4V6W

Structure of the D. melanogaster 80S ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structures of the human and Drosophila 80S ribosome.

Anger, A.M.Armache, J.P.Berninghausen, O.Habeck, M.Subklewe, M.Wilson, D.N.Beckmann, R.

(2013) Nature 497: 80-85

  • DOI: 10.1038/nature12104
  • Primary Citation of Related Structures:  
    4V6W, 4V6X

  • PubMed Abstract: 
  • Protein synthesis in all cells is carried out by macromolecular machines called ribosomes. Although the structures of prokaryotic, yeast and protist ribosomes have been determined, the more complex molecular architecture of metazoan 80S ribosomes has ...

    Protein synthesis in all cells is carried out by macromolecular machines called ribosomes. Although the structures of prokaryotic, yeast and protist ribosomes have been determined, the more complex molecular architecture of metazoan 80S ribosomes has so far remained elusive. Here we present structures of Drosophila melanogaster and Homo sapiens 80S ribosomes in complex with the translation factor eEF2, E-site transfer RNA and Stm1-like proteins, based on high-resolution cryo-electron-microscopy density maps. These structures not only illustrate the co-evolution of metazoan-specific ribosomal RNA with ribosomal proteins but also reveal the presence of two additional structural layers in metazoan ribosomes, a well-ordered inner layer covered by a flexible RNA outer layer. The human and Drosophila ribosome structures will provide the basis for more detailed structural, biochemical and genetic experiments.


