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-Universität München, 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: eEF2, EF2, Ef2b, CG2238
Find proteins for P13060 (Drosophila melanogaster)
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Entity ID: 2
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Guanine nucleotide-binding protein subunit beta-like proteinAg318Drosophila melanogasterMutation(s): 0 
Gene Names: Rack1, CG7111
Find proteins for O18640 (Drosophila melanogaster)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S20AU120Drosophila melanogasterMutation(s): 0 
Gene Names: RpS20, CG15693
Find proteins for P55828 (Drosophila melanogaster)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S10aAK163Drosophila melanogasterMutation(s): 0 
Gene Names: RpS10a, RpS10, CG12275
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Entity ID: 5
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40S ribosomal protein S14AO151Drosophila melanogasterMutation(s): 0 
Gene Names: RpS14a, CG1524
Find proteins for C0HKA0 (Drosophila melanogaster)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S23AX143Drosophila melanogasterMutation(s): 0 
Gene Names: RpS23, CG8415
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S12AM139Drosophila melanogasterMutation(s): 0 
Gene Names: RpS12, RpS12E, CG11271
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S18AS152Drosophila melanogasterMutation(s): 0 
Gene Names: RpS18, CG8900
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Entity ID: 9
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40S ribosomal protein S29Ad56Drosophila melanogasterMutation(s): 0 
Gene Names: RpS29, CG8495
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Entity ID: 10
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40S ribosomal protein S13AN151Drosophila 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 S11AL155Drosophila melanogasterMutation(s): 0 
Gene Names: RpS11, CG8857
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Entity ID: 12
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40S ribosomal protein S17AR131Drosophila 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 AAP148Drosophila 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 S19aAT156Drosophila melanogasterMutation(s): 0 
Gene Names: RpS19a, RpS19, CG4464
Find proteins for P39018 (Drosophila melanogaster)
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Entity ID: 15
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40S ribosomal protein S3aAB268Drosophila melanogasterMutation(s): 0 
Gene Names: RpS3A, C3, M(4)101, CG2168
Find proteins for P55830 (Drosophila melanogaster)
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Entity ID: 16
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40S ribosomal protein SAAA313Drosophila melanogasterMutation(s): 0 
Gene Names: sta, CG14792
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Entity ID: 17
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40S ribosomal protein S21AV83Drosophila melanogasterMutation(s): 0 
Gene Names: RpS21, oho23B, CG2986
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Entity ID: 18
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40S ribosomal protein S24AY131Drosophila 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 S25AZ117Drosophila melanogasterMutation(s): 0 
Gene Names: RpS25, RpS31, CG6684
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Entity ID: 20
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40S ribosomal protein S26Aa114Drosophila melanogasterMutation(s): 0 
Gene Names: RpS26, CG10305
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Entity ID: 21
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40S ribosomal protein S27Ab84Drosophila melanogasterMutation(s): 0 
Gene Names: RpS27, anon-EST:Posey295, Dmel\CG10423, Q9VBU9_DROME, Rp S27, CG10423, Dmel_CG10423
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Entity ID: 22
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40S ribosomal protein S28Ac65Drosophila melanogasterMutation(s): 0 
Gene Names: RpS28b, CG2998
Find proteins for Q9W334 (Drosophila melanogaster)
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Entity ID: 23
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40S ribosomal protein S3AD246Drosophila 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 AAe132Drosophila 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 S27aAf80Drosophila 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 S9AJ195Drosophila melanogasterMutation(s): 0 
Gene Names: RpS9, CG3395
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Entity ID: 27
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40S ribosomal protein S4AE261Drosophila melanogasterMutation(s): 0 
Gene Names: RpS4, RP4, CG11276
Find proteins for P41042 (Drosophila melanogaster)
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Entity ID: 28
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40S ribosomal protein S2AC267Drosophila melanogasterMutation(s): 0 
Gene Names: RpS2, sop, CG5920
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Entity ID: 29
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40S ribosomal protein S6AG248Drosophila melanogasterMutation(s): 0 
Gene Names: RpS6, hen, l(1)air8, CG10944
Find proteins for P29327 (Drosophila melanogaster)
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Entity ID: 30
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40S ribosomal protein S5aAF228Drosophila melanogasterMutation(s): 0 
Gene Names: RpS5a, M(1)15D, RpS5, CG8922
Find proteins for Q24186 (Drosophila melanogaster)
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Entity ID: 31
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40S ribosomal protein S7AH194Drosophila melanogasterMutation(s): 0 
Gene Names: RpS7, CG1883
Find proteins for Q9VA91 (Drosophila melanogaster)
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Entity ID: 32
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40S ribosomal protein S15AaAW130Drosophila melanogasterMutation(s): 0 
Gene Names: RpS15Aa, RpS15A, CG2033
Find proteins for P48149 (Drosophila melanogaster)
