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Structure of the Thermus thermophilus 30S ribosomal subunit bound to codon and near-cognate transfer rna anticodon stem-loop mismatched at the second codon position at the a site with paromomycin
DOI:10.2210/pdb1n33/pdb   NDB ID: RR0057
1N33
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Ribosome
    Structure Weight: 793101.68
    Molecule: 16S RIBOSOMAL RNA
    Polymer: 1 Type: rna Length: 1522
    Chains: A
    Organism Thermus thermophilus
    Molecule: ANTICODON STEM-LOOP OF SER TRANSFER RNA
    Polymer: 2 Type: rna Length: 17
    Chains: Y
    Organism Thermus thermophilus
    Molecule: A-SITE MESSENGER RNA FRAGMENT
    Polymer: 3 Type: rna Length: 6
    Chains: Z
    Organism Thermus thermophilus
    Molecule: 30S RIBOSOMAL PROTEIN S2
    Polymer: 4 Type: protein Length: 256
    Chains: B
    Organism Thermus thermophilus
    Gene Names rpsB rps2 TTHA0861
    UniProtKB:   Protein Feature View | Search PDB | P80371  
    Molecule: 30S RIBOSOMAL PROTEIN S3
    Polymer: 5 Type: protein Length: 239
    Chains: C
    Organism Thermus thermophilus
    Gene Names rpsC rps3 TTHA1686
    UniProtKB:   Protein Feature View | Search PDB | P80372  
    Molecule: 30S RIBOSOMAL PROTEIN S4
    Polymer: 6 Type: protein Length: 208
    Chains: D
    Organism Thermus thermophilus
    Gene Names rpsD rps4 TTHA1665
    UniProtKB:   Protein Feature View | Search PDB | P80373  
    Molecule: 30S RIBOSOMAL PROTEIN S5
    Polymer: 7 Type: protein Length: 161
    Chains: E
    Organism Thermus thermophilus
    Gene Names rpsE TTHA1675
    UniProtKB:   Protein Feature View | Search PDB | Q5SHQ5  
    Molecule: 30S RIBOSOMAL PROTEIN S6
    Polymer: 8 Type: protein Length: 101
    Chains: F
    Organism Thermus thermophilus
    Gene Names rpsF TTHA0245
    UniProtKB:   Protein Feature View | Search PDB | Q5SLP8  
    Molecule: 30S RIBOSOMAL PROTEIN S7
    Polymer: 9 Type: protein Length: 155
    Chains: G
    Organism Thermus thermophilus
    Gene Names rpsG rps7 TTHA1696
    UniProtKB:   Protein Feature View | Search PDB | P17291  
    Molecule: 30S RIBOSOMAL PROTEIN S8
    Polymer: 10 Type: protein Length: 138
    Chains: H
    Organism Thermus thermophilus
    Gene Names rpsH TTHA1678
    UniProtKB:   Protein Feature View | Search PDB | Q5SHQ2  
    Molecule: 30S RIBOSOMAL PROTEIN S9
    Polymer: 11 Type: protein Length: 128
    Chains: I
    Organism Thermus thermophilus
    Gene Names rpsI rps9 TTHA1464
    UniProtKB:   Protein Feature View | Search PDB | P80374  
    Molecule: 30S RIBOSOMAL PROTEIN S10
    Polymer: 12 Type: protein Length: 104
    Chains: J
    Organism Thermus thermophilus
    Gene Names rpsJ TTHA1693
    UniProtKB:   Protein Feature View | Search PDB | Q5SHN7  
    Molecule: 30S RIBOSOMAL PROTEIN S11
    Polymer: 13 Type: protein Length: 129
    Chains: K
    Organism Thermus thermophilus
    Gene Names rpsK rps11 TTHA1666
    UniProtKB:   Protein Feature View | Search PDB | P80376  
    Molecule: 30S RIBOSOMAL PROTEIN S12
    Polymer: 14 Type: protein Length: 135
    Chains: L
    Organism Thermus thermophilus
    Gene Names rpsL TTHA1697
    UniProtKB:   Protein Feature View | Search PDB | Q5SHN3  
    Molecule: 30S RIBOSOMAL PROTEIN S13
    Polymer: 15 Type: protein Length: 126
    Chains: M
    Organism Thermus thermophilus
    Gene Names rpsM rps13 TTHA1667
    UniProtKB:   Protein Feature View | Search PDB | P80377  
    Molecule: 30S RIBOSOMAL PROTEIN S14
    Polymer: 16 Type: protein Length: 60
    Chains: N
    Organism Thermus thermophilus
    Gene Names rpsZ rpsN TTHA1679
    UniProtKB:   Protein Feature View | Search PDB | Q5SHQ1  
    Molecule: 30S RIBOSOMAL PROTEIN S15
    Polymer: 17 Type: protein Length: 88
    Chains: O
    Organism Thermus thermophilus
    Gene Names rpsO TTHA1138
    UniProtKB:   Protein Feature View | Search PDB | Q5SJ76  
    Molecule: 30S RIBOSOMAL PROTEIN S16
    Polymer: 18 Type: protein Length: 88
    Chains: P
    Organism Thermus thermophilus
    Gene Names rpsP TTHA1035
    UniProtKB:   Protein Feature View | Search PDB | Q5SJH3  
    Molecule: 30S RIBOSOMAL PROTEIN S17
    Polymer: 19 Type: protein Length: 104
    Chains: Q
    Organism Thermus thermophilus
    Gene Names rpsQ TTHA1683
    UniProtKB:   Protein Feature View | Search PDB | Q5SHP7  
    Molecule: 30S RIBOSOMAL PROTEIN S18
    Polymer: 20 Type: protein Length: 88
    Chains: R
    Organism Thermus thermophilus
    Gene Names rpsR TTHA0243
    UniProtKB:   Protein Feature View | Search PDB | Q5SLQ0  
    Molecule: 30S RIBOSOMAL PROTEIN S19
    Polymer: 21 Type: protein Length: 92
    Chains: S
    Organism Thermus thermophilus
    Gene Names rpsS TTHA1688
    UniProtKB:   Protein Feature View | Search PDB | Q5SHP2  
    Molecule: 30S RIBOSOMAL PROTEIN S20
    Polymer: 22 Type: protein Length: 106
    Chains: T
    Organism Thermus thermophilus
    Gene Names rpsT rps20 TTHA1397
    UniProtKB:   Protein Feature View | Search PDB | P80380  
    Molecule: 30S RIBOSOMAL PROTEIN THX
    Polymer: 23 Type: protein Length: 26
    Chains: V
    Organism Thermus thermophilus
    Gene Names rpsU TTHA1396
    UniProtKB:   Protein Feature View | Search PDB | Q5SIH3  
     
