10.1038/nsmb866 Nat Struct Mol Biol 11:1251-1252 (2004)
PubMed id: 15558050  
 
 
Structure of a purine-purine wobble base pair in the decoding center of the ribosome.
F.V.Murphy, V.Ramakrishnan.
 
  ABSTRACT  
 
Here we report the crystal structures of I.C and I.A wobble base pairs in the context of the ribosomal decoding center, clearly showing that the I.A base pair is of an I(anti).A(anti) conformation, as predicted by Crick. Additionally, the structures enable the observation of changes in the anticodon to allow purine-purine base pairing, the 'widest' base pair geometry allowed in the wobble position.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Cartoon structures of the I C and I A base pairs. 		Figure 2.
Figure 2. Details of base pairs. (a) I C base pair (I, green; C, yellow) with 2F[o] - F[c] map contoured to 1.6 . (b) I A base pair (I, green; A, cyan) with 2F[o] - F[c] map contoured to 1.6 . (c) I C base pair with hydrogen bonds as dashed lines. (d) I A base pairs (both anti-anti and syn-anti).
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2004, 11, 1251-1252) copyright 2004.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19931536 E.M.Phizicky, and J.D.Alfonzo (2010).
Do all modifications benefit all tRNAs?
  FEBS Lett, 584, 265-271.  
19151083 C.Takemoto, L.L.Spremulli, L.A.Benkowski, T.Ueda, T.Yokogawa, and K.Watanabe (2009).
Unconventional decoding of the AUA codon as methionine by mitochondrial tRNAMet with the anticodon f5CAU as revealed with a mitochondrial in vitro translation system.
  Nucleic Acids Res, 37, 1616-1627.  
19089882 E.Zimmerman, and A.Yonath (2009).
Biological implications of the ribosome's stunning stereochemistry.
  Chembiochem, 10, 63-72.  
19861423 F.A.Vendeix, A.M.Munoz, and P.F.Agris (2009).
Free energy calculation of modified base-pair formation in explicit solvent: A predictive model.
  RNA, 15, 2278-2287.  
18346970 J.Kondo, and E.Westhof (2008).
The bacterial and mitochondrial ribosomal A-site molecular switches possess different conformational substates.
  Nucleic Acids Res, 36, 2654-2666.
PDB codes: 3bnl 3bnn 3bno 3bnp 3bnq 3bnr 3bns 3bnt
18193063 M.Rogalski, D.Karcher, and R.Bock (2008).
Superwobbling facilitates translation with reduced tRNA sets.
  Nat Struct Mol Biol, 15, 192-198.  
17916576 K.W.Gaston, M.A.Rubio, J.L.Spears, I.Pastar, F.N.Papavasiliou, and J.D.Alfonzo (2007).
C to U editing at position 32 of the anticodon loop precedes tRNA 5' leader removal in trypanosomatids.
  Nucleic Acids Res, 35, 6740-6749.  
17218280 U.Kothe, and M.V.Rodnina (2007).
Codon reading by tRNAAla with modified uridine in the wobble position.
  Mol Cell, 25, 167-174.  
16522645 A.Mokdad, M.V.Krasovska, J.Sponer, and N.B.Leontis (2006).
Structural and evolutionary classification of G/U wobble basepairs in the ribosome.
  Nucleic Acids Res, 34, 1326-1341.  
17120123 A.Travers (2006).
The evolution of the genetic code revisited.
  Orig Life Evol Biosph, 36, 549-555.  
16600899 C.Marck, R.Kachouri-Lafond, I.Lafontaine, E.Westhof, B.Dujon, and H.Grosjean (2006).
The RNA polymerase III-dependent family of genes in hemiascomycetes: comparative RNomics, decoding strategies, transcription and evolutionary implications.
  Nucleic Acids Res, 34, 1816-1835.  
16415880 H.C.Losey, A.J.Ruthenburg, and G.L.Verdine (2006).
Crystal structure of Staphylococcus aureus tRNA adenosine deaminase TadA in complex with RNA.
  Nat Struct Mol Biol, 13, 153-159.
PDB code: 2b3j
16455492 K.B.Gromadski, T.Daviter, and M.V.Rodnina (2006).
A uniform response to mismatches in codon-anticodon complexes ensures ribosomal fidelity.
  Mol Cell, 21, 369-377.  
15578054 L.Cochella, and R.Green (2004).
Wobble during decoding: more than third-position promiscuity.
  Nat Struct Mol Biol, 11, 1160-1162.  
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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