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Entity ID: 33
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40S ribosomal protein S8AI208Drosophila melanogasterMutation(s): 0 
Gene Names: RpS8, CG7808
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Entity ID: 34
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40S ribosomal protein S16AQ148Drosophila melanogasterMutation(s): 0 
Gene Names: RpS16, CG4046
Find proteins for Q9W237 (Drosophila melanogaster)
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Entity ID: 35
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Vig2, isoform BAh121Drosophila 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-2Cz218Drosophila melanogasterMutation(s): 0 
Gene Names: RpL10Ab, CG7283
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Entity ID: 39
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60S acidic ribosomal protein P0Cq223Drosophila melanogasterMutation(s): 0 
Find proteins for P05388 (Homo sapiens)
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PHAROS  P05388
GTEx  ENSG00000089157
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Entity ID: 40
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60S ribosomal protein L12CK165Drosophila 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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Entity ID: 41
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60S ribosomal protein L13aCO205Drosophila melanogasterMutation(s): 0 
Gene Names: RpL13A, CG1475
Find proteins for Q9VNE9 (Drosophila melanogaster)
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Entity ID: 42
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60S ribosomal protein L13CL218Drosophila melanogasterMutation(s): 0 
Gene Names: RpL13, bbc1, CG4651
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Entity ID: 43
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60S ribosomal protein L23CV140Drosophila melanogasterMutation(s): 0 
Gene Names: RpL23, RpL17A, CG3661
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Entity ID: 44
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60S ribosomal protein L14CM166Drosophila melanogasterMutation(s): 0 
Gene Names: RpL14, CG6253
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Entity ID: 45
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60S ribosomal protein L27aCa149Drosophila melanogasterMutation(s): 0 
Gene Names: RpL27A, RpL27a2, RpL27Aa, RpL27Ab, CG15442
Find proteins for P41092 (Drosophila melanogaster)
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Entity ID: 46
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60S ribosomal protein L15CN204Drosophila melanogasterMutation(s): 0 
Gene Names: RpL15, ZITI, CG17420
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Entity ID: 47
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60S ribosomal protein L10CI218Drosophila melanogasterMutation(s): 0 
Gene Names: RpL10, Qm, CG17521
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Entity ID: 48
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60S ribosomal protein L5CD299Drosophila melanogasterMutation(s): 0 
Gene Names: RpL5, yip6, CG17489
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Entity ID: 49
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60S ribosomal protein L18CQ188Drosophila melanogasterMutation(s): 0 
Gene Names: RpL18, CG8615
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Entity ID: 50
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60S ribosomal protein L19CR203Drosophila melanogasterMutation(s): 0 
Gene Names: RpL19, M(2)60E, CG2746
Find proteins for P36241 (Drosophila melanogaster)
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Entity ID: 51
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60S ribosomal protein L8CA256Drosophila melanogasterMutation(s): 0 
Gene Names: RpL8, CG1263
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Entity ID: 52
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60S ribosomal protein L18aCS177Drosophila melanogasterMutation(s): 0 
Gene Names: RpL18A, CG6510
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Entity ID: 53
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60S ribosomal protein L21CT159Drosophila melanogasterMutation(s): 0 
Gene Names: RpL21, anon-EST:Posey18, anon-EST:Posey30, BcDNA:RH06526, Dmel\CG12775, Rp L21, RPL21, CG12775, Dmel_CG12775
Find proteins for Q9V9M7 (Drosophila melanogaster)
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Entity ID: 54
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60S ribosomal protein L17CP186Drosophila melanogasterMutation(s): 0 
Gene Names: RpL17, CG3203
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Entity ID: 55
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60S ribosomal protein L22CU299Drosophila melanogasterMutation(s): 0 
Gene Names: RpL22, CG7434
Find proteins for P50887 (Drosophila melanogaster)
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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: RpL26, Dmel\CG6846, L26, lincRNA.S5499, Rp L26, RPL26, CG6846, Dmel_CG6846
Find proteins for Q9VVU2 (Drosophila melanogaster)
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Entity ID: 58
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60S ribosomal protein L24CW155Drosophila melanogasterMutation(s): 0 
Gene Names: RpL24, CG9282
Find proteins for Q9VJY6 (Drosophila melanogaster)
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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L27CZ135Drosophila melanogasterMutation(s): 0 
Gene Names: RpL27, chr3R:21510055..21510241, Dmel\CG4759, RPL27, RpL27e, CG4759, Dmel_CG4759
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Entity ID: 60
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60S ribosomal protein L28Cr144Drosophila melanogasterMutation(s): 0 
Gene Names: RpL28, CG12740
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Entity ID: 61
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60S ribosomal protein L35Ch123Drosophila melanogasterMutation(s): 0 
Gene Names: RpL35, anon-EST:fe1C12, anon-EST:Posey157, BcDNA:RE09547, Dmel\CG4111, Rp L35, RpL35-RB, RpL35e, CG4111, Dmel_CG4111
