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Structure of RelE nuclease bound to the 70S ribosome (precleavage state; Part 1 of 4)
DOI:10.2210/pdb3kiq/pdb   NDB ID: NA0323
3KIQ
Split Entry
The asymmetric unit for this structure is composed of multiple PDB entries:
3KIQ   3KIR   3KIS   3KIT  
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The complete entry has been assigned PDB ID 4V7J 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/4v7j.cif.gz
ftp://ftp.wwpdb.org/pub/pdb/data/large_structures/XML/4v7j.xml.gz
 
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Ribosome
    Structure Weight: 852670.63
    Molecule: 30S ribosomal protein S2
    Polymer: 1 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: 2 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: 3 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: 4 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: 5 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: 6 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: 7 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: 8 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: 9 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: 10 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: 11 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: 12 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: 13 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: 14 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: 15 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: 16 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: 17 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: 18 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: 19 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: 20 Type: protein Length: 27
    Chains: u
    Organism: Thermus thermophilus HB8
    Gene Names: rpsU TTHA1396
    UniProtKB: Protein Feature View | Search PDB | Q5SIH3  
    Molecule: Toxin relE
    Polymer: 21 Type: protein Length: 95
    Chains: y
    EC#: 3.1   
    Mutation: R45A, R81A
    Organism: Escherichia coli K-12
    Gene Names: relE b1563 JW1555
    UniProtKB: Protein Feature View | Search PDB | P0C077  
    Molecule: RNA (1504-MER)
    Polymer: 22 Type: rna Length: 1504
    Chains: a
    Organism: Thermus thermophilus
    Molecule: RNA (5'-R(*GP*GP*CP*AP*AP*GP*GP*AP*GP*GP*UP*A*AP*AP*AP*AP*UP*GP*(OMU)P*(A2M)P*(OMG)P*AP*AP*AP*A)-3')
    Polymer: 23 Type: rna Length: 25
    Chains: x
    Molecule: RNA (77-MER)
    Polymer: 24 Type: rna Length: 77
    Chains: v
    Organism: Thermus thermophilus
    Molecule: RNA (77-MER)
    Polymer: 25 Type: rna Length: 77
    Chains: w
    Organism: Thermus thermophilus
     
  •   Structure Validation Hide

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  • MolProbity Ramachandran Plot
     

  •   Related Citations in PDB Entry (REMARK 1) Hide
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Thermus thermophilus hb8   Taxonomy    
    Polymer: 2
    Scientific Name: Thermus thermophilus hb8   Taxonomy    
    Polymer: 3
    Scientific Name: Thermus thermophilus hb8   Taxonomy    
    Polymer: 4
    Scientific Name: Thermus thermophilus hb8   Taxonomy    
    Polymer: 5
    Scientific Name: Thermus thermophilus hb8   Taxonomy    
    Polymer: 6
    Scientific Name: Thermus thermophilus hb8   Taxonomy    
    Polymer: 7
    Scientific Name: Thermus thermophilus hb8   Taxonomy    
    Polymer: 8
    Scientific Name: Thermus thermophilus hb8   Taxonomy    
    Polymer: 9
    Scientific Name: Thermus thermophilus hb8   Taxonomy    
    Polymer: 10
    Scientific Name: Thermus thermophilus hb8   Taxonomy    
    Polymer: 11
    Scientific Name: Thermus thermophilus hb8   Taxonomy    
    Polymer: 12
    Scientific Name: Thermus thermophilus hb8   Taxonomy    
    Polymer: 13
    Scientific Name: Thermus thermophilus hb8   Taxonomy    
    Polymer: 14
    Scientific Name: Thermus thermophilus hb8   Taxonomy    
    Polymer: 15
    Scientific Name: Thermus thermophilus hb8   Taxonomy    
    Polymer: 16
    Scientific Name: Thermus thermophilus hb8   Taxonomy    
    Polymer: 17
    Scientific Name: Thermus thermophilus hb8   Taxonomy    
    Polymer: 18
    Scientific Name: Thermus thermophilus hb8   Taxonomy    
    Polymer: 19
    Scientific Name: Thermus thermophilus hb8   Taxonomy    
    Polymer: 20
    Scientific Name: Thermus thermophilus hb8   Taxonomy    
    Polymer: 21
    Scientific Name: Escherichia coli k-12   Taxonomy   Expression System: Escherichia coli  
    Polymer: 22
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 23
    Scientific Name: Synthetic construct   Taxonomy    
    Polymer: 24
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 25
    Scientific Name: Thermus thermophilus   Taxonomy    
     
  •   Related PDB Entries Hide
    Identifier Details
    3KIU   
    3KIW   
    3KIX   
    3KIY   
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    MG
    Search 
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    MG Mg
    MAGNESIUM ION
    ZN
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    ZN Zn
    ZINC ION
     
  •   Modified Residues Hide
    Identifier Formula Parent Type
    OMU
    Search 
    OMU C10 H15 N2 O9 P U rnaLinking
    A2M
    Search 
    A2M C11 H16 N5 O7 P A rnaLinking
    OMG
    Search 
    OMG C11 H16 N5 O8 P G rnaLinking
    5MU
    Search 
    5MU C10 H15 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: NA0323
     
 
Data in orange boxes are gathered from external resources (when available).
 
  Biological Assembly       
Composite of PDB entries (3KIQ and 3KIR)