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PDBsum entry 2uxc
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protein dna_rna ligands metals Protein-protein interface(s) links
Ribosome PDB id
2uxc

 

 

 

 

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Contents
Protein chains
235 a.a. *
207 a.a. *
208 a.a. *
151 a.a. *
101 a.a. *
155 a.a. *
138 a.a. *
127 a.a. *
99 a.a. *
119 a.a. *
125 a.a. *
125 a.a. *
60 a.a. *
88 a.a. *
84 a.a. *
104 a.a. *
73 a.a. *
81 a.a. *
99 a.a. *
25 a.a. *
DNA/RNA
Ligands
PAR
Metals
_ZN ×2
_MG ×192
__K ×26
* Residue conservation analysis
PDB id:
2uxc
Name: Ribosome
Title: Crystal structure of an extended tRNA anticodon stem loop in complex with its cognate mRNA ucgu in the context of the thermus thermophilus 30s subunit.
Structure: 16s ribosomal RNA. Chain: a. Other_details: chain a (16s RNA) has e. Coli numbering. Ribosomal protein s2. Chain: b. Ribosomal protein s3. Chain: c. Ribosomal protein s4. Chain: d.
Source: Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Atcc: 27634. Synthetic: yes. Synthetic construct. Organism_taxid: 32630. Organism_taxid: 32630
Resolution:
2.90Å     R-factor:   0.217     R-free:   0.255
Authors: C.M.Dunham,M.Selmer,S.S.Phelps,A.C.Kelley,T.Suzuki,S.Joseph, V.Ramakrishnan
Key ref: C.M.Dunham et al. (2007). Structures of tRNAs with an expanded anticodon loop in the decoding center of the 30S ribosomal subunit. Rna, 13, 817-823. PubMed id: 17416634
Date:
28-Mar-07     Release date:   08-May-07    
PROCHECK
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 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.
235 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.
207 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.
151 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.
99 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.
125 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.
84 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.
81 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.
25 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- ... 1513 bases
  A-C-G-A-A-A-U-C-U 9 bases
  U-C-G-U-U 5 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, U: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
Rna 13:817-823 (2007)
PubMed id: 17416634  
 
 
Structures of tRNAs with an expanded anticodon loop in the decoding center of the 30S ribosomal subunit.
C.M.Dunham, M.Selmer, S.S.Phelps, A.C.Kelley, T.Suzuki, S.Joseph, V.Ramakrishnan.
 
  ABSTRACT  
 
During translation, some +1 frameshift mRNA sites are decoded by frameshift suppressor tRNAs that contain an extra base in their anticodon loops. Similarly engineered tRNAs have been used to insert nonnatural amino acids into proteins. Here, we report crystal structures of two anticodon stem-loops (ASLs) from tRNAs known to facilitate +1 frameshifting bound to the 30S ribosomal subunit with their cognate mRNAs. ASL(CCCG) and ASL(ACCC) (5'-3' nomenclature) form unpredicted anticodon-codon interactions where the anticodon base 34 at the wobble position contacts either the fourth codon base or the third and fourth codon bases. In addition, we report the structure of ASL(ACGA) bound to the 30S ribosomal subunit with its cognate mRNA. The tRNA containing this ASL was previously shown to be unable to facilitate +1 frameshifting in competition with normal tRNAs (Hohsaka et al. 2001), and interestingly, it displays a normal anticodon-codon interaction. These structures show that the expanded anticodon loop of +1 frameshift promoting tRNAs are flexible enough to adopt conformations that allow three bases of the anticodon to span four bases of the mRNA. Therefore it appears that normal triplet pairing is not an absolute constraint of the decoding center.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20416503 G.Hayashi, Y.Goto, and H.Suga (2010).
Ribosome evolution for two artificial amino acids in E. coli.
  Chem Biol, 17, 320-321.  
20377916 H.S.Bernhardt, and W.P.Tate (2010).
The transition from noncoded to coded protein synthesis: did coding mRNAs arise from stability-enhancing binding partners to tRNA?
  Biol Direct, 5, 16.  
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.  
19479032 P.V.Baranov, M.Venin, and G.Provan (2009).
Codon size reduction as the origin of the triplet genetic code.
  PLoS One, 4, e5708.  
18842120 A.Tats, T.Tenson, and M.Remm (2008).
Preferred and avoided codon pairs in three domains of life.
  BMC Genomics, 9, 463.  
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
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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