    Organizational Affiliation

    Gene Center, Department of Biochemistry and Center for integrated Protein Science Munich, Ludwig-Maximilians-Universit√§t M√ľnchen, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Elongation factor 2Az844Drosophila melanogasterMutation(s): 0 
Gene Names: eEF2EF2Ef2bCG2238
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Entity ID: 2
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Guanine nucleotide-binding protein subunit beta-like proteinAg318Drosophila melanogasterMutation(s): 0 
Gene Names: Rack1CG7111
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Entity ID: 3
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40S ribosomal protein S20AU120Drosophila melanogasterMutation(s): 0 
Gene Names: RpS20CG15693
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S10aAK163Drosophila melanogasterMutation(s): 0 
Gene Names: RpS10aRpS10CG12275
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Entity ID: 5
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40S ribosomal protein S14AO151Drosophila melanogasterMutation(s): 0 
Gene Names: RpS14aCG1524
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Entity ID: 6
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40S ribosomal protein S23AX143Drosophila melanogasterMutation(s): 0 
Gene Names: RpS23CG8415
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S12AM139Drosophila melanogasterMutation(s): 0 
Gene Names: RpS12RpS12ECG11271
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Entity ID: 8
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40S ribosomal protein S18AS152Drosophila melanogasterMutation(s): 0 
Gene Names: RpS18CG8900
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Entity ID: 9
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40S ribosomal protein S29Ad56Drosophila melanogasterMutation(s): 0 
Gene Names: RpS29CG8495
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Entity ID: 10
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40S ribosomal protein S13AN151Drosophila melanogasterMutation(s): 0 
Gene Names: RpS13M(2)32ARp17CG13389
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Entity ID: 11
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40S ribosomal protein S11AL155Drosophila melanogasterMutation(s): 0 
Gene Names: RpS11CG8857
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Entity ID: 12
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40S ribosomal protein S17AR131Drosophila melanogasterMutation(s): 0 
Gene Names: RpS17M(3)67CCG3922
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Entity ID: 13
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40S ribosomal protein S15, isoform AAP148Drosophila melanogasterMutation(s): 0 
Gene Names: RpS15anon-EST:Posey137anon-EST:Posey185Dmel\CG8332S15s15CG8332Dmel_CG8332
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Entity ID: 14
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40S ribosomal protein S19aAT156Drosophila melanogasterMutation(s): 0 
Gene Names: RpS19aRpS19CG4464
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Entity ID: 15
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40S ribosomal protein S3aAB268Drosophila melanogasterMutation(s): 0 
Gene Names: RpS3AC3M(4)101CG2168
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Entity ID: 16
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40S ribosomal protein SAAA313Drosophila melanogasterMutation(s): 0 
Gene Names: staCG14792
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Entity ID: 17
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40S ribosomal protein S21AV83Drosophila melanogasterMutation(s): 0 
Gene Names: RpS21oho23BCG2986
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Entity ID: 18
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40S ribosomal protein S24AY131Drosophila melanogasterMutation(s): 0 
Gene Names: RpS24BcDNA:RE59324Dmel\CG3751l(2)SH2 2053l(2)SH2053Rp S24S24CG3751Dmel_CG3751
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Entity ID: 19
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40S ribosomal protein S25AZ117Drosophila melanogasterMutation(s): 0 
Gene Names: RpS25RpS31CG6684
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Entity ID: 20
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40S ribosomal protein S26Aa114Drosophila melanogasterMutation(s): 0 
Gene Names: RpS26CG10305
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Entity ID: 21
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40S ribosomal protein S27Ab84Drosophila melanogasterMutation(s): 0 
Gene Names: RpS27anon-EST:Posey295Dmel\CG10423Q9VBU9_DROMERp S27CG10423Dmel_CG10423
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Entity ID: 22
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40S ribosomal protein S28Ac65Drosophila melanogasterMutation(s): 0 
Gene Names: RpS28bCG2998
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Entity ID: 23
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40S ribosomal protein S3AD246Drosophila melanogasterMutation(s): 0 
Gene Names: RpS3M(3)95ACG6779
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Entity ID: 24
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40S ribosomal protein S30, isoform AAe132Drosophila melanogasterMutation(s): 0 
Gene Names: RpS30anon-EST:Posey127Dmel\CG15697Q9VDH8_DROMERps30RpS30aS30CG15697Dmel_CG15697
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Entity ID: 25
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40S ribosomal protein S27aAf80Drosophila melanogasterMutation(s): 0 
Gene Names: RpS27AUB3-DUBI-F80Ubi-mCG5271
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Entity ID: 26
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40S ribosomal protein S9AJ195Drosophila melanogasterMutation(s): 0 
Gene Names: RpS9CG3395
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Entity ID: 27
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40S ribosomal protein S4AE261Drosophila melanogasterMutation(s): 0 
Gene Names: RpS4RP4CG11276
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Entity ID: 28
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40S ribosomal protein S2AC267Drosophila melanogasterMutation(s): 0 
Gene Names: RpS2sopCG5920
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Entity ID: 29
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40S ribosomal protein S6AG248Drosophila melanogasterMutation(s): 0 
