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 so far remained elusive ...

    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-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Elongation factor 2A [auth Az]844Drosophila melanogasterMutation(s): 0 
Gene Names: eEF2, EF2, Ef2b, CG2238
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Entity ID: 2
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Guanine nucleotide-binding protein subunit beta-like proteinB [auth Ag]318Drosophila melanogasterMutation(s): 0 
Gene Names: Rack1, CG7111
UniProt
Find proteins for O18640 (Drosophila melanogaster)
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Entity ID: 3
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40S ribosomal protein S20C [auth AU]120Drosophila melanogasterMutation(s): 0 
Gene Names: RpS20, CG15693
UniProt
Find proteins for P55828 (Drosophila melanogaster)
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Entity ID: 4
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40S ribosomal protein S10aD [auth AK]163Drosophila melanogasterMutation(s): 0 
Gene Names: RpS10a, RpS10, CG12275
UniProt
Find proteins for Q9VB14 (Drosophila melanogaster)
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Entity ID: 5
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40S ribosomal protein S14E [auth AO]151Drosophila melanogasterMutation(s): 0 
Gene Names: RpS14a, CG1524
UniProt
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Entity ID: 6
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40S ribosomal protein S23F [auth AX]143Drosophila melanogasterMutation(s): 0 
Gene Names: RpS23, CG8415
UniProt
Find proteins for Q8T3U2 (Drosophila melanogaster)
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Entity ID: 7
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40S ribosomal protein S12G [auth AM]139Drosophila melanogasterMutation(s): 0 
Gene Names: RpS12, RpS12E, CG11271
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Entity ID: 8
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40S ribosomal protein S18H [auth AS]152Drosophila melanogasterMutation(s): 0 
Gene Names: RpS18, CG8900
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Find proteins for P41094 (Drosophila melanogaster)
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Entity ID: 9
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40S ribosomal protein S29I [auth Ad]56Drosophila melanogasterMutation(s): 0 
Gene Names: RpS29, CG8495
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Entity ID: 10
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40S ribosomal protein S13J [auth AN]151Drosophila melanogasterMutation(s): 0 
Gene Names: RpS13, M(2)32A, Rp17, CG13389
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Entity ID: 11
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40S ribosomal protein S11K [auth AL]155Drosophila melanogasterMutation(s): 0 
Gene Names: RpS11, CG8857
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Entity ID: 12
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40S ribosomal protein S17L [auth AR]131Drosophila melanogasterMutation(s): 0 
Gene Names: RpS17, M(3)67C, CG3922
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Entity ID: 13
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40S ribosomal protein S15, isoform AM [auth AP]148Drosophila melanogasterMutation(s): 0 
Gene Names: RpS15, anon-EST:Posey137, anon-EST:Posey185, Dmel\CG8332, S15, s15, CG8332, Dmel_CG8332
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Entity ID: 14
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40S ribosomal protein S19aN [auth AT]156Drosophila melanogasterMutation(s): 0 
Gene Names: RpS19a, RpS19, CG4464
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Entity ID: 15
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40S ribosomal protein S3aO [auth AB]268Drosophila melanogasterMutation(s): 0 
Gene Names: RpS3A, C3, M(4)101, CG2168
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Entity ID: 16
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40S ribosomal protein SAP [auth AA]313Drosophila melanogasterMutation(s): 0 
Gene Names: sta, CG14792
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Entity ID: 17
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40S ribosomal protein S21Q [auth AV]83Drosophila melanogasterMutation(s): 0 
Gene Names: RpS21, oho23B, CG2986
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Entity ID: 18
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40S ribosomal protein S24R [auth AY]131Drosophila melanogasterMutation(s): 0 
Gene Names: RpS24, BcDNA:RE59324, Dmel\CG3751, l(2)SH2 2053, l(2)SH2053, Rp S24, S24, CG3751, Dmel_CG3751
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Entity ID: 19
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40S ribosomal protein S25S [auth AZ]117Drosophila melanogasterMutation(s): 0 
Gene Names: RpS25, RpS31, CG6684
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Entity ID: 20
