Structure of the Thermus thermophilus 30S ribosomal subunit complexed with a human mitochondrial anticodon stem loop (ASL) of transfer RNA Methionine (TRNAMET) bound to an mRNA with an AUG-codon in the A-site and paromomycin.
DOI:10.2210/pdb4gkj/pdb   NDB ID: NA1971
4GKJ
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Ribosome/antibiotic
    Structure Weight: 777329.32
    Molecule: 16S rRNA
    Polymer: 1 Type: rna Length: 1513
    Chains: A
    Organism: Thermus thermophilus HB8
    Molecule: 30S ribosomal protein S2
    Polymer: 2 Type: protein Length: 234
    Chains: B
    Organism: Thermus thermophilus HB8
    Gene Names: rpsB rps2 TTHA0861
    UniProtKB: Search PDB | P80371   Protein Feature View
    Molecule: 30S ribosomal protein S3
    Polymer: 3 Type: protein Length: 206
    Chains: C
    Organism: Thermus thermophilus HB8
    Gene Names: rpsC rps3 TTHA1686
    UniProtKB: Search PDB | P80372   Protein Feature View
    Molecule: 30S ribosomal protein S4
    Polymer: 4 Type: protein Length: 208
    Chains: D
    Organism: Thermus thermophilus HB8
    Gene Names: rpsD rps4 TTHA1665
    UniProtKB: Search PDB | P80373   Protein Feature View
    Molecule: 30S ribosomal protein S5
    Polymer: 5 Type: protein Length: 150
    Chains: E
    Organism: Thermus thermophilus HB8
    Gene Names: rpsE TTHA1675
    UniProtKB: Search PDB | Q5SHQ5   Protein Feature View
    Molecule: 30S ribosomal protein S6
    Polymer: 6 Type: protein Length: 101
    Chains: F
    Organism: Thermus thermophilus HB8
    Gene Names: rpsF TTHA0245
    UniProtKB: Search PDB | Q5SLP8   Protein Feature View
    Molecule: 30S ribosomal protein S7
    Polymer: 7 Type: protein Length: 155
    Chains: G
    Organism: Thermus thermophilus HB8
    Gene Names: rpsG rps7 TTHA1696
    UniProtKB: Search PDB | P17291   Protein Feature View
    Molecule: 30S ribosomal protein S8
    Polymer: 8 Type: protein Length: 138
    Chains: H
    Organism: Thermus thermophilus HB8
    Gene Names: rpsH TTHA1678
    UniProtKB: Search PDB | Q5SHQ2   Protein Feature View
    Molecule: 30S ribosomal protein S9
    Polymer: 9 Type: protein Length: 127
    Chains: I
    Organism: Thermus thermophilus HB8
    Gene Names: rpsI rps9 TTHA1464
    UniProtKB: Search PDB | P80374   Protein Feature View
    Molecule: 30S ribosomal protein S10
    Polymer: 10 Type: protein Length: 98
    Chains: J
    Organism: Thermus thermophilus HB8
    Gene Names: rpsJ TTHA1693
    UniProtKB: Search PDB | Q5SHN7   Protein Feature View
    Molecule: 30S ribosomal protein S11
    Polymer: 11 Type: protein Length: 119
    Chains: K
    Organism: Thermus thermophilus HB8
    Gene Names: rpsK rps11 TTHA1666
    UniProtKB: Search PDB | P80376   Protein Feature View
    Molecule: 30S ribosomal protein S12
    Polymer: 12 Type: protein Length: 124
    Chains: L
    Organism: Thermus thermophilus HB8
    Gene Names: rpsL TTHA1697
    UniProtKB: Search PDB | Q5SHN3   Protein Feature View
    Molecule: 30S ribosomal protein S13
    Polymer: 13 Type: protein Length: 125
    Chains: M
    Organism: Thermus thermophilus HB8
    Gene Names: rpsM rps13 TTHA1667
    UniProtKB: Search PDB | P80377   Protein Feature View
    Molecule: 30S ribosomal protein S14 type Z
    Polymer: 14 Type: protein Length: 60
    Chains: N
    Organism: Thermus thermophilus HB8
    Gene Names: rpsZ rpsN TTHA1679
    UniProtKB: Search PDB | Q5SHQ1   Protein Feature View
    Molecule: 30S ribosomal protein S15
    Polymer: 15 Type: protein Length: 88
    Chains: O
    Organism: Thermus thermophilus HB8
    Gene Names: rpsO TTHA1138
    UniProtKB: Search PDB | Q5SJ76   Protein Feature View
    Molecule: 30S ribosomal protein S16
    Polymer: 16 Type: protein Length: 83
    Chains: P
    Organism: Thermus thermophilus HB8
    Gene Names: rpsP TTHA1035
    UniProtKB: Search PDB | Q5SJH3   Protein Feature View
    Molecule: 30S ribosomal protein S17
    Polymer: 17 Type: protein Length: 104
    Chains: Q
    Organism: Thermus thermophilus HB8
    Gene Names: rpsQ TTHA1683
    UniProtKB: Search PDB | Q5SHP7   Protein Feature View
    Molecule: 30S ribosomal protein S18
    Polymer: 18 Type: protein Length: 73
    Chains: R
    Organism: Thermus thermophilus HB8
    Gene Names: rpsR TTHA0243
    UniProtKB: Search PDB | Q5SLQ0   Protein Feature View
    Molecule: 30S ribosomal protein S19
    Polymer: 19 Type: protein Length: 80
    Chains: S
    Organism: Thermus thermophilus HB8
    Gene Names: rpsS TTHA1688
    UniProtKB: Search PDB | Q5SHP2   Protein Feature View
    Molecule: 30S ribosomal protein S20
    Polymer: 20 Type: protein Length: 99
    Chains: T
    Organism: Thermus thermophilus HB8
    Gene Names: rpsT rps20 TTHA1397
    UniProtKB: Search PDB | P80380   Protein Feature View
    Molecule: 30S ribosomal protein Thx
    Polymer: 21 Type: protein Length: 24
    Chains: V
    Organism: Thermus thermophilus HB8
    Gene Names: rpsU TTHA1396
    UniProtKB: Search PDB | Q5SIH3   Protein Feature View
    Molecule: mRNA A-site fragment
    Polymer: 22 Type: rna Length: 6
    Chains: W
    Organism: synthetic construct
    Molecule: tRNA ASL human mitochondrial Met
    Polymer: 23 Type: rna Length: 17
    Chains: X
    Organism: synthetic construct
     