Find proteins for Q9W499 (Drosophila melanogaster)
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Entity ID: 62
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60S ribosomal protein L29Cb76Drosophila melanogasterMutation(s): 0 
Gene Names: RpL29, RpL43, CG10071
Find proteins for Q24154 (Drosophila melanogaster)
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Entity ID: 63
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60S ribosomal protein L3CB416Drosophila melanogasterMutation(s): 0 
Gene Names: RpL3, CG4863
Find proteins for O16797 (Drosophila melanogaster)
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Entity ID: 64
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60S ribosomal protein L7CF252Drosophila melanogasterMutation(s): 0 
Gene Names: RpL7, CG4897
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Entity ID: 65
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60S ribosomal protein L30Cc111Drosophila melanogasterMutation(s): 0 
Gene Names: 
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Entity ID: 66
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60S ribosomal protein L31Cd124Drosophila melanogasterMutation(s): 0 
Gene Names: RpL31, CG1821
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Entity ID: 67
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60S ribosomal protein L32Ce134Drosophila melanogasterMutation(s): 0 
Gene Names: RpL32, M(3)99D, rp49, CG7939
Find proteins for P04359 (Drosophila melanogaster)
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Entity ID: 68
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60S ribosomal protein L35ACf157Drosophila melanogasterMutation(s): 0 
Gene Names: RpL35A, anon-EST:Posey39, Dmel\CG2099, L35a, Rp L35A, Rpl35A, CG2099, Dmel_CG2099
Find proteins for Q9VNB9 (Drosophila melanogaster)
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Entity ID: 69
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60S ribosomal protein L34aCg162Drosophila melanogasterMutation(s): 0 
Gene Names: RpL34a, CG6090-RA, Dmel\CG6090, L34, RpL34, CG6090, Dmel_CG6090
Find proteins for Q9VBH8 (Drosophila melanogaster)
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Entity ID: 70
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60S ribosomal protein L36Ci115Drosophila melanogasterMutation(s): 0 
Gene Names: RpL36, M(1)1B, CG7622
Find proteins for P49630 (Drosophila melanogaster)
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Entity ID: 71
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60S ribosomal protein L37-ACj93Drosophila melanogasterMutation(s): 0 
Gene Names: RpL37a, CG9091
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Entity ID: 72
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60S ribosomal protein L38Ck70Drosophila melanogasterMutation(s): 0 
Gene Names: RpL38, CG18001
Find proteins for Q9W5N2 (Drosophila melanogaster)
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Entity ID: 73
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60S ribosomal protein L39Cl51Drosophila melanogasterMutation(s): 0 
Gene Names: RpL39, rp46, RpL46, CG3997
Find proteins for O16130 (Drosophila melanogaster)
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Entity ID: 74
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60S ribosomal protein L4CC401Drosophila melanogasterMutation(s): 0 
Gene Names: RpL4, RpL1, CG5502
Find proteins for P09180 (Drosophila melanogaster)
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Entity ID: 75
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60S ribosomal protein L40Cm52Drosophila melanogasterMutation(s): 0 
Gene Names: RpL40, Ubi-f, UBI-F52, CG2960
Find proteins for P18101 (Drosophila melanogaster)
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Entity ID: 76
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60S ribosomal protein L41Cn25Drosophila melanogasterMutation(s): 0 
Gene Names: 
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Entity ID: 77
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60S ribosomal protein L37aCp92Drosophila melanogasterMutation(s): 0 
Gene Names: RpL37A, CG5827
Find proteins for Q9VMU4 (Drosophila melanogaster)
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Entity ID: 78
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60S ribosomal protein L36ACo104Drosophila melanogasterMutation(s): 0 
Gene Names: RpL36A, anon-EST:fe1B2, Dmel\CG7424, CG7424, Dmel_CG7424
Find proteins for Q9VLT7 (Drosophila melanogaster)
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Entity ID: 79
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60S ribosomal protein L11CJ184Drosophila melanogasterMutation(s): 0 
Gene Names: RpL11, RPL11A, CG7726
Find proteins for P46222 (Drosophila melanogaster)
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Entity ID: 80
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60S ribosomal protein L9CH190Drosophila melanogasterMutation(s): 0 
Gene Names: RpL9, M(2)32D, CG6141
Find proteins for P50882 (Drosophila melanogaster)
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Entity ID: 81
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60S ribosomal protein L6, isoform ACE243Drosophila melanogasterMutation(s): 0 
Gene Names: RpL6, Dmel\CG11522, Rp L6, RPL6, rpl6, CG11522, Dmel_CG11522
Find proteins for Q9V9W2 (Drosophila melanogaster)
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Entity ID: 82
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60S ribosomal protein L7aCG271Drosophila melanogasterMutation(s): 0 
Gene Names: RpL7A, SURF-3, CG3314
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
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E-tRNABC75Drosophila melanogaster
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Entity ID: 83
MoleculeChainsLengthOrganismImage
28S ribosomal RNAA53970Drosophila melanogaster
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Entity ID: 84
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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


View more in-depth experimental data

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