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Structural basis for translation termination on the 70S ribosome. This file contains the 30S subunit, release factor 1 (RF1), two tRNA, and mRNA molecules of the second 70S ribosome. The entire crystal structure contains two 70S ribosomes as described in remark 400.
DOI:10.2210/pdb3d5c/pdb   NDB ID: RR0225
3D5C
Split Entry
The asymmetric unit for this structure is composed of multiple PDB entries:
3D5A   3D5B   3D5C   3D5D  
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The complete entry has been assigned PDB ID 4V63 and is available for download in PDBx/mmCIF and PDBML/XML formats from the FTP archive at:
ftp://ftp.wwpdb.org/pub/pdb/data/large_structures/mmCIF/4v63.cif.gz
ftp://ftp.wwpdb.org/pub/pdb/data/large_structures/XML/4v63.xml.gz
 
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Ribosome
    Structure Weight: 895349.58
    Molecule: 16S RRNA
    Polymer: 1 Type: rna Length: 1525
    Chains: A
    Organism: Thermus thermophilus HB27
    Molecule: P and E-site tRNA(fMet)
    Polymer: 2 Type: rna Length: 77
    Chains: Y, Z
    Organism: Escherichia coli
    Molecule: mRNA
    Polymer: 3 Type: rna Length: 27
    Chains: V
    Molecule: 30S ribosomal protein S2
    Polymer: 4 Type: protein Length: 256
    Chains: B
    Organism: Thermus thermophilus HB27
    Gene Names: rpsB rps2 TT_C0509
    UniProtKB: Protein Feature View | Search PDB | P62662  
    Molecule: 30S ribosomal protein S3
    Polymer: 5 Type: protein Length: 239
    Chains: C
    Organism: Thermus thermophilus HB27
    Gene Names: rpsC rps3 TT_C1322
    UniProtKB: Protein Feature View | Search PDB | P62663  
    Molecule: 30S ribosomal protein S4
    Polymer: 6 Type: protein Length: 209
    Chains: D
    Organism: Thermus thermophilus HB27
    Gene Names: rpsD rps4 TT_C1301
    UniProtKB: Protein Feature View | Search PDB | P62664  
    Molecule: 30S ribosomal protein S5
    Polymer: 7 Type: protein Length: 162
    Chains: E
    Organism: Thermus thermophilus HB27
    Gene Names: rpsE rps5 TT_C1311
    UniProtKB: Protein Feature View | Search PDB | P62665  
    Molecule: 30S ribosomal protein S6
    Polymer: 8 Type: protein Length: 101
    Chains: F
    Organism: Thermus thermophilus HB27
    Gene Names: rpsF rps6 TT_C1740
    UniProtKB: Protein Feature View | Search PDB | P62666  
    Molecule: 30S ribosomal protein S7
    Polymer: 9 Type: protein Length: 156
    Chains: G
    Organism: Thermus thermophilus HB27
    Gene Names: rpsG rps7 TT_C1332
    UniProtKB: Protein Feature View | Search PDB | P62667  
    Molecule: 30S ribosomal protein S8
    Polymer: 10 Type: protein Length: 138
    Chains: H
    Organism: Thermus thermophilus HB27
    Gene Names: rpsH rps8 TT_C1314
    UniProtKB: Protein Feature View | Search PDB | P62668  
    Molecule: 30S ribosomal protein S9
    Polymer: 11 Type: protein Length: 128
    Chains: I
    Organism: Thermus thermophilus HB27
    Gene Names: rpsI rps9 TT_C1100
    UniProtKB: Protein Feature View | Search PDB | P62669  
    Molecule: 30S ribosomal protein S10
    Polymer: 12 Type: protein Length: 105
    Chains: J
    Organism: Thermus thermophilus HB27
    Gene Names: rpsJ rps10 TT_C1329
    UniProtKB: Protein Feature View | Search PDB | P62653  
    Molecule: 30S ribosomal protein S11
    Polymer: 13 Type: protein Length: 129
    Chains: K
    Organism: Thermus thermophilus HB27
    Gene Names: rpsK rps11 TT_C1302
    UniProtKB: Protein Feature View | Search PDB | P62654  