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40S ribosomal protein S26T [auth Aa]114Drosophila melanogasterMutation(s): 0 
Gene Names: RpS26, CG10305
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Entity ID: 21
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40S ribosomal protein S27U [auth Ab]84Drosophila melanogasterMutation(s): 0 
Gene Names: RpS27, anon-EST:Posey295, Dmel\CG10423, Q9VBU9_DROME, Rp S27, CG10423, Dmel_CG10423
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Find proteins for Q9VBU9 (Drosophila melanogaster)
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Entity ID: 22
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40S ribosomal protein S28V [auth Ac]65Drosophila melanogasterMutation(s): 0 
Gene Names: RpS28b, CG2998
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Entity ID: 23
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40S ribosomal protein S3W [auth AD]246Drosophila melanogasterMutation(s): 0 
Gene Names: RpS3, M(3)95A, CG6779
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Entity ID: 24
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40S ribosomal protein S30, isoform AX [auth Ae]132Drosophila melanogasterMutation(s): 0 
Gene Names: RpS30, anon-EST:Posey127, Dmel\CG15697, Q9VDH8_DROME, Rps30, RpS30a, S30, CG15697, Dmel_CG15697
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Entity ID: 25
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40S ribosomal protein S27aY [auth Af]80Drosophila melanogasterMutation(s): 0 
Gene Names: RpS27A, UB3-D, UBI-F80, Ubi-m, CG5271
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Entity ID: 26
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40S ribosomal protein S9Z [auth AJ]195Drosophila melanogasterMutation(s): 0 
Gene Names: RpS9, CG3395
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40S ribosomal protein S4AA [auth AE]261Drosophila melanogasterMutation(s): 0 
Gene Names: RpS4, RP4, CG11276
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Entity ID: 28
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40S ribosomal protein S2BA [auth AC]267Drosophila melanogasterMutation(s): 0 
Gene Names: RpS2, sop, CG5920
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Entity ID: 29
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40S ribosomal protein S6CA [auth AG]248Drosophila melanogasterMutation(s): 0 
Gene Names: RpS6, hen, l(1)air8, CG10944
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Entity ID: 30
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40S ribosomal protein S5aDA [auth AF]228Drosophila melanogasterMutation(s): 0 
Gene Names: RpS5a, M(1)15D, RpS5, CG8922
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40S ribosomal protein S7EA [auth AH]194Drosophila melanogasterMutation(s): 0 
Gene Names: RpS7, CG1883
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Entity ID: 32
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40S ribosomal protein S15AaFA [auth AW]130Drosophila melanogasterMutation(s): 0 
Gene Names: RpS15Aa, RpS15A, CG2033
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40S ribosomal protein S8GA [auth AI]208Drosophila melanogasterMutation(s): 0 
Gene Names: RpS8, CG7808
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40S ribosomal protein S16HA [auth AQ]148Drosophila melanogasterMutation(s): 0 
Gene Names: RpS16, CG4046
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Vig2, isoform BIA [auth Ah]121Drosophila melanogasterMutation(s): 0 
Gene Names: vig2, anon-WO0118547.290, BcDNA:SD06613, Dmel\CG11844, vig-2, Vig2, CG11844, Dmel_CG11844
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Entity ID: 38
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60S ribosomal protein L10a-2LA [auth Cz]218Drosophila melanogasterMutation(s): 0 
Gene Names: RpL10Ab, CG7283
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Entity ID: 39
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60S acidic ribosomal protein P0MA [auth Cq]223Drosophila melanogasterMutation(s): 0 
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GTEx:  ENSG00000089157
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Entity ID: 40
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60S ribosomal protein L12NA [auth CK]165Drosophila melanogasterMutation(s): 0 
Gene Names: RpL12, anon-EST:Posey236, Dmel\CG3195, L12, Q9W1B9_DROME, Rp L12, RPL12, Rpl12, CG3195, Dmel_CG3195
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60S ribosomal protein L13aOA [auth CO]205Drosophila melanogasterMutation(s): 0 
Gene Names: RpL13A, CG1475
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60S ribosomal protein L13PA [auth CL]218Drosophila melanogasterMutation(s): 0 
Gene Names: RpL13, bbc1, CG4651
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60S ribosomal protein L23QA [auth CV]140Drosophila melanogasterMutation(s): 0 
Gene Names: RpL23, RpL17A, CG3661
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60S ribosomal protein L14RA [auth CM]166Drosophila melanogasterMutation(s): 0 