  •   Structure Validation Hide

    Download full validation report    

     
  •   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: Thermus thermophilus   Taxonomy    
    Polymer: 23
    Scientific Name: Thermus thermophilus   Taxonomy    
     
  •   Related PDB Entries Hide
    Identifier Details
    1FJG  STRUCTURE OF THE 30S PARTICLE IN COMPLEX WITH THE ANTIBIOTICS STREPTOMYCIN, SPECTINOMYCIN AND PAROMOMYCIN 
    1IBK  STRUCTURE OF THE 30S PARTICLE IN COMPLEX WITH P-SITE MESSENGER RNA FRAGMENT AND WITH THE ANTIBIOTIC PAROMOMYCIN 
    1IBL  STRUCTURE OF THE 30S PARTICLE IN COMPLEX WITH MESSENGER RNA FRAGMENT AND COGNATE TRANSFER RNA ANTICODON STEM-LOOP BOUND TO THE A SITE AND WITH THE ANTIBIOTIC PAROMOMYCIN 
    1IBM  STRUCTURE OF THE 30S PARTICLE IN COMPLEX WITH MESSENGER RNA FRAGMENT AND COGNATE TRANSFER RNA ANTICODON STEM-LOOP BOUND TO THE A SITE 
    1J5E  NATIVE STRUCTURE OF THE 30S PARTICLE 
    1N32  STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNIT BOUND TO CODON AND NEAR-COGNATE TRANSFER RNA ANTICODON STEM-LOOP MISMATCHED AT THE FIRST CODON POSITION AT THE A SITE WITH PAROMOMYCIN 
    1N34  STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNIT IN THE PRESENCE OF CODON AND CRYSTALLOGRAPHICALLY DISORDERED NEAR-COGNATE TRANSFER RNA ANTICODON STEM-LOOP MISMATCHED AT THE FIRST CODON POSITION 
    1N36  STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNIT IN THE PRESENCE OF CRYSTALLOGRAPHICALLY DISORDERED CODON AND NEAR-COGNATE TRANSFER RNA ANTICODON STEM-LOOP MISMATCHED AT THE SECOND CODON POSITION 
     
  •   Ligand Chemical Component Hide
     
  •   Modified Residues Hide
    Identifier Formula Parent Type
    PSU
    Search 
    PSU C9 H13 N2 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: RR0057
     
 
Data in orange boxes are gathered from external resources (when available).
 
  Biological Assembly       
Biological assembly 1 assigned by authors
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