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Crystal structure of the Thermus thermophilus 70S ribosome in the pre-attack state of peptide bond formation containing short substrate-mimic Cytidine-Cytidine-Puromycin in the A site and acylated tRNA in the P site. This entry contains the 30S subunit of the first 70S ribosome in the ASU.
DOI:10.2210/pdb4qcy/pdb   NDB ID: NA3015
4QCY
Split Entry
The asymmetric unit for this structure is composed of multiple PDB entries:
4QCY   4QCZ   4QD0   4QD1  
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The complete entry has been assigned PDB ID 1VY7 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/1vy7.cif.gz
ftp://ftp.wwpdb.org/pub/pdb/data/large_structures/XML/1vy7.xml.gz
 
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Ribosome
    Structure Weight: 847670.97
    Molecule: 16S Ribosomal RNA
    Polymer: 1 Type: rna Length: 1521
    Chains: A
    Organism: Thermus thermophilus HB8
    Molecule: 30S ribosomal protein S2
    Polymer: 2 Type: protein Length: 256
    Chains: B
    Organism: Thermus thermophilus HB8
    Gene Names: rpsB rps2 TTHA0861
    UniProtKB: Protein Feature View | Search PDB | P80371  
    Molecule: 30S ribosomal protein S3
    Polymer: 3 Type: protein Length: 239
    Chains: C
    Organism: Thermus thermophilus HB8
    Gene Names: rpsC rps3 TTHA1686
    UniProtKB: Protein Feature View | Search PDB | P80372  
    Molecule: 30S ribosomal protein S4
    Polymer: 4 Type: protein Length: 209
    Chains: D
    Organism: Thermus thermophilus HB8
    Gene Names: rpsD rps4 TTHA1665
    UniProtKB: Protein Feature View | Search PDB | P80373  
    Molecule: 30S ribosomal protein S5
    Polymer: 5 Type: protein Length: 162
    Chains: E
    Organism: Thermus thermophilus HB8
    Gene Names: rpsE TTHA1675
    UniProtKB: Protein Feature View | Search PDB | Q5SHQ5  
    Molecule: 30S ribosomal protein S6
    Polymer: 6 Type: protein Length: 101
    Chains: F
    Organism: Thermus thermophilus HB8
    Gene Names: rpsF TTHA0245
    UniProtKB: Protein Feature View | Search PDB | Q5SLP8  
    Molecule: 30S ribosomal protein S7
    Polymer: 7 Type: protein Length: 156
    Chains: G
    Organism: Thermus thermophilus HB8
    Gene Names: rpsG rps7 TTHA1696
    UniProtKB: Protein Feature View | Search PDB | P17291  
    Molecule: 30S ribosomal protein S8
    Polymer: 8 Type: protein Length: 138
    Chains: H
    Organism: Thermus thermophilus HB8
    Gene Names: rpsH TTHA1678
    UniProtKB: Protein Feature View | Search PDB | Q5SHQ2  
    Molecule: 30S ribosomal protein S9
    Polymer: 9 Type: protein Length: 128
    Chains: I
    Organism: Thermus thermophilus HB8
    Gene Names: rpsI rps9 TTHA1464
    UniProtKB: Protein Feature View | Search PDB | P80374  
    Molecule: 30S ribosomal protein S10
    Polymer: 10 Type: protein Length: 105
    Chains: J
    Organism: Thermus thermophilus HB8
    Gene Names: rpsJ TTHA1693
    UniProtKB: Protein Feature View | Search PDB | Q5SHN7  
    Molecule: 30S ribosomal protein S11
    Polymer: 11 Type: protein Length: 129
    Chains: K
    Organism: Thermus thermophilus HB8
    Gene Names: rpsK rps11 TTHA1666
    UniProtKB: Protein Feature View | Search PDB | P80376  
    Molecule: 30S ribosomal protein S12
    Polymer: 12 Type: protein Length: 132
    Chains: L
    Organism: Thermus thermophilus HB8
    Gene Names: rpsL TTHA1697
    UniProtKB: Protein Feature View | Search PDB | Q5SHN3  
    Molecule: 30S ribosomal protein S13
    Polymer: 13 Type: protein Length: 126
