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Crystal structure of a complex containing domain 3 from the PSIV IGR IRES RNA bound to the 70S ribosome. This file contains the 50S subunit of the second 70S ribosome.
DOI:10.2210/pdb3pyr/pdb   NDB ID: NA0929
3PYR
Split Entry
The asymmetric unit for this structure is composed of multiple PDB entries:
3PYN   3PYO   3PYQ   3PYR  
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The complete entry has been assigned PDB ID 4V83 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/4v83.cif.gz
ftp://ftp.wwpdb.org/pub/pdb/data/large_structures/XML/4v83.xml.gz
 
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Ribosome
    Structure Weight: 1388544.20
    Molecule: 23S ribosomal RNA
    Polymer: 1 Type: rna Length: 2879
    Chains: A
    Organism: Thermus thermophilus HB27
    Molecule: 5S ribosomal RNA
    Polymer: 2 Type: rna Length: 119
    Chains: B
    Organism: Thermus thermophilus HB27
    Molecule: 50S ribosomal protein L2
    Polymer: 3 Type: protein Length: 271
    Chains: C
    Organism: Thermus thermophilus HB27
    Gene Names: rplB TT_C1325
    UniProtKB: Protein Feature View | Search PDB | Q72I07  
    Molecule: 50S ribosomal protein L3
    Polymer: 4 Type: protein Length: 204
    Chains: D
    Organism: Thermus thermophilus HB27
    Gene Names: rplC TT_C1328
    UniProtKB: Protein Feature View | Search PDB | Q72I04  
    Molecule: 50S ribosomal protein L4
    Polymer: 5 Type: protein Length: 202
    Chains: E
    Organism: Thermus thermophilus HB27
    Gene Names: rplD TT_C1327
    UniProtKB: Protein Feature View | Search PDB | Q72I05  
    Molecule: 50S ribosomal protein L5
    Polymer: 6 Type: protein Length: 181
    Chains: F
    Organism: Thermus thermophilus HB27
    Gene Names: rplE TT_C1316
    UniProtKB: Protein Feature View | Search PDB | Q72I16  
    Molecule: 50S ribosomal protein L6
    Polymer: 7 Type: protein Length: 159
    Chains: G
    Organism: Thermus thermophilus HB27
    Gene Names: rplF TT_C1313
    UniProtKB: Protein Feature View | Search PDB | Q72I19  
    Molecule: 50S ribosomal protein L9
    Polymer: 8 Type: protein Length: 145
    Chains: H
    Organism: Thermus thermophilus HB27
    Gene Names: rplI TT_C1743
    UniProtKB: Protein Feature View | Search PDB | Q72GV5  
    Molecule: 50S ribosomal protein L10
    Polymer: 9 Type: protein Length: 65
    Chains: I
    Organism: Thermus thermophilus HB27
    Gene Names: rplJ TT_C1777
    UniProtKB: Protein Feature View | Search PDB | Q72GS1  
    Molecule: 50S ribosomal protein L13
    Polymer: 10 Type: protein Length: 137
    Chains: J
    Organism: Thermus thermophilus HB27
    Gene Names: rplM TT_C1101
    UniProtKB: Protein Feature View | Search PDB | Q72IN1  
    Molecule: 50S ribosomal protein L14
    Polymer: 11 Type: protein Length: 122
    Chains: K
    Organism: Thermus thermophilus HB27
    Gene Names: rplN TT_C1318
    UniProtKB: Protein Feature View | Search PDB | Q72I14  
    Molecule: 50S ribosomal protein L15
    Polymer: 12 Type: protein Length: 146
    Chains: L
    Organism: Thermus thermophilus HB27
    Gene Names: rplO TT_C1309
    UniProtKB: Protein Feature View | Search PDB | Q72I23  
    Molecule: 50S ribosomal protein L16
    Polymer: 13 Type: protein Length: 136
    Chains: M
    Organism: Thermus thermophilus HB27
    Gene Names: rplP TT_C1321
    UniProtKB: Protein Feature View | Search PDB | Q72I11  
    Molecule: 50S ribosomal protein L17
    Polymer: 14 Type: protein Length: 117
    Chains: N
    Organism: Thermus thermophilus HB27
    Gene Names: rplQ TT_C1299
    UniProtKB: Protein Feature View | Search PDB | Q72I33  
    Molecule: 50S ribosomal protein L18
    Polymer: 15 Type: protein Length: 98
    Chains: O
    Organism: Thermus thermophilus HB27
    Gene Names: rplR TT_C1312
    UniProtKB: Protein Feature View | Search PDB | Q72I20  
    Molecule: 50S ribosomal protein L19
    Polymer: 16 Type: protein Length: 137
    Chains: P
    Organism: Thermus thermophilus HB27
    Gene Names: rplS TT_C0669
    UniProtKB: Protein Feature View | Search PDB | Q72JU9  
    Molecule: 50S ribosomal protein L20
    Polymer: 17 Type: protein Length: 116
    Chains: Q
    Organism: Thermus thermophilus HB27
    Gene Names: rplT TT_C0185
    UniProtKB: Protein Feature View | Search PDB | Q72L76  
    Molecule: 50S ribosomal protein L21
    Polymer: 18 Type: protein Length: 101
    Chains: R
