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Yeast 80S ribosome. This entry consists of the 60S subunit of the second 80S in the asymmetric unit.
DOI:10.2210/pdb3o5h/pdb   NDB ID: NA0744
3O5H
Split Entry
The asymmetric unit for this structure is composed of multiple PDB entries:
3O2Z   3O30   3O58   3O5H  
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The complete entry has been assigned PDB ID 4V7R 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/4v7r.cif.gz
ftp://ftp.wwpdb.org/pub/pdb/data/large_structures/XML/4v7r.xml.gz
 
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Ribosome
    Structure Weight: 1872096.21
    Molecule: 25S ribosomal RNA
    Polymer: 1 Type: rna Length: 3396
    Chains: 1
    Organism: Saccharomyces cerevisiae
    Molecule: 5S ribosomal RNA
    Polymer: 2 Type: rna Length: 121
    Chains: 2
    Organism: Saccharomyces cerevisiae
    Molecule: 5.8S ribosomal RNA
    Polymer: 3 Type: rna Length: 158
    Chains: 3
    Organism: Saccharomyces cerevisiae
    Molecule: 60S ribosomal protein L1
    Polymer: 4 Type: protein Length: 217
    Chains: A
    Organism: Saccharomyces cerevisiae
    Gene Names: RPL1A SSM1 SSM1A YPL220W
    UniProtKB: Protein Feature View | Search PDB | P0CX43  
    Molecule: 60S ribosomal protein L2
    Polymer: 5 Type: protein Length: 254
    Chains: B
    Organism: Saccharomyces cerevisiae
    Gene Names: RPL2A RPL5B YFR031C-A YFR031BC
    UniProtKB: Protein Feature View | Search PDB | P0CX45  
    Molecule: 60S ribosomal protein L3
    Polymer: 6 Type: protein Length: 387
    Chains: C
    Organism: Saccharomyces cerevisiae
    Gene Names: Gene View for RPL3 MAK8 TCM1 YOR063W YOR29-14
    UniProtKB: Protein Feature View | Search PDB | P14126  
    Molecule: 60S ribosomal protein L4-A
    Polymer: 7 Type: protein Length: 362
    Chains: D
    Organism: Saccharomyces cerevisiae
    Gene Names: RPL4A RPL2 RPL2A YBR031W YBR0315
    UniProtKB: Protein Feature View | Search PDB | P10664  
    Molecule: 60S ribosomal protein L5
    Polymer: 8 Type: protein Length: 297
    Chains: E
    Organism: Saccharomyces cerevisiae
    Gene Names: Gene View for RPL5 RPL1 RPL1A YPL131W LPI14W
    UniProtKB: Protein Feature View | Search PDB | P26321  
    Molecule: 60S ribosomal protein L6-A
    Polymer: 9 Type: protein Length: 176
    Chains: F
    Organism: Saccharomyces cerevisiae
    Gene Names: RPL6A RPL17A YL16A YML073C
    UniProtKB: Protein Feature View | Search PDB | Q02326  
    Molecule: 60S ribosomal protein L7-A
    Polymer: 10 Type: protein Length: 244
    Chains: G
    Organism: Saccharomyces cerevisiae
    Gene Names: Gene View for RPL7A RPL6A RPL8A YL8A YGL076C
    UniProtKB: Protein Feature View | Search PDB | P05737  
    Molecule: 60S ribosomal protein L8-A
    Polymer: 11 Type: protein Length: 256
    Chains: H
    Organism: Saccharomyces cerevisiae
    Gene Names: RPL8A MAK7 RPL4A YHL033C
    UniProtKB: Protein Feature View | Search PDB | P17076  
    Molecule: 60S ribosomal protein L9-A
    Polymer: 12 Type: protein Length: 191
    Chains: I
    Organism: Saccharomyces cerevisiae
    Gene Names: RPL9A RPL8A Gene View for RPL9 YGL147C
    UniProtKB: Protein Feature View | Search PDB | P05738  
    Molecule: 60S ribosomal protein L10
    Polymer: 13 Type: protein Length: 221
    Chains: J
    Organism: Saccharomyces cerevisiae
    Gene Names: Gene View for RPL10 GRC5 QSR1 YLR075W
    UniProtKB: Protein Feature View | Search PDB | P41805  
    Molecule: 60S ribosomal protein L11-A
    Polymer: 14 Type: protein Length: 174
    Chains: K
    Organism: Saccharomyces cerevisiae
    Gene Names: RPL11A RP39A RPL16A YPR102C P8283.14
    UniProtKB: Protein Feature View | Search PDB | P0C0W9  
    Molecule: 60S ribosomal protein L12
    Polymer: 15 Type: protein Length: 165
    Chains: L
    Organism: Saccharomyces cerevisiae
    Gene Names: RPL12A RPL15B YEL054C
    UniProtKB: Protein Feature View | Search PDB | P0CX53  
    Molecule: 60S acidic ribosomal protein P0
    Polymer: 16 Type: protein Length: 312
    Chains: M
    Organism: Saccharomyces cerevisiae
    Gene Names: RPP0 L10E RPA0 RPL10E RPLA0 YLR340W L8300.8
    UniProtKB: Protein Feature View | Search PDB | P05317  
    Molecule: 60S ribosomal protein L14-A
    Polymer: 17 Type: protein Length: 138
    Chains: N
    Organism: Saccharomyces cerevisiae
    Gene Names: RPL14A YKL006W YKL153
    UniProtKB: Protein Feature View | Search PDB | P36105  
    Molecule: 60S ribosomal protein L15-A
    Polymer: 18 Type: protein Length: 204
    Chains: O
    Organism: Saccharomyces cerevisiae
    Gene Names: RPL15A Gene View for RPL10A Gene View for RPL13A YL10A YLR029C
    UniProtKB: Protein Feature View | Search PDB | P05748  
    Molecule: 60S ribosomal protein L16-A
    Polymer: 19 Type: protein Length: 199
    Chains: P
    Organism: Saccharomyces cerevisiae
    Gene Names: RPL16A Gene View for RPL13 RPL21A YIL133C
