ISDA

Deposition Date 2007-03-01

Release Date 2007-05-15

Last Version Date 2024-11-06

Entry Detail

PDB ID:

2UUB

Keywords:

RIBOSOME

Title:

Structure of the Thermus thermophilus 30S ribosomal subunit complexed with a Valine-ASL with cmo5U in position 34 bound to an mRNA with a GUU-codon in the A-site and paromomycin.

Biological Source:

Source Organism:

synthetic construct (Taxon ID: 32630)
THERMUS THERMOPHILUS (Taxon ID: 300852)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.80 Å

R-Value Free:

0.24

R-Value Work:

0.21

R-Value Observed:

0.21

Space Group:

P 41 21 2

Download 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

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S2
Gene (Uniprot):rpsB
Chain IDs:B
Chain Length:256
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P80371 Pfam ID:PF00318

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S3
Gene (Uniprot):rpsC
Chain IDs:C
Chain Length:239
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P80372 Pfam ID:PF07650, PF00189

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S4
Gene (Uniprot):rpsD
Chain IDs:D
Chain Length:209
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P80373 Pfam ID:PF00163, PF01479

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S5
Gene (Uniprot):rpsE
Chain IDs:E
Chain Length:162
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHQ5 Pfam ID:PF00333, PF03719

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S6
Gene (Uniprot):rpsF
Chain IDs:F
Chain Length:101
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SLP8 Pfam ID:PF01250

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S7
Gene (Uniprot):rpsG
Chain IDs:G
Chain Length:156
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P17291 Pfam ID:PF00177

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S8
Chain IDs:H
Chain Length:138
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P0DOY9 Pfam ID:PF00410

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S9
Gene (Uniprot):rpsI
Chain IDs:I
Chain Length:128
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P80374 Pfam ID:PF00380

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S10
Gene (Uniprot):rpsJ
Chain IDs:J
Chain Length:105
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHN7 Pfam ID:PF00338

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S11
Gene (Uniprot):rpsK
Chain IDs:K
Chain Length:129
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P80376 Pfam ID:PF00411

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S12
Gene (Uniprot):rpsL
Chain IDs:L
Chain Length:135
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHN3 Pfam ID:PF00164

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S13
Gene (Uniprot):rpsM
Chain IDs:M
Chain Length:126
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P80377 Pfam ID:PF00416

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S14
Chain IDs:N
Chain Length:61
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P0DOY6 Pfam ID:PF00253

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S15
Gene (Uniprot):rpsO
Chain IDs:O
Chain Length:89
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SJ76 Pfam ID:PF00312

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S16
Gene (Uniprot):rpsP
Chain IDs:P
Chain Length:88
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SJH3 Pfam ID:PF00886

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S17
Chain IDs:Q
Chain Length:105
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P0DOY7 Pfam ID:PF00366

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S18
Gene (Uniprot):rpsR
Chain IDs:R
Chain Length:88
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SLQ0 Pfam ID:PF01084

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S19
Gene (Uniprot):rpsS
Chain IDs:S
Chain Length:93
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHP2 Pfam ID:PF00203

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S20
Gene (Uniprot):rpsT
Chain IDs:T
Chain Length:106
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P80380 Pfam ID:PF01649

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN THX
Gene (Uniprot):rpsU
Chain IDs:U
Chain Length:27
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SIH3 Pfam ID:PF17070

Polymer Type:polyribonucleotide
Molecule:5'-R(*GP*UP*UP*AP*AP*AP)-3'
Chain IDs:V (auth: X)
Chain Length:6
Number of Molecules:1
Biological Source:synthetic construct

Polymer Type:polyribonucleotide
Molecule:5'-R(*CP*CP*UP*CP*CP*CP*UP*CM0P*AP*CP*6MZP*AP *GP*GP*AP*GP*G)-3'
Chain IDs:W (auth: Y)
Chain Length:17
Number of Molecules:1
Biological Source:synthetic construct

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details	2D Image
6MZ	W	A	N6-METHYLADENOSINE-5'-MONOPHOSPHATE

Ligand Molecules

PAR

Primary Citation

Mechanism for Expanding the Decoding Capacity of Transfer Rnas by Modification of Uridines

Weixlbaumer, A, Murphy, F.V, Dziergowska, A, Malkiewicz, A, Vendeix, F.A.P, Agris, P.F, Ramakrishnan, V.Show

Nat.Struct.Mol.Biol. 14 498 ? (2007)

PMID: 17496902 DOI: 10.1038/NSMB1242

Abstact

One of the most prevalent base modifications involved in decoding is uridine 5-oxyacetic acid at the wobble position of tRNA. It has been known for several decades that this modification enables a single tRNA to decode all four codons in a degenerate codon box. We have determined structures of an anticodon stem-loop of tRNA(Val) containing the modified uridine with all four valine codons in the decoding site of the 30S ribosomal subunit. An intramolecular hydrogen bond involving the modification helps to prestructure the anticodon loop. We found unusual base pairs with the three noncomplementary codon bases, including a G.U base pair in standard Watson-Crick geometry, which presumably involves an enol form for the uridine. These structures suggest how a modification in the uridine at the wobble position can expand the decoding capability of a tRNA.

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Protein

Chemical

Disease

Primary Citation of related structures