Gene Names: RpS6henl(1)air8CG10944
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Entity ID: 30
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40S ribosomal protein S5aAF228Drosophila melanogasterMutation(s): 0 
Gene Names: RpS5aM(1)15DRpS5CG8922
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Entity ID: 31
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40S ribosomal protein S7AH194Drosophila melanogasterMutation(s): 0 
Gene Names: RpS7CG1883
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Entity ID: 32
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40S ribosomal protein S15AaAW130Drosophila melanogasterMutation(s): 0 
Gene Names: RpS15AaRpS15ACG2033
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Entity ID: 33
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40S ribosomal protein S8AI208Drosophila melanogasterMutation(s): 0 
Gene Names: RpS8CG7808
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Entity ID: 34
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40S ribosomal protein S16AQ148Drosophila melanogasterMutation(s): 0 
Gene Names: RpS16CG4046
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Entity ID: 35
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Vig2, isoform BAh121Drosophila melanogasterMutation(s): 0 
Gene Names: vig2anon-WO0118547.290BcDNA:SD06613Dmel\CG11844vig-2Vig2CG11844Dmel_CG11844
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Entity ID: 38
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60S ribosomal protein L10a-2Cz218Drosophila melanogasterMutation(s): 0 
Gene Names: RpL10AbCG7283
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Entity ID: 39
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60S acidic ribosomal protein P0Cq223Drosophila melanogasterMutation(s): 0 
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Entity ID: 40
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60S ribosomal protein L12CK165Drosophila melanogasterMutation(s): 0 
Gene Names: RpL12anon-EST:Posey236Dmel\CG3195L12Q9W1B9_DROMERp L12RPL12Rpl12CG3195Dmel_CG3195
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Entity ID: 41
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60S ribosomal protein L13aCO205Drosophila melanogasterMutation(s): 0 
Gene Names: RpL13ACG1475
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Entity ID: 42
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60S ribosomal protein L13CL218Drosophila melanogasterMutation(s): 0 
Gene Names: RpL13bbc1CG4651
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Entity ID: 43
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60S ribosomal protein L23CV140Drosophila melanogasterMutation(s): 0 
Gene Names: RpL23RpL17ACG3661
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Entity ID: 44
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60S ribosomal protein L14CM166Drosophila melanogasterMutation(s): 0 
Gene Names: RpL14CG6253
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Entity ID: 45
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60S ribosomal protein L27aCa149Drosophila melanogasterMutation(s): 0 
Gene Names: RpL27ARpL27a2RpL27AaRpL27AbCG15442
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Entity ID: 46
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60S ribosomal protein L15CN204Drosophila melanogasterMutation(s): 0 
Gene Names: RpL15ZITICG17420
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Entity ID: 47
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60S ribosomal protein L10CI218Drosophila melanogasterMutation(s): 0 
Gene Names: RpL10QmCG17521
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Entity ID: 48
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60S ribosomal protein L5CD299Drosophila melanogasterMutation(s): 0 
Gene Names: RpL5yip6CG17489
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Entity ID: 49
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60S ribosomal protein L18CQ188Drosophila melanogasterMutation(s): 0 
Gene Names: RpL18CG8615
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Entity ID: 50
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60S ribosomal protein L19CR203Drosophila melanogasterMutation(s): 0 
Gene Names: RpL19M(2)60ECG2746
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Entity ID: 51
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60S ribosomal protein L8CA256Drosophila melanogasterMutation(s): 0 
Gene Names: RpL8CG1263
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Entity ID: 52
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60S ribosomal protein L18aCS177Drosophila melanogasterMutation(s): 0 
Gene Names: RpL18ACG6510
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Entity ID: 53
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60S ribosomal protein L21CT159Drosophila melanogasterMutation(s): 0 
Gene Names: RpL21anon-EST:Posey18anon-EST:Posey30BcDNA:RH06526Dmel\CG12775Rp L21RPL21CG12775Dmel_CG12775
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Entity ID: 54
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60S ribosomal protein L17CP186Drosophila melanogasterMutation(s): 0 
Gene Names: RpL17CG3203
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Entity ID: 55
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60S ribosomal protein L22CU299Drosophila melanogasterMutation(s): 0 
Gene Names: RpL22CG7434
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Entity ID: 56
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60S ribosomal protein L23ACX277Drosophila melanogasterMutation(s): 0 
Gene Names: 
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Entity ID: 57
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60S ribosomal protein L26CY149Drosophila melanogasterMutation(s): 0 
Gene Names: RpL26Dmel\CG6846L26lincRNA.S5499Rp L26RPL26CG6846Dmel_CG6846
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Entity ID: 58
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60S ribosomal protein L24CW155Drosophila melanogasterMutation(s): 0 
Gene Names: RpL24CG9282
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Entity ID: 59
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60S ribosomal protein L27CZ135Drosophila melanogasterMutation(s): 0 
Gene Names: RpL27chr3R:21510055..21510241Dmel\CG4759RPL27RpL27eCG4759Dmel_CG4759
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Entity ID: 60
