ISDA: 1XNR

Deposition Date 2004-10-05

Release Date 2004-12-14

Last Version Date 2024-11-13

Entry Detail

PDB ID:

1XNR

Keywords:

RIBOSOME

Title:

Crystal Structure of an Inosine-Cytosine Wobble Base Pair in the Context of the Decoding Center

Biological Source:

Source Organism:

Thermus thermophilus (Taxon ID: 274)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

3.10 Å

R-Value Free:

0.27

R-Value Work:

0.22

R-Value Observed:

0.23

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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:16S 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:16S 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:16S 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:16S 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:16S 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:16S 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:16S 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:16S 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:16S 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:16S 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:16S 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:16S 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:16S 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:16S 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:16S 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:16S 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:16S 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:16S 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:16S 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:16S 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

Ligand Molecules

PAR

Primary Citation

Structure of a purine-purine wobble base pair in the decoding center of the ribosome.

Murphy, F.V, Ramakrishnan, V.Show

Nat.Struct.Mol.Biol. 11 1251 1252 (2004)

PMID: 15558050 DOI: 10.1038/nsmb866

Abstact

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.

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Disease

Primary Citation of related structures