    Chains: M
    Organism: Thermus thermophilus HB8
    Gene Names: rpsM rps13 TTHA1667
    UniProtKB: Protein Feature View | Search PDB | P80377  
    Molecule: 30S ribosomal protein S14 type Z
    Polymer: 14 Type: protein Length: 61
    Chains: N
    Organism: Thermus thermophilus HB8
    Gene Names: rpsZ rpsN TTHA1679
    UniProtKB: Protein Feature View | Search PDB | Q5SHQ1  
    Molecule: 30S ribosomal protein S15
    Polymer: 15 Type: protein Length: 89
    Chains: O
    Organism: Thermus thermophilus HB8
    Gene Names: rpsO TTHA1138
    UniProtKB: Protein Feature View | Search PDB | Q5SJ76  
    Molecule: 30S ribosomal protein S16
    Polymer: 16 Type: protein Length: 88
    Chains: P
    Organism: Thermus thermophilus HB8
    Gene Names: rpsP TTHA1035
    UniProtKB: Protein Feature View | Search PDB | Q5SJH3  
    Molecule: 30S ribosomal protein S17
    Polymer: 17 Type: protein Length: 105
    Chains: Q
    Organism: Thermus thermophilus HB8
    Gene Names: rpsQ TTHA1683
    UniProtKB: Protein Feature View | Search PDB | Q5SHP7  
    Molecule: 30S ribosomal protein S18
    Polymer: 18 Type: protein Length: 88
    Chains: R
    Organism: Thermus thermophilus HB8
    Gene Names: rpsR TTHA0243
    UniProtKB: Protein Feature View | Search PDB | Q5SLQ0  
    Molecule: 30S ribosomal protein S19
    Polymer: 19 Type: protein Length: 93
    Chains: S
    Organism: Thermus thermophilus HB8
    Gene Names: rpsS TTHA1688
    UniProtKB: Protein Feature View | Search PDB | Q5SHP2  
    Molecule: 30S ribosomal protein S20
    Polymer: 20 Type: protein Length: 106
    Chains: T
    Organism: Thermus thermophilus HB8
    Gene Names: rpsT rps20 TTHA1397
    UniProtKB: Protein Feature View | Search PDB | P80380  
    Molecule: 30S ribosomal protein Thx
    Polymer: 21 Type: protein Length: 27
    Chains: U
    Organism: Thermus thermophilus HB8
    Gene Names: rpsU TTHA1396
    UniProtKB: Protein Feature View | Search PDB | Q5SIH3  
    Molecule: mRNA
    Polymer: 22 Type: rna Length: 24
    Chains: V
    Organism: synthetic construct
    Molecule: Cytidine-Puromycin
    Polymer: 23 Type: rna Length: 3
    Chains: W
    Organism: synthetic construct
    Molecule: P-site tRNA
    Polymer: 24 Type: rna Length: 77
    Chains: X
    Organism: Escherichia coli
    Molecule: E-site tRNA
    Polymer: 25 Type: rna Length: 76
    Chains: Y
    Organism: Escherichia coli
     
  •   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: 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    
    Polymer: 24
    Scientific Name: Escherichia coli   Taxonomy   Expression System: Escherichia coli  
    Polymer: 25
    Scientific Name: Escherichia coli   Taxonomy   Expression System: Escherichia coli  
     
  •   Ligand Chemical Component Hide
     
  •   Modified Residues Hide
    Identifier Formula Parent Type
    PPU
    Search 
    PPU C22 H30 N7 O8 P A rnaLinking
    4SU
    Search 
    4SU C9 H13 N2 O8 P S U rnaLinking
    5MC
    Search 
    5MC C10 H16 N3 O8 P C rnaLinking
    5MU
    Search 
    5MU C10 H15 N2 O9 P U rnaLinking
    PSU
    Search 
    PSU C9 H13 N2 O9 P U rnaLinking
    31H
    Search 
    31H C16 H24 N7 O8 P S A rnaLinking
    MIA
    Search 
    MIA C16 H26 N5 O7 P S A rnaLinking
    7MG
    Search 
    7MG C11 H18 N5 O8 P G rnaLinking
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure: NA3015
     
 
Data in orange boxes are gathered from external resources (when available).
 
  Biological Assembly       
Composite of PDB entries (4QCY and 4QCZ)