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60S ribosomal protein L28Cr144Drosophila melanogasterMutation(s): 0 
Gene Names: RpL28CG12740
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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L35Ch123Drosophila melanogasterMutation(s): 0 
Gene Names: RpL35anon-EST:fe1C12anon-EST:Posey157BcDNA:RE09547Dmel\CG4111Rp L35RpL35-RBRpL35eCG4111Dmel_CG4111
Find proteins for Q9W499 (Drosophila melanogaster)
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Entity ID: 62
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L29Cb76Drosophila melanogasterMutation(s): 0 
Gene Names: RpL29RpL43CG10071
Find proteins for Q24154 (Drosophila melanogaster)
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Entity ID: 63
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L3CB416Drosophila melanogasterMutation(s): 0 
Gene Names: RpL3CG4863
Find proteins for O16797 (Drosophila melanogaster)
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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L7CF252Drosophila melanogasterMutation(s): 0 
Gene Names: RpL7CG4897
Find proteins for P32100 (Drosophila melanogaster)
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Entity ID: 65
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L30Cc111Drosophila melanogasterMutation(s): 0 
Gene Names: 
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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L31Cd124Drosophila melanogasterMutation(s): 0 
Gene Names: RpL31CG1821
Find proteins for Q9V597 (Drosophila melanogaster)
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Entity ID: 67
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60S ribosomal protein L32Ce134Drosophila melanogasterMutation(s): 0 
Gene Names: RpL32M(3)99Drp49CG7939
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Entity ID: 68
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L35ACf157Drosophila melanogasterMutation(s): 0 
Gene Names: RpL35Aanon-EST:Posey39Dmel\CG2099L35aRp L35ARpl35ACG2099Dmel_CG2099
Find proteins for Q9VNB9 (Drosophila melanogaster)
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Entity ID: 69
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L34aCg162Drosophila melanogasterMutation(s): 0 
Gene Names: RpL34aCG6090-RADmel\CG6090L34RpL34CG6090Dmel_CG6090
Find proteins for Q9VBH8 (Drosophila melanogaster)
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Entity ID: 70
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L36Ci115Drosophila melanogasterMutation(s): 0 
Gene Names: RpL36M(1)1BCG7622
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Entity ID: 71
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L37-ACj93Drosophila melanogasterMutation(s): 0 
Gene Names: RpL37aCG9091
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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L38Ck70Drosophila melanogasterMutation(s): 0 
Gene Names: RpL38CG18001
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Entity ID: 73
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L39Cl51Drosophila melanogasterMutation(s): 0 
Gene Names: RpL39rp46RpL46CG3997
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Entity ID: 74
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60S ribosomal protein L4CC401Drosophila melanogasterMutation(s): 0 
Gene Names: RpL4RpL1CG5502
Find proteins for P09180 (Drosophila melanogaster)
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Entity ID: 75
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L40Cm52Drosophila melanogasterMutation(s): 0 
Gene Names: RpL40Ubi-fUBI-F52CG2960
Find proteins for P18101 (Drosophila melanogaster)
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Entity ID: 76
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L41Cn25Drosophila melanogasterMutation(s): 0 
Gene Names: 
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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L37aCp92Drosophila melanogasterMutation(s): 0 
Gene Names: RpL37ACG5827
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Entity ID: 78
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L36ACo104Drosophila melanogasterMutation(s): 0 
Gene Names: RpL36Aanon-EST:fe1B2Dmel\CG7424CG7424Dmel_CG7424
Find proteins for Q9VLT7 (Drosophila melanogaster)
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Entity ID: 79
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L11CJ184Drosophila melanogasterMutation(s): 0 
Gene Names: RpL11RPL11ACG7726
Find proteins for P46222 (Drosophila melanogaster)
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Entity ID: 80
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L9CH190Drosophila melanogasterMutation(s): 0 
Gene Names: RpL9M(2)32DCG6141
Find proteins for P50882 (Drosophila melanogaster)
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Entity ID: 81
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L6, isoform ACE243Drosophila melanogasterMutation(s): 0 
Gene Names: RpL6Dmel\CG11522Rp L6RPL6rpl6CG11522Dmel_CG11522
Find proteins for Q9V9W2 (Drosophila melanogaster)
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Entity ID: 82
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L7aCG271Drosophila melanogasterMutation(s): 0 
Gene Names: RpL7ASURF-3CG3314
Find proteins for P46223 (Drosophila melanogaster)
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Entity ID: 36
MoleculeChainsLengthOrganismImage
18S ribosomal RNAB21995Drosophila melanogaster
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Entity ID: 37
MoleculeChainsLengthOrganismImage
E-tRNABC75Drosophila melanogaster
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Entity ID: 83
MoleculeChainsLengthOrganismImage
28S ribosomal RNAA53970Drosophila melanogaster
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Entity ID: 84
MoleculeChainsLengthOrganismImage
2S ribosomal RNAA930Drosophila melanogaster
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Entity ID: 85
MoleculeChainsLengthOrganismImage
5S ribosomal RNAA7120Drosophila melanogaster
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Entity ID: 86
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5.8S ribosomal RNAA8123Drosophila melanogaster
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other
  • Version 1.2: 2015-04-08
    Changes: Other
  • Version 1.3: 2018-07-18
    Changes: Data collection
  • Version 1.4: 2019-12-18
    Changes: Database references, Other