    UniProtKB: Protein Feature View | Search PDB | P26784  
    Molecule: 60S ribosomal protein L17-A
    Polymer: 20 Type: protein Length: 184
    Chains: Q
    Organism: Saccharomyces cerevisiae
    Gene Names: RPL17A Gene View for RPL17 RPL20A YKL180W
    UniProtKB: Protein Feature View | Search PDB | P05740  
    Molecule: 60S ribosomal protein L18
    Polymer: 21 Type: protein Length: 186
    Chains: R
    Organism: Saccharomyces cerevisiae
    Gene Names: Gene View for RPL18A RP28A YOL120C
    UniProtKB: Protein Feature View | Search PDB | P0CX49  
    Molecule: 60S ribosomal protein L19
    Polymer: 22 Type: protein Length: 189
    Chains: S
    Organism: Saccharomyces cerevisiae
    Gene Names: RPL19A Gene View for RPL23A YL14A YBR084C-A YBR084BC
    UniProtKB: Protein Feature View | Search PDB | P0CX82  
    Molecule: 60S ribosomal protein L21-A
    Polymer: 23 Type: protein Length: 160
    Chains: T
    Organism: Saccharomyces cerevisiae
    Gene Names: RPL21A URP1 YBR191W YBR1401
    UniProtKB: Protein Feature View | Search PDB | Q02753  
    Molecule: 60S ribosomal protein L23
    Polymer: 24 Type: protein Length: 137
    Chains: U
    Organism: Saccharomyces cerevisiae
    Gene Names: Gene View for RPL23A RPL17A RPL17AA YBL087C YBL0713
    UniProtKB: Protein Feature View | Search PDB | P0CX41  
    Molecule: 60S ribosomal protein L24-A
    Polymer: 25 Type: protein Length: 155
    Chains: V
    Organism: Saccharomyces cerevisiae
    Gene Names: RPL24A RP29 RPL30A YGL031C
    UniProtKB: Protein Feature View | Search PDB | P04449  
    Molecule: 60S ribosomal protein L25
    Polymer: 26 Type: protein Length: 142
    Chains: W
    Organism: Saccharomyces cerevisiae
    Gene Names: RPL25 YOL127W
    UniProtKB: Protein Feature View | Search PDB | P04456  
    Molecule: 60S ribosomal protein L26-A
    Polymer: 27 Type: protein Length: 127
    Chains: X
    Organism: Saccharomyces cerevisiae
    Gene Names: RPL26A Gene View for RPL26 RPL33A YLR344W L8300.4
    UniProtKB: Protein Feature View | Search PDB | P05743  
    Molecule: 60S ribosomal protein L28
    Polymer: 28 Type: protein Length: 149
    Chains: Y
    Organism: Saccharomyces cerevisiae
    Gene Names: Gene View for RPL28 CYH2 YGL103W
    UniProtKB: Protein Feature View | Search PDB | P02406  
    Molecule: 60S ribosomal protein L30
    Polymer: 29 Type: protein Length: 105
    Chains: Z
    Organism: Saccharomyces cerevisiae
    Gene Names: Gene View for RPL30 Gene View for RPL32 YGL030W
    UniProtKB: Protein Feature View | Search PDB | P14120  
    Molecule: 60S ribosomal protein L31-A
    Polymer: 30 Type: protein Length: 113
    Chains: a
    Organism: Saccharomyces cerevisiae
    Gene Names: RPL31A Gene View for RPL34 RPL34A YDL075W D2478
    UniProtKB: Protein Feature View | Search PDB | P0C2H8  
    Molecule: 60S ribosomal protein L32
    Polymer: 31 Type: protein Length: 130
    Chains: b
    Organism: Saccharomyces cerevisiae
    Gene Names: Gene View for RPL32 YBL092W YBL0838
    UniProtKB: Protein Feature View | Search PDB | P38061  
    Molecule: 60S ribosomal protein L35
    Polymer: 32 Type: protein Length: 120
    Chains: c
    Organism: Saccharomyces cerevisiae
    Gene Names: RPL35B Gene View for SOS2 YDL136W D2170
    UniProtKB: Protein Feature View | Search PDB | P0CX85  
    Molecule: 60S ribosomal protein L37-A
    Polymer: 33 Type: protein Length: 88
    Chains: d
    Organism: Saccharomyces cerevisiae
    Gene Names: Gene View for RPL37A Gene View for RPL35A YLR185W L9470.6
    UniProtKB: Protein Feature View | Search PDB | P49166  
    Molecule: 60S ribosomal protein L39
    Polymer: 34 Type: protein Length: 51
    Chains: e
    Organism: Saccharomyces cerevisiae
    Gene Names: Gene View for RPL39 RPL46 SPB2 YJL189W J0360
    UniProtKB: Protein Feature View | Search PDB | P04650  
    Molecule: 60S ribosomal protein L42
    Polymer: 35 Type: protein Length: 106
    Chains: f
    Organism: Saccharomyces cerevisiae
    Gene Names: RPL42A RPL41A SCL41A YNL162W N1722
    UniProtKB: Protein Feature View | Search PDB | P0CX27  
    Molecule: 60S ribosomal protein L43
    Polymer: 36 Type: protein Length: 92
    Chains: g
    Organism: Saccharomyces cerevisiae
    Gene Names: RPL43A YPR043W YP9499.02
    UniProtKB: Protein Feature View | Search PDB | P0CX25  
    Molecule: Unassigned secondary structure
    Polymer: 37 Type: protein Length: 44
    Chains: h
    Organism: Saccharomyces cerevisiae
    Molecule: Unassigned secondary structure
    Polymer: 38 Type: protein Length: 12
    Chains: i
    Organism: Saccharomyces cerevisiae
    Molecule: Unassigned secondary structure
    Polymer: 39 Type: protein Length: 21
    Chains: j
    Organism: Saccharomyces cerevisiae
    Molecule: Unassigned secondary structure
    Polymer: 40 Type: protein Length: 16
    Chains: k
    Organism: Saccharomyces cerevisiae
     