Gene Names: RpL14, CG6253
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Entity ID: 45
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60S ribosomal protein L27aSA [auth Ca]149Drosophila melanogasterMutation(s): 0 
Gene Names: RpL27A, RpL27a2, RpL27Aa, RpL27Ab, CG15442
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Entity ID: 46
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60S ribosomal protein L15TA [auth CN]204Drosophila melanogasterMutation(s): 0 
Gene Names: RpL15, ZITI, CG17420
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60S ribosomal protein L10UA [auth CI]218Drosophila melanogasterMutation(s): 0 
Gene Names: RpL10, Qm, CG17521
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Entity ID: 48
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60S ribosomal protein L5VA [auth CD]299Drosophila melanogasterMutation(s): 0 
Gene Names: RpL5, yip6, CG17489
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Entity ID: 49
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60S ribosomal protein L18WA [auth CQ]188Drosophila melanogasterMutation(s): 0 
Gene Names: RpL18, CG8615
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Entity ID: 50
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60S ribosomal protein L19XA [auth CR]203Drosophila melanogasterMutation(s): 0 
Gene Names: RpL19, M(2)60E, CG2746
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Entity ID: 51
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60S ribosomal protein L8YA [auth CA]256Drosophila melanogasterMutation(s): 0 
Gene Names: RpL8, CG1263
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Entity ID: 52
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60S ribosomal protein L18aZA [auth CS]177Drosophila melanogasterMutation(s): 0 
Gene Names: RpL18A, CG6510
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Entity ID: 53
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60S ribosomal protein L21AB [auth CT]159Drosophila melanogasterMutation(s): 0 
Gene Names: RpL21, anon-EST:Posey18, anon-EST:Posey30, BcDNA:RH06526, Dmel\CG12775, Rp L21, RPL21, CG12775, Dmel_CG12775
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Entity ID: 54
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60S ribosomal protein L17BB [auth CP]186Drosophila melanogasterMutation(s): 0 
Gene Names: RpL17, CG3203
UniProt
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L22CB [auth CU]299Drosophila melanogasterMutation(s): 0 
Gene Names: RpL22, CG7434
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Entity ID: 56
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60S ribosomal protein L23ADB [auth CX]277Drosophila melanogasterMutation(s): 0 
Gene Names: 
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L26EB [auth CY]149Drosophila melanogasterMutation(s): 0 
Gene Names: RpL26, Dmel\CG6846, L26, lincRNA.S5499, Rp L26, RPL26, CG6846, Dmel_CG6846
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L24FB [auth CW]155Drosophila melanogasterMutation(s): 0 
Gene Names: RpL24, CG9282
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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L27GB [auth CZ]135Drosophila melanogasterMutation(s): 0 
Gene Names: RpL27, chr3R:21510055..21510241, Dmel\CG4759, RPL27, RpL27e, CG4759, Dmel_CG4759
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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L28HB [auth Cr]144Drosophila melanogasterMutation(s): 0 
Gene Names: RpL28, CG12740
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Entity ID: 61
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60S ribosomal protein L35IB [auth Ch]123Drosophila melanogasterMutation(s): 0 
Gene Names: RpL35, anon-EST:fe1C12, anon-EST:Posey157, BcDNA:RE09547, Dmel\CG4111, Rp L35, RpL35-RB, RpL35e, CG4111, Dmel_CG4111
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Entity ID: 62
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60S ribosomal protein L29JB [auth Cb]76Drosophila melanogasterMutation(s): 0 
Gene Names: RpL29, RpL43, CG10071
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Entity ID: 63
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60S ribosomal protein L3KB [auth CB]416Drosophila melanogasterMutation(s): 0 
Gene Names: RpL3, CG4863
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Entity ID: 64
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60S ribosomal protein L7LB [auth CF]252Drosophila melanogasterMutation(s): 0 
Gene Names: RpL7, CG4897
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Entity ID: 65
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60S ribosomal protein L30MB [auth Cc]111Drosophila melanogasterMutation(s): 0 
Gene Names: 
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Entity ID: 66
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60S ribosomal protein L31NB [auth Cd]124Drosophila melanogasterMutation(s): 0 
Gene Names: RpL31, CG1821
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Entity ID: 67