    Molecule: 30S ribosomal protein S12
    Polymer: 14 Type: protein Length: 134
    Chains: L
    Organism: Thermus thermophilus HB27
    Gene Names: rpsL rps12 TT_C1333
    UniProtKB: Protein Feature View | Search PDB | P61941  
    Molecule: 30S ribosomal protein S13
    Polymer: 15 Type: protein Length: 126
    Chains: M
    Organism: Thermus thermophilus HB27
    Gene Names: rpsM rps13 TT_C1303
    UniProtKB: Protein Feature View | Search PDB | P62655  
    Molecule: 30S ribosomal protein S14
    Polymer: 16 Type: protein Length: 61
    Chains: N
    Organism: Thermus thermophilus HB27
    Gene Names: rpsZ rps14 rpsN TT_C1315
    UniProtKB: Protein Feature View | Search PDB | P62656  
    Molecule: 30S ribosomal protein S15
    Polymer: 17 Type: protein Length: 89
    Chains: O
    Organism: Thermus thermophilus HB27
    Gene Names: rpsO rps15 TT_C0773
    UniProtKB: Protein Feature View | Search PDB | P62657  
    Molecule: 30S ribosomal protein S16
    Polymer: 18 Type: protein Length: 88
    Chains: P
    Organism: Thermus thermophilus HB27
    Gene Names: rpsP rps16 TT_C0673
    UniProtKB: Protein Feature View | Search PDB | P62238  
    Molecule: 30S ribosomal protein S17
    Polymer: 19 Type: protein Length: 105
    Chains: Q
    Organism: Thermus thermophilus HB27
    Gene Names: rpsQ rps17 TT_C1319
    UniProtKB: Protein Feature View | Search PDB | P62658  
    Molecule: 30S ribosomal protein S18
    Polymer: 20 Type: protein Length: 88
    Chains: R
    Organism: Thermus thermophilus HB27
    Gene Names: rpsR rps18 TT_C1742
    UniProtKB: Protein Feature View | Search PDB | P62659  
    Molecule: 30S ribosomal protein S19
    Polymer: 21 Type: protein Length: 93
    Chains: S
    Organism: Thermus thermophilus HB27
    Gene Names: rpsS rps19 TT_C1324
    UniProtKB: Protein Feature View | Search PDB | P62660  
    Molecule: 30S ribosomal protein S20
    Polymer: 22 Type: protein Length: 106
    Chains: T
    Organism: Thermus thermophilus HB27
    Gene Names: rpsT rps20 TT_C1031
    UniProtKB: Protein Feature View | Search PDB | P62661  
    Molecule: 30S ribosomal protein Thx
    Polymer: 23 Type: protein Length: 27
    Chains: U
    Organism: Thermus thermophilus HB27
    Gene Names: rpsU TT_C1030
    UniProtKB: Protein Feature View | Search PDB | P62613  
    Molecule: Peptide chain release factor 1
    Polymer: 24 Type: protein Length: 354
    Chains: X
    Organism: Thermus thermophilus HB27
    Gene Names: prfA TT_C1577
    UniProtKB: Protein Feature View | Search PDB | Q72HB8  
     
  •   Structure Validation Hide

    Download 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: Escherichia coli   Taxonomy    
    Polymer: 3
    Scientific Name: Synthetic construct   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    
    Polymer: 24
    Scientific Name: Thermus thermophilus   Taxonomy    
     
  •   Related PDB Entries Hide
    Identifier Details
    3D5A  30S SUBUNIT OF 70S RIBOSOME ONE 
    3D5B  50S SUBUNIT OF 70S RIBOSOME ONE 
    3D5D  50S SUBUNIT OF 70S RIBOSOME TWO 
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    MG
    Search 
    Download 
    MG Mg
    MAGNESIUM ION
    ZN
    Search 
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    ZN Zn
    ZINC ION
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure: RR0225
     
 
Data in orange boxes are gathered from external resources (when available).
 
  Biological Assembly       
Composite of PDB entries (3D5A and 3D5B)