Structure of a mammalian Ribosomal 60S subunit within an 80S complex obtained by docking homology models of the RNA and proteins into an 8.7 A cryo-EM map
2ZKR
Split Entry
The asymmetric unit for this structure is composed of multiple PDB entries:
2ZKQ    2ZKR   
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The complete entry has been assigned PDB ID 4V5Z 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/4v5z.cif.gz
ftp://ftp.wwpdb.org/pub/pdb/data/large_structures/XML/4v5z.xml.gz
 
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Ribosomal Protein/rna
    Structure Weight: 2016187.63
    Molecule: 5.8S Ribosomal RNA
    Polymer: 1 Type: rna Length: 123
    Chains: 1
    Organism: Canis lupus familiaris
    Molecule: 28S Ribosomal RNA
    Polymer: 2 Type: rna Length: 2903
    Chains: 0
    Organism: Canis lupus familiaris
    Molecule: RNA Expansion segment ES3
    Polymer: 3 Type: rna Length: 21
    Chains: A
    Details: Expansion segment in 5.8S
    Organism: Canis lupus familiaris
    Molecule: RNA Expansion segment ES4
    Polymer: 4 Type: rna Length: 27
    Chains: B
    Details: Expansion segment at the 3' end of 5.8S and 5' end of 28S
    Organism: Canis lupus familiaris
    Molecule: RNA Expansion segment ES5
    Polymer: 5 Type: rna Length: 17
    Chains: C
    Organism: Canis lupus familiaris
    Molecule: RNA Expansion segment ES7 part I
    Polymer: 6 Type: rna Length: 16
    Chains: D
    Organism: Canis lupus familiaris
    Molecule: RNA Expansion segment ES7 part II
    Polymer: 7 Type: rna Length: 54
    Chains: E
    Organism: Canis lupus familiaris
    Molecule: RNA Expansion segment ES7 part III
    Polymer: 8 Type: rna Length: 120
    Chains: F
    Organism: Canis lupus familiaris
    Molecule: RNA Expansion segment ES9
    Polymer: 9 Type: rna Length: 48
    Chains: G
    Organism: Canis lupus familiaris
    Molecule: RNA Expansion segment ES12
    Polymer: 10 Type: rna Length: 25
    Chains: H
    Organism: Canis lupus familiaris
    Molecule: RNA Expansion segment ES15 part I
    Polymer: 11 Type: rna Length: 72
    Chains: I
    Organism: Canis lupus familiaris
    Molecule: RNA Expansion segment ES15 part II
    Polymer: 12 Type: rna Length: 30
    Chains: J
    Organism: Canis lupus familiaris
    Molecule: RNA Expansion segment ES19
    Polymer: 13 Type: rna Length: 26
    Chains: K
    Organism: Canis lupus familiaris
    Molecule: RNA Expansion segment ES20
    Polymer: 14 Type: rna Length: 20
    Chains: L
    Organism: Canis lupus familiaris
    Molecule: RNA Expansion segment ES24
    Polymer: 15 Type: rna Length: 19
    Chains: M
    Organism: Canis lupus familiaris
    Molecule: RNA Expansion segment ES27
    Polymer: 16 Type: rna Length: 78
    Chains: N
    Organism: Canis lupus familiaris
    Molecule: RNA Expansion segment ES30
    Polymer: 17 Type: rna Length: 20
    Chains: O
    Organism: Canis lupus familiaris
    Molecule: RNA Expansion segment ES31 part I
    Polymer: 18 Type: rna Length: 15
    Chains: P
    Organism: Canis lupus familiaris
    Molecule: RNA Expansion segment ES31 part II
    Polymer: 19 Type: rna Length: 30
    Chains: Q
    Organism: Canis lupus familiaris
    Molecule: RNA Expansion segment ES39 part I
    Polymer: 20 Type: rna Length: 30
    Chains: R
    Organism: Canis lupus familiaris
    Molecule: RNA Expansion segment ES39 part II
    Polymer: 21 Type: rna Length: 38
    Chains: S
    Organism: Canis lupus familiaris
    Molecule: RNA Expansion segment ES39 part III
    Polymer: 22 Type: rna Length: 30
    Chains: T
    Organism: Canis lupus familiaris
    Molecule: RNA Expansion segment ES41
    Polymer: 23 Type: rna Length: 16
    Chains: U
    Organism: Canis lupus familiaris
    Molecule: RNA Expansion segment ES9 part2
    Polymer: 24 Type: rna Length: 22
    Chains: V
    Organism: Canis lupus familiaris
    Molecule: RNA Expansion segment ES10
    Polymer: 25 Type: rna Length: 16
    Chains: W
    Organism: Canis lupus familiaris
    Molecule: RNA helices
    Polymer: 26 Type: rna Length: 113