  •   Structure Validation Hide

    View the full validation report  

     

  • MolProbity Ramachandran Plot
     

  •   Related Citations in PDB Entry (REMARK 1) Hide
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 2
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 3
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 4
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 5
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 6
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 7
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 8
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 9
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 10
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 11
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 12
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 13
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 14
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 15
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 16
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 17
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 18
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 19
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 20
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 21
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 22
    Scientific Name: Synthetic construct (synthetic construct)   Taxonomy    
    Polymer: 23
    Scientific Name: Synthetic construct (synthetic construct)   Taxonomy    
     
  •   Related PDB Entries Hide
    Identifier Details
    2KRY   Same ASL in solution. 
    2UUC   Similar structure with a different ASL-mRNA pair. 
    3T1Y   Same crystallization conditions and used for phasing. 
     
  •   Ligand Chemical Component Hide
     
  •   Modified Residues Hide
    Identifier Formula Parent Type
    PSU
    Search 
    PSU C9 H13 N2 O9 P U rnaLinking
    RSQ
    Search 
    RSQ C10 H14 N3 O9 P U rnaLinking
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure:NA1971
     
 
Data in orange boxes are gathered from external resources (when available).
  Biological Assembly       
Biological assembly 1 assigned by authors and generated by PISA (software)
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  •   MyPDB Personal Annotations Hide
     
  •   Deposition Summary Hide
    Authors:   Cantara, W.A.,  Murphy IV, F.V.,  Spears, J.L.,  Demirci, H.,  Agris, P.F.

    Deposition:   2012-08-11
    Release:   2013-06-05
    Last Modified (REVDAT):   2013-07-17
     
  •   Revision History    Hide
    Mouse over text for details
    2013-07-17
    Citation
    2013-07-03
    Citation
    2013-06-19
    Citation
    2013-06-12
    Polymer description
     
  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    Resolution[Å]:   3.30
    R-Value: 0.190 (obs.)
    R-Free: 0.222
    Space Group: P 41 21 2
    Unit Cell:
      Length [Å] Angles [°]
    a = 400.55 α = 90.00 
    b = 400.55 β = 90.00 
    c = 176.19 γ = 90.00