ISDA

Deposition Date 2013-03-05

Release Date 2013-11-06

Last Version Date 2025-02-12

Entry Detail

PDB ID:

4JI3

Keywords:

RIBOSOME

Title:

Crystal Structure of 30S ribosomal subunit from Thermus thermophilus

Biological Source:

Source Organism:

Thermus thermophilus (Taxon ID: 300852)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

3.35 Å

R-Value Free:

0.21

R-Value Work:

0.16

R-Value Observed:

0.17

Space Group:

P 41 21 2

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:16S rRNA
Chain IDs:A
Chain Length:1522
Number of Molecules:1
Biological Source:Thermus thermophilus

Protein Blast

Polymer Type:polypeptide(L)
Molecule: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: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: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: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: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: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: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: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: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: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:RIBOSOMAL PROTEIN S12
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: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: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: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: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: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: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: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: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: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

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details
2MG	A	G	2N-METHYLGUANOSINE-5'-MONOPHOSPHATE
4OC	A	C	4N,O2'-METHYLCYTIDINE-5'-MONOPHOSPHATE
5MC	A	C	5-METHYLCYTIDINE-5'-MONOPHOSPHATE
7MG	A	G	?
M2G	A	G	N2-DIMETHYLGUANOSINE-5'-MONOPHOSPHATE
MA6	A	A	6N-DIMETHYLADENOSINE-5'-MONOPHOSHATE
PSU	A	U	PSEUDOURIDINE-5'-MONOPHOSPHATE
UR3	A	U	3-METHYLURIDINE-5'-MONOPHOSHATE

Ligand Molecules

SRY

Primary Citation

The central role of protein S12 in organizing the structure of the decoding site of the ribosome.

Demirci, H, Wang, L, Murphy, F.V, Murphy, E.L, Carr, J.F, Blanchard, S.C, Jogl, G, Dahlberg, A.E, Gregory, S.T.Show

Rna 19 1791 1801 (2013)

PMID: 24152548 DOI: 10.1261/rna.040030.113

Abstact

The ribosome decodes mRNA by monitoring the geometry of codon-anticodon base-pairing using a set of universally conserved 16S rRNA nucleotides within the conformationally dynamic decoding site. By applying single-molecule FRET and X-ray crystallography, we have determined that conditional-lethal, streptomycin-dependence mutations in ribosomal protein S12 interfere with tRNA selection by allowing conformational distortions of the decoding site that impair GTPase activation of EF-Tu during the tRNA selection process. Distortions in the decoding site are reversed by streptomycin or by a second-site suppressor mutation in 16S rRNA. These observations encourage a refinement of the current model for decoding, wherein ribosomal protein S12 and the decoding site collaborate to optimize codon recognition and substrate discrimination during the early stages of the tRNA selection process.

Legend

Protein

Chemical

Disease

Primary Citation of related structures