    Chains: X
    Organism: Canis lupus familiaris
    Molecule: 5S Ribosomal RNA
    Polymer: 27 Type: rna Length: 115
    Chains: Y
    Organism: Canis lupus familiaris
    Molecule: E site t-RNA
    Polymer: 28 Type: rna Length: 72
    Chains: Z
    Organism: Canis lupus familiaris
    Molecule: 60S Ribosomal protein L8
    Polymer: 29 Type: protein Length: 257
    Chains: a
    Organism: Canis lupus familiaris
    Gene Name: Gene View for RPL8
    UniProtKB: Protein Feature View | Search PDB | E2RIA8  
    Molecule: 60S Ribosomal protein L3
    Polymer: 30 Type: protein Length: 403
    Chains: b
    Organism: Canis lupus familiaris
    Gene Name: Gene View for RPL3
    UniProtKB: Protein Feature View | Search PDB | J9P6X5  
    Molecule: 60S Ribosomal protein L4
    Polymer: 31 Type: protein Length: 421
    Chains: c
    Organism: Canis lupus familiaris
    Gene Names: Gene View for RPL4 RPL1
    UniProtKB: Protein Feature View | Search PDB | Q28346  
    Molecule: 60S Ribosomal protein L11
    Polymer: 32 Type: protein Length: 178
    Chains: d
    Organism: Canis lupus familiaris
    Gene Name: Gene View for RPL11
    UniProtKB: Protein Feature View | Search PDB | E2R9G7  
    Molecule: 60S Ribosomal protein L9
    Polymer: 33 Type: protein Length: 192
    Chains: e
    Organism: Canis lupus familiaris
    Gene Name: Gene View for RPL9
    UniProtKB: Protein Feature View | Search PDB | E2R149  
    Molecule: 60S Ribosomal protein L7a
    Polymer: 34 Type: protein Length: 266
    Chains: f
    Organism: Canis lupus familiaris
    Gene Name: Gene View for RPL7A
    UniProtKB: Protein Feature View | Search PDB | F2Z4P2  
    Molecule: 60S acidic ribosomal protein P0
    Polymer: 35 Type: protein Length: 317
    Chains: g
    Organism: Canis lupus familiaris
    Gene Name: Gene View for RPLP0
    UniProtKB: Protein Feature View | Search PDB | F1PUX4  
    Molecule: 60S Ribosomal protein L10
    Polymer: 36 Type: protein Length: 214
    Chains: h
    Organism: Canis lupus familiaris
    Gene Name: Gene View for RPL10L
    UniProtKB: Protein Feature View | Search PDB | J9PBD3  
    Molecule: 60S Ribosomal protein L12
    Polymer: 37 Type: protein Length: 165
    Chains: i
    Organism: Canis lupus familiaris
    Gene Name: Gene View for RPL12
    UniProtKB: Protein Feature View | Search PDB | E2RR58  
    Molecule: 60S ribosomal protein L13a
    Polymer: 38 Type: protein Length: 203
    Chains: j
    Organism: Canis lupus familiaris
    Gene Name: Gene View for RPL13A
    UniProtKB: Protein Feature View | Search PDB | Q9XSU0  
    Molecule: 60S Ribosomal protein L23
    Polymer: 39 Type: protein Length: 140
    Chains: k
    Organism: Canis lupus familiaris
    Gene Name: Gene View for RPL23
    UniProtKB: Protein Feature View | Search PDB | F2Z4P3  
    Molecule: 60S Ribosomal protein L27a
    Polymer: 40 Type: protein Length: 148
    Chains: l
    Organism: Canis lupus familiaris
    Gene Name: LOC100688656
    UniProtKB: Protein Feature View | Search PDB | E2RI34  
    Molecule: 60S Ribosomal protein L15e
    Polymer: 41 Type: protein Length: 204
    Chains: m
    Organism: Canis lupus familiaris
    Gene Name: Gene View for RPL15
    UniProtKB: Protein Feature View | Search PDB | E2QXF3  
    Molecule: 60S Ribosomal protein L5
    Polymer: 42 Type: protein Length: 297
    Chains: n
    Organism: Canis lupus familiaris
    Gene Name: Gene View for RPL5
    UniProtKB: Protein Feature View | Search PDB | F1P7B0  
    Molecule: 60S Ribosomal protein L18
    Polymer: 43 Type: protein Length: 188
    Chains: o
    Organism: Canis lupus familiaris
    Gene Name: Gene View for RPL18
    UniProtKB: Protein Feature View | Search PDB | D0VWQ3  
    Molecule: 60S Ribosomal protein L19
    Polymer: 44 Type: protein Length: 196
    Chains: p
    Organism: Canis lupus familiaris
    Gene Name: Gene View for RPL19
    UniProtKB: Protein Feature View | Search PDB | D0VWQ5  
    Molecule: 60S Ribosomal protein L19
    Polymer: 45 Type: protein Length: 13
    Chains: 7