    Organism: Thermus thermophilus HB27
    Gene Names: rplU TT_C1424
    UniProtKB: Protein Feature View | Search PDB | Q72HR2  
    Molecule: 50S ribosomal protein L22
    Polymer: 19 Type: protein Length: 112
    Chains: S
    Organism: Thermus thermophilus HB27
    Gene Names: rplV TT_C1323
    UniProtKB: Protein Feature View | Search PDB | Q72I09  
    Molecule: 50S ribosomal protein L23
    Polymer: 20 Type: protein Length: 92
    Chains: T
    Organism: Thermus thermophilus HB27
    Gene Names: rplW TT_C1326
    UniProtKB: Protein Feature View | Search PDB | Q72I06  
    Molecule: 50S ribosomal protein L24
    Polymer: 21 Type: protein Length: 100
    Chains: U
    Organism: Thermus thermophilus HB27
    Gene Names: rplX TT_C1317
    UniProtKB: Protein Feature View | Search PDB | Q72I15  
    Molecule: 50S ribosomal protein L25
    Polymer: 22 Type: protein Length: 188
    Chains: V
    Organism: Thermus thermophilus HB27
    Gene Names: rplY ctc TT_C1225
    UniProtKB: Protein Feature View | Search PDB | Q72IA7  
    Molecule: 50S ribosomal protein L27
    Polymer: 23 Type: protein Length: 76
    Chains: W
    Organism: Thermus thermophilus HB27
    Gene Names: rpmA TT_C1423
    UniProtKB: Protein Feature View | Search PDB | Q72HR3  
    Molecule: 50S ribosomal protein L28
    Polymer: 24 Type: protein Length: 88
    Chains: X
    Organism: Thermus thermophilus HB27
    Gene Names: rpmB TT_C1964
    UniProtKB: Protein Feature View | Search PDB | Q72G84  
    Molecule: 50S ribosomal protein L29
    Polymer: 25 Type: protein Length: 62
    Chains: Y
    Organism: Thermus thermophilus HB27
    Gene Names: rpmC TT_C1320
    UniProtKB: Protein Feature View | Search PDB | Q72I12  
    Molecule: 50S ribosomal protein L30
    Polymer: 26 Type: protein Length: 59
    Chains: Z
    Organism: Thermus thermophilus HB27
    Gene Names: rpmD TT_C1310
    UniProtKB: Protein Feature View | Search PDB | Q72I22  
    Molecule: 50S ribosomal protein L31
    Polymer: 27 Type: protein Length: 30
    Chains: 1
    Organism: Thermus thermophilus HB27
    Gene Names: rpmE TT_C0708
    UniProtKB: Protein Feature View | Search PDB | Q72JR0  
    Molecule: 50S ribosomal protein L32
    Polymer: 28 Type: protein Length: 52
    Chains: 2
    Organism: Thermus thermophilus HB27
    Gene Names: rpmF rpl32 TT_C0050
    UniProtKB: Protein Feature View | Search PDB | P62652  
    Molecule: 50S ribosomal protein L33
    Polymer: 29 Type: protein Length: 44
    Chains: 3
    Organism: Thermus thermophilus HB27
    Gene Names: rpmG TT_C1735
    UniProtKB: Protein Feature View | Search PDB | Q72GW3  
    Molecule: 50S ribosomal protein L34
    Polymer: 30 Type: protein Length: 48
    Chains: 4
    Organism: Thermus thermophilus HB27
    Gene Names: rpmH rpl34 TTHA0446
    UniProtKB: Protein Feature View | Search PDB | P80340  
    Molecule: 50S ribosomal protein L35
    Polymer: 31 Type: protein Length: 63
    Chains: 5
    Organism: Thermus thermophilus HB27
    Gene Names: rpmI TT_C0184
    UniProtKB: Protein Feature View | Search PDB | Q72L77  
     
  •   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: Thermus thermophilus   Taxonomy    
    Polymer: 23
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 24
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 25
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 26
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 27
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 28
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 29
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 30
    Scientific Name: Thermus thermophilus   Taxonomy    
    Polymer: 31
    Scientific Name: Thermus thermophilus   Taxonomy    
     
  •   Related PDB Entries Hide
    Identifier Details
    3PYN  30S subunit of 70S Ribosome 1 
    3PYO  50S subunit of 70S Ribosome 1 
    3PYQ  30S subunit of 70S Ribosome 2 
    3PYS  30S subunit of 70S Ribosome 1 
    3PYT  50S subunit of 70S Ribosome 1 
    3PYU  30S subunit of 70S Ribosome 2 
    3PYV  50S subunit of 70S Ribosome 2 
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    MG
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    MG Mg
    MAGNESIUM ION
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure: NA0929
     
 
Data in orange boxes are gathered from external resources (when available).
 
  Biological Assembly       
Composite of PDB entries (3PYN and 3PYO)