1XMO image
Deposition Date 2004-10-04
Release Date 2004-12-14
Last Version Date 2024-10-09
Entry Detail
PDB ID:
1XMO
Keywords:
RIBOSOME
Title:
Crystal Structure of mnm5U34t6A37-tRNALysUUU Complexed with AAG-mRNA in the Decoding Center
Biological Source:
Source Organism:
Thermus thermophilus (Taxon ID: 262724)
Thermus thermophilus (Taxon ID: 274)
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
3.25 Å
R-Value Free:
0.28
R-Value Work:
0.23
R-Value Observed:
0.23
Space Group:
P 41 21 2
1XMO validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:16S ribosomal RNA
Chain IDs:A
Chain Length:1522
Number of Molecules:1
Biological Source:Thermus thermophilus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:D (auth: B)
Chain Length:256
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P80371 Pfam ID:PF00318
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:E (auth: C)
Chain Length:239
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P80372 Pfam ID:PF07650, PF00189
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Gene (Uniprot):rpsD
Chain IDs:F (auth: D)
Chain Length:209
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P80373 Pfam ID:PF00163, PF01479
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Chain IDs:G (auth: E)
Chain Length:162
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SHQ5 Pfam ID:PF00333, PF03719
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Chain IDs:H (auth: F)
Chain Length:101
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SLP8 Pfam ID:PF01250
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:I (auth: G)
Chain Length:156
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P17291 Pfam ID:PF00177
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Chain IDs:J (auth: H)
Chain Length:138
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P0DOY9 Pfam ID:PF00410
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:K (auth: I)
Chain Length:128
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P80374 Pfam ID:PF00380
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Chain IDs:L (auth: J)
Chain Length:105
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SHN7 Pfam ID:PF00338
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:M (auth: K)
Chain Length:129
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P80376 Pfam ID:PF00411
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Chain IDs:N (auth: L)
Chain Length:135
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SHN3 Pfam ID:PF00164
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:O (auth: M)
Chain Length:126
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P80377 Pfam ID:PF00416
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14
Chain IDs:P (auth: N)
Chain Length:61
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P0DOY6 Pfam ID:PF00253
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Chain IDs:Q (auth: O)
Chain Length:89
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SJ76 Pfam ID:PF00312
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Chain IDs:R (auth: P)
Chain Length:88
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SJH3 Pfam ID:PF00886
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Chain IDs:S (auth: Q)
Chain Length:105
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P0DOY7 Pfam ID:PF00366
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Chain IDs:T (auth: R)
Chain Length:88
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SLQ0 Pfam ID:PF01084
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Chain IDs:U (auth: S)
Chain Length:93
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SHP2 Pfam ID:PF00203
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:V (auth: T)
Chain Length:106
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P80380 Pfam ID:PF01649
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein Thx
Chain IDs:W (auth: V)
Chain Length:27
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SIH3 Pfam ID:PF17070
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
MNU C U ?
T6A C A ?
Ligand Molecules
MG
PAR
ZN
Primary Citation
The role of modifications in codon discrimination by tRNA(Lys)(UUU).
Nat.Struct.Mol.Biol. 11 1186 1191 (2004)
PMID: 15558052 DOI: 10.1038/nsmb861

Abstact

The natural modification of specific nucleosides in many tRNAs is essential during decoding of mRNA by the ribosome. For example, tRNA(Lys)(UUU) requires the modification N6-threonylcarbamoyladenosine at position 37 (t(6)A37), adjacent and 3' to the anticodon, to bind AAA in the A site of the ribosomal 30S subunit. Moreover, it can only bind both AAA and AAG lysine codons when doubly modified with t(6)A37 and either 5-methylaminomethyluridine or 2-thiouridine at the wobble position (mnm(5)U34 or s(2)U34). Here we report crystal structures of modified tRNA anticodon stem-loops bound to the 30S ribosomal subunit with lysine codons in the A site. These structures allow the rationalization of how modifications in the anticodon loop enable decoding of both lysine codons AAA and AAG.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
1IBL
1IBK
1IBM
1FKA
1XMQ
1XNQ
1XNR
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