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60S ribosomal protein L32OB [auth Ce]134Drosophila melanogasterMutation(s): 0 
Gene Names: RpL32, M(3)99D, rp49, CG7939
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Entity ID: 68
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60S ribosomal protein L35APB [auth Cf]157Drosophila melanogasterMutation(s): 0 
Gene Names: RpL35A, anon-EST:Posey39, Dmel\CG2099, L35a, Rp L35A, Rpl35A, CG2099, Dmel_CG2099
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Entity ID: 69
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60S ribosomal protein L34aQB [auth Cg]162Drosophila melanogasterMutation(s): 0 
Gene Names: RpL34a, CG6090-RA, Dmel\CG6090, L34, RpL34, CG6090, Dmel_CG6090
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Entity ID: 70
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60S ribosomal protein L36RB [auth Ci]115Drosophila melanogasterMutation(s): 0 
Gene Names: RpL36, M(1)1B, CG7622
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Entity ID: 71
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60S ribosomal protein L37-ASB [auth Cj]93Drosophila melanogasterMutation(s): 0 
Gene Names: RpL37a, CG9091
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Entity ID: 72
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60S ribosomal protein L38TB [auth Ck]70Drosophila melanogasterMutation(s): 0 
Gene Names: RpL38, CG18001
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Entity ID: 73
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60S ribosomal protein L39UB [auth Cl]51Drosophila melanogasterMutation(s): 0 
Gene Names: RpL39, rp46, RpL46, CG3997
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Entity ID: 74
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60S ribosomal protein L4VB [auth CC]401Drosophila melanogasterMutation(s): 0 
Gene Names: RpL4, RpL1, CG5502
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Entity ID: 75
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60S ribosomal protein L40WB [auth Cm]52Drosophila melanogasterMutation(s): 0 
Gene Names: RpL40, Ubi-f, UBI-F52, CG2960
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Entity ID: 76
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60S ribosomal protein L41XB [auth Cn]25Drosophila melanogasterMutation(s): 0 
Gene Names: 
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Entity ID: 77
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60S ribosomal protein L37aYB [auth Cp]92Drosophila melanogasterMutation(s): 0 
Gene Names: RpL37A, CG5827
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Entity ID: 78
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60S ribosomal protein L36AZB [auth Co]104Drosophila melanogasterMutation(s): 0 
Gene Names: RpL36A, anon-EST:fe1B2, Dmel\CG7424, CG7424, Dmel_CG7424
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Entity ID: 79
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60S ribosomal protein L11AC [auth CJ]184Drosophila melanogasterMutation(s): 0 
Gene Names: RpL11, RPL11A, CG7726
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Entity ID: 80
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60S ribosomal protein L9BC [auth CH]190Drosophila melanogasterMutation(s): 0 
Gene Names: RpL9, M(2)32D, CG6141
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Entity ID: 81
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60S ribosomal protein L6, isoform ACC [auth CE]243Drosophila melanogasterMutation(s): 0 
Gene Names: RpL6, Dmel\CG11522, Rp L6, RPL6, rpl6, CG11522, Dmel_CG11522
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Entity ID: 82
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60S ribosomal protein L7aDC [auth CG]271Drosophila melanogasterMutation(s): 0 
Gene Names: RpL7A, SURF-3, CG3314
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Entity ID: 36
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18S ribosomal RNAJA [auth B2]1995Drosophila melanogaster
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Entity ID: 37
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E-tRNAKA [auth BC]75Drosophila melanogaster
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Entity ID: 83
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28S ribosomal RNAEC [auth A5]3970Drosophila melanogaster
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Entity ID: 84
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2S ribosomal RNAFC [auth A9]30Drosophila melanogaster
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Entity ID: 85
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5S ribosomal RNAGC [auth A7]120Drosophila melanogaster
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Entity ID: 86
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5.8S ribosomal RNAHC [auth A8]123Drosophila melanogaster
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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



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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