    Details: C-terminal extension
    Organism: Canis lupus familiaris
    Gene Name: Gene View for RPL19
    UniProtKB: Protein Feature View | Search PDB | D0VWQ5  
    Molecule: 60S Ribosomal protein L21
    Polymer: 46 Type: protein Length: 160
    Chains: q
    Organism: Canis lupus familiaris
    Gene Name: LOC607788
    UniProtKB: Protein Feature View | Search PDB | F1PWM2  
    Molecule: 60S Ribosomal protein L17
    Polymer: 47 Type: protein Length: 184
    Chains: r
    Organism: Canis lupus familiaris
    Gene Name: LOC100855554
    UniProtKB: Protein Feature View | Search PDB | E2R3D3  
    Molecule: 60S Ribosomal protein L23a
    Polymer: 48 Type: protein Length: 156
    Chains: s
    Organism: Canis lupus familiaris
    Gene Name: LOC610129
    UniProtKB: Protein Feature View | Search PDB | E2QZG2  
    Molecule: 60S Ribosomal protein L26
    Polymer: 49 Type: protein Length: 145
    Chains: t
    Organism: Canis lupus familiaris
    Gene Name: LOC608703
    UniProtKB: Protein Feature View | Search PDB | E2QUE7  
    Molecule: 60S Ribosomal protein L24
    Polymer: 50 Type: protein Length: 157
    Chains: u
    Organism: Canis lupus familiaris
    Gene Name: Gene View for RPL24
    UniProtKB: Protein Feature View | Search PDB | F1PGD7  
    Molecule: 60S Ribosomal protein L35
    Polymer: 51 Type: protein Length: 123
    Chains: v
    Organism: Canis lupus familiaris
    Gene Name: Gene View for RPL35
    UniProtKB: Protein Feature View | Search PDB | E2RPE5  
    Molecule: 60S Ribosomal protein L35
    Polymer: 52 Type: protein Length: 10
    Chains: 8
    Details: C-terminal extension
    Organism: Canis lupus familiaris
    Gene Name: Gene View for RPL35
    UniProtKB: Protein Feature View | Search PDB | E2RPE5  
    Molecule: 60S Ribosomal protein L7
    Polymer: 53 Type: protein Length: 270
    Chains: w
    Organism: Canis lupus familiaris
    Gene Name: Gene View for RPL7
    UniProtKB: Protein Feature View | Search PDB | F1Q0Z2  
    Molecule: 60S Ribosomal protein L31
    Polymer: 54 Type: protein Length: 125
    Chains: x
    Organism: Canis lupus familiaris
    Gene Names: LOC100855789 Gene View for RPL31
    UniProtKB: Protein Feature View | Search PDB | E2R8G3  
    Molecule: 60S Ribosomal protein L32
    Polymer: 55 Type: protein Length: 135
    Chains: y
    Organism: Canis lupus familiaris
    Gene Name: Gene View for RPL32
    UniProtKB: Protein Feature View | Search PDB | E2RKA8  
    Molecule: 60S Ribosomal protein L32
    Polymer: 56 Type: protein Length: 58
    Chains: 9
    Details: C-terminal extension
    Organism: Canis lupus familiaris
    Gene Name: Gene View for RPL32
    UniProtKB: Protein Feature View | Search PDB | E2RKA8  
    Molecule: 60S Ribosomal protein L37a
    Polymer: 57 Type: protein Length: 92
    Chains: z
    Organism: Canis lupus familiaris
    Gene Name: Gene View for RPL37A
    UniProtKB: Protein Feature View | Search PDB | J9NVE6  
    Molecule: 60S Ribosomal protein L37e
    Polymer: 58 Type: protein Length: 97
    Chains: 2
    Organism: Canis lupus familiaris
    Gene Name: LOC100855714
    UniProtKB: Protein Feature View | Search PDB | E2RR77  
    Molecule: 60S Ribosomal protein L39e
    Polymer: 59 Type: protein Length: 51
    Chains: 3
    Organism: Canis lupus familiaris
    Gene Name: LOC100855964
    UniProtKB: Protein Feature View | Search PDB | J9NZS7  
    Molecule: 60S Ribosomal protein L44e
    Polymer: 60 Type: protein Length: 106
    Chains: 4
    Organism: Canis lupus familiaris
    Gene Names: Rpl36a Rpl44
    UniProtKB: Protein Feature View | Search PDB | D0VWQ4  
    Molecule: 60S Ribosomal protein L10a
    Polymer: 61 Type: protein Length: 212
    Chains: 5
    Organism: Canis lupus familiaris
    UniProtKB: Protein Feature View | Search PDB | D0VWQ6  
    Molecule: 60S Ribosomal protein L30e
    Polymer: 62 Type: protein Length: 115
    Chains: 6
    Organism: Canis lupus familiaris
    Gene Name: Gene View for RPL30
    UniProtKB: Protein Feature View | Search PDB | J9NU88  
     