  •   Structure Validation Hide

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  • MolProbity Ramachandran Plot
     

  •   Related Citations in PDB Entry (REMARK 1) Hide
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Yeast  
    Polymer: 2
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Yeast  
    Polymer: 3
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Yeast  
    Polymer: 4
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Yeast  
    Polymer: 5
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Yeast  
    Polymer: 6
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Yeast  
    Polymer: 7
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Yeast  
    Polymer: 8
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Yeast  
    Polymer: 9
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Yeast  
    Polymer: 10
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Yeast  
    Polymer: 11
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Yeast  
    Polymer: 12
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Yeast  
    Polymer: 13
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Yeast  
    Polymer: 14
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Yeast  
    Polymer: 15
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Yeast  
    Polymer: 16
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Yeast  
    Polymer: 17
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Yeast  
    Polymer: 18
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Yeast  
    Polymer: 19
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Yeast  
    Polymer: 20
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Yeast  
    Polymer: 21
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Yeast  
    Polymer: 22
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Yeast  
    Polymer: 23
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Yeast  
    Polymer: 24
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Yeast  
    Polymer: 25
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Yeast  
    Polymer: 26
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Yeast  
    Polymer: 27
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Yeast  
    Polymer: 28
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Yeast  
    Polymer: 29
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Yeast  
    Polymer: 30
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Yeast  
    Polymer: 31
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Yeast  
    Polymer: 32
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Yeast  
    Polymer: 33
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Yeast  
    Polymer: 34
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Yeast  
    Polymer: 35
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Yeast  
    Polymer: 36
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Yeast  
    Polymer: 37
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Yeast  
    Polymer: 38
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Yeast  
    Polymer: 39
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Yeast  
    Polymer: 40
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Yeast  
     
  •   Modified Residues Hide
    Identifier Formula Parent Type
    UNK
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    UNK C4 H9 N O2 lPeptideLinking
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure: NA0744
     
 
Data in orange boxes are gathered from external resources (when available).
 
  Biological Assembly       
Composite of PDB entries (3O2Z and 3O58)