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PDBsum entry 4k0m

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protein dna_rna Protein-protein interface(s) links
Ribosome PDB id
4k0m
Jmol PyMol
Contents
Protein chains
190 a.a.
271 a.a.
204 a.a.
207 a.a.
181 a.a.
159 a.a.
145 a.a.
130 a.a.
138 a.a.
122 a.a.
146 a.a.
141 a.a.
117 a.a.
98 a.a.
137 a.a.
117 a.a.
101 a.a.
113 a.a.
92 a.a.
100 a.a.
176 a.a.
84 a.a.
93 a.a.
71 a.a.
59 a.a.
30 a.a.
59 a.a.
44 a.a.
48 a.a.
63 a.a.
36 a.a.
DNA/RNA
PDB id:
4k0m
Name: Ribosome
Title: Crystal structure of thermus thermophilus 70s containing trn mRNA stop codon with pseudouridine
Structure: 23s ribosomal RNA. Chain: a. 5s ribosomal RNA. Chain: b. 50s ribosomal protein l1. Chain: c. 50s ribosomal protein l2. Chain: d. 50s ribosomal protein l3.
Source: Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Strain: hb8
Resolution:
3.30Å     R-factor:   0.228     R-free:   0.279
Authors: I.S.Fernandez,C.L.Ng,A.C.Kelley,W.Guowei,Y.T.Yu,V.Ramakrishn
Key ref: I.S.Fernández et al. (2013). Unusual base pairing during the decoding of a stop codon by the ribosome. Nature, 500, 107-110. PubMed id: 23812587 DOI: 10.1038/nature12302
Date:
04-Apr-13     Release date:   03-Jul-13    
PROCHECK
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 Headers
 References

Protein chain
No UniProt id for this chain
Struc: 190 a.a.
Protein chain
Pfam   ArchSchema ?
P60405  (RL2_THET8) -  50S ribosomal protein L2
Seq:
Struc:
276 a.a.
271 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHN8  (RL3_THET8) -  50S ribosomal protein L3
Seq:
Struc:
206 a.a.
204 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHN9  (RL4_THET8) -  50S ribosomal protein L4
Seq:
Struc:
210 a.a.
207 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHQ0  (RL5_THET8) -  50S ribosomal protein L5
Seq:
Struc:
182 a.a.
181 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHQ3  (RL6_THET8) -  50S ribosomal protein L6
Seq:
Struc:
180 a.a.
159 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SLQ1  (RL9_THET8) -  50S ribosomal protein L9
Seq:
Struc:
148 a.a.
145 a.a.
Protein chain
No UniProt id for this chain
Struc: 130 a.a.
Protein chain
Pfam   ArchSchema ?
P60488  (RL13_THET8) -  50S ribosomal protein L13
Seq:
Struc:
140 a.a.
138 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHP8  (RL14_THET8) -  50S ribosomal protein L14
Seq:
Struc:
122 a.a.
122 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHQ7  (RL15_THET8) -  50S ribosomal protein L15
Seq:
Struc:
150 a.a.
146 a.a.
Protein chain
Pfam   ArchSchema ?
P60489  (RL16_THET8) -  50S ribosomal protein L16
Seq:
Struc:
141 a.a.
141 a.a.
Protein chain
Pfam   ArchSchema ?
Q9Z9H5  (RL17_THET8) -  50S ribosomal protein L17
Seq:
Struc:
118 a.a.
117 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHQ4  (RL18_THET8) -  50S ribosomal protein L18
Seq:
Struc:
112 a.a.
98 a.a.
Protein chain
Pfam   ArchSchema ?
P60490  (RL19_THET8) -  50S ribosomal protein L19
Seq:
Struc:
146 a.a.
137 a.a.
Protein chain
Pfam   ArchSchema ?
P60491  (RL20_THET8) -  50S ribosomal protein L20
Seq:
Struc:
118 a.a.
117 a.a.*
Protein chain
Pfam   ArchSchema ?
P60492  (RL21_THET8) -  50S ribosomal protein L21
Seq:
Struc:
101 a.a.
101 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHP3  (RL22_THET8) -  50S ribosomal protein L22
Seq:
Struc:
113 a.a.
113 a.a.*
Protein chain
Pfam   ArchSchema ?
Q5SHP0  (RL23_THET8) -  50S ribosomal protein L23
Seq:
Struc:
96 a.a.
92 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHP9  (RL24_THET8) -  50S ribosomal protein L24
Seq:
Struc:
110 a.a.
100 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHZ1  (RL25_THET8) -  50S ribosomal protein L25
Seq:
Struc:
206 a.a.
176 a.a.
Protein chain
Pfam   ArchSchema ?
P60493  (RL27_THET8) -  50S ribosomal protein L27
Seq:
Struc:
85 a.a.
84 a.a.
Protein chain
Pfam   ArchSchema ?
P60494  (RL28_THET8) -  50S ribosomal protein L28
Seq:
Struc:
98 a.a.
93 a.a.*
Protein chain
Pfam   ArchSchema ?
Q5SHP6  (RL29_THET8) -  50S ribosomal protein L29
Seq:
Struc:
72 a.a.
71 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHQ6  (RL30_THET8) -  50S ribosomal protein L30
Seq:
Struc:
60 a.a.
59 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SJE1  (RL31_THET8) -  50S ribosomal protein L31
Seq:
Struc:
71 a.a.
30 a.a.
Protein chain
Pfam   ArchSchema ?
P80339  (RL32_THET8) -  50S ribosomal protein L32
Seq:
Struc:
60 a.a.
59 a.a.
Protein chain
Pfam   ArchSchema ?
P35871  (RL33_THET8) -  50S ribosomal protein L33
Seq:
Struc:
54 a.a.
44 a.a.
Protein chain
Pfam   ArchSchema ?
P80340  (RL34_THET8) -  50S ribosomal protein L34
Seq:
Struc:
49 a.a.
48 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SKU1  (RL35_THET8) -  50S ribosomal protein L35
Seq:
Struc:
65 a.a.
63 a.a.
Protein chain
Pfam   ArchSchema ?
Q5SHR2  (RL36_THET8) -  50S ribosomal protein L36
Seq:
Struc:
37 a.a.
36 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 

 
DOI no: 10.1038/nature12302 Nature 500:107-110 (2013)
PubMed id: 23812587  
 
 
Unusual base pairing during the decoding of a stop codon by the ribosome.
I.S.Fernández, C.L.Ng, A.C.Kelley, G.Wu, Y.T.Yu, V.Ramakrishnan.
 
  ABSTRACT  
 
During normal translation, the binding of a release factor to one of the three stop codons (UGA, UAA or UAG) results in the termination of protein synthesis. However, modification of the initial uridine to a pseudouridine (Ψ) allows efficient recognition and read-through of these stop codons by a transfer RNA (tRNA), although it requires the formation of two normally forbidden purine-purine base pairs. Here we determined the crystal structure at 3.1 Å resolution of the 30S ribosomal subunit in complex with the anticodon stem loop of tRNA(Ser) bound to the ΨAG stop codon in the A site. The ΨA base pair at the first position is accompanied by the formation of purine-purine base pairs at the second and third positions of the codon, which show an unusual Watson-Crick/Hoogsteen geometry. The structure shows a previously unsuspected ability of the ribosomal decoding centre to accommodate non-canonical base pairs.
 

 

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