  • MolProbity Ramachandran Plot
     

  •   Related Citations in PDB Entry (REMARK 1) Hide
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 2
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 3
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 4
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 5
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 6
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 7
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 8
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 9
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 10
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 11
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 12
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 13
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 14
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 15
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 16
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 17
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 18
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 19
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 20
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 21
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 22
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 23
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 24
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 25
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 26
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 27
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 28
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 29
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 30
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 31
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 32
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 33
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 34
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 35
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 36
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 37
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 38
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 39
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 40
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 41
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 42
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 43
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 44
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 45
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 46
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 47
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 48
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 49
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 50
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 51
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 52
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 53
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 54
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 55
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 56
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 57
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 58
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 59
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 60
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 61
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
    Polymer: 62
    Scientific Name: Canis familiaris   Taxonomy   Common Name: Dog  
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
 
Data in orange boxes are gathered from external resources (when available).
  Biological Assembly       
Composite of PDB entries (2ZKQ and 2ZKR)
 
 
 
  •   MyPDB Personal Annotations Hide
     
  •   Deposition Summary Hide
    Authors:   Chandramouli, P.,  Akey, C.W.

    Deposition:   2008-03-27
    Release:   2008-05-06
    Last Modified (REVDAT):   2014-04-23
     
  •   Revision History    Hide
    Mouse over text for details
    2014-04-23
    Data collection
    2012-05-30
    Source and taxonomy
    2011-07-13
    Version format compliance
     
  •   Experimental Details Hide
    Method:   ELECTRON MICROSCOPY
    Exp. Data:


    EM Resolution [Å]: 8.7
    Aggregation State: PARTICLE
    Symmetry Type: ASYMMETRIC Reconstruction Method: SINGLE PARTICLE
    Specimen Type: VITREOUS ICE (CRYO EM)