7DUL image
Deposition Date 2021-01-09
Release Date 2022-01-26
Last Version Date 2025-02-12
Entry Detail
PDB ID:
7DUL
Keywords:
RIBOSOME
Title:
Crystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with mRNA and cognate transfer RNA anticodon stem-loop and sisomicin derivative N3''MS bound
Biological Source:
Source Organism:
Thermus thermophilus HB8 (Taxon ID: 300852)
Thermus thermophilus (Taxon ID: 274)
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
3.62 Å
R-Value Free:
0.22
R-Value Work:
0.18
R-Value Observed:
0.18
Space Group:
P 41 21 2
7DUL validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:30S Ribosomal RNA rRNA
Chain IDs:A
Chain Length:1522
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
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 HB8
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 HB8
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 HB8
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 HB8
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 HB8
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 HB8
UniProt ID:P17291 Pfam ID:PF00177
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Gene (Uniprot):rpsH
Chain IDs:H
Chain Length:138
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
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 HB8
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 HB8
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 HB8
UniProt ID:P80376 Pfam ID:PF00411
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Chain IDs:L
Chain Length:135
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
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 HB8
UniProt ID:P80377 Pfam ID:PF00416
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14 type Z
Gene (Uniprot):rpsZ
Chain IDs:N
Chain Length:61
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
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 HB8
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 HB8
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 HB8
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 HB8
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 HB8
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 HB8
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 HB8
UniProt ID:Q5SIH3 Pfam ID:PF17070
Polymer Type:polyribonucleotide
Molecule:RNA (5'-R(*GP*GP*GP*AP*UP*UP*GP*AP*AP*AP*AP*UP*CP*CP*C)-3')
Chain IDs:W
Chain Length:15
Number of Molecules:1
Biological Source:Thermus thermophilus
Polymer Type:polyribonucleotide
Molecule:RNA (5'-R(*UP*UP*UP*UP*UP*U)-3')
Chain IDs:V (auth: Y)
Chain Length:6
Number of Molecules:1
Biological Source:Thermus thermophilus
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
0TD L ASP modified residue
Ligand Molecules
MG
SIS
ZN
Primary Citation
Crystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with mRNA and cognate transfer RNA anticodon stem-loop and sisomicin derivative N3''MS bound
To Be Published ? ? ? (?)
Primary Citation of related structures
7DUL