4V6X

Structure of the human 80S ribosome

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.6 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: https://doi.org/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. 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
MoleculeChains Sequence LengthOrganismDetailsImage
Elongation factor 2A [auth Az]858Homo sapiensMutation(s): 0 
EC: 3.6.5
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GTEx:  ENSG00000167658 
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UniProt GroupP13639
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein subunit beta-2-like 1B [auth Ag]317Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000204628 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S20C [auth AU]119Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000008988 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S10D [auth AK]165Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000124614 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14E [auth AO]151Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000164587 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23F [auth AX]143Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000186468 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12G [auth AM]132Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112306 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18H [auth AS]152Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000231500 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S29I [auth Ad]56Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000213741 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13J [auth AN]151Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000110700 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11K [auth AL]158Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142534 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17L [auth AR]135Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182774 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15M [auth AP]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115268 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19N [auth AT]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105372 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aO [auth AB]264Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000145425 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein SAP [auth AA]295Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000168028 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21Q [auth AV]83Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171858 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24R [auth AY]133Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000138326 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25S [auth AZ]125Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000118181 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26T [auth Aa]115Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197728 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27U [auth Ab]84Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000177954 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28V [auth Ac]69Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000233927 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3W [auth AD]243Homo sapiensMutation(s): 0 
EC: 4.2.99.18
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GTEx:  ENSG00000149273 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30X [auth Ae]59Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000149806 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27aY [auth Af]80Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143947 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9Z [auth AJ]194Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000170889 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4, X isoformAA [auth AE]263Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198034 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2BA [auth AC]293Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000140988 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6CA [auth AG]249Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000137154 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S5DA [auth AF]204Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000083845 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7EA [auth AH]194Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171863 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15aFA [auth AW]130Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000134419 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8GA [auth AI]208Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142937 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16HA [auth AQ]146Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105193 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Plasminogen activator inhibitor 1 RNA-binding proteinIA [auth Ah]408Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142864 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10aLA [auth Cz]217Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198755 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
60S acidic ribosomal protein P0MA [auth Cq]317Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000089157 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L12NA [auth CK]165Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197958 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13aOA [auth CO]203Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142541 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13PA [auth CL]211Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000167526 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23QA [auth CV]140Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125691 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14RA [auth CM]215Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000188846 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27aSA [auth Ca]148Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000166441 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L15TA [auth CN]204Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174748 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10-likeUA [auth CI]214Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000165496 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5VA [auth CD]297Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000122406 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18WA [auth CQ]188Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000063177 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19XA [auth CR]196Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108298 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8YA [auth CA]257Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000161016 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18aZA [auth CS]176Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105640 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21AB [auth CT]160Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000122026 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17BB [auth CP]184Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000265681 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22CB [auth CU]128Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000116251 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23aDB [auth CX]156Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198242 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26EB [auth CY]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000161970 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L24FB [auth CW]157Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000114391 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27GB [auth CZ]136Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000131469 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28HB [auth Cr]137Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108107 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35IB [auth Ch]123Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000136942 
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29JB [auth Cb]159Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000162244 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3KB [auth CB]403Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100316 
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7LB [auth CF]248Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000147604 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30MB [auth Cc]115Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000156482 
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31NB [auth Cd]125Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000071082 
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32OB [auth Ce]135Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000144713 
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35aPB [auth Cf]110Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182899 
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34QB [auth Cg]117Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000109475 
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36RB [auth Ci]105Homo sapiensMutation(s): 0 
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Find proteins for Q9Y3U8 (Homo sapiens)
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GTEx:  ENSG00000130255 
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37SB [auth Cj]97Homo sapiensMutation(s): 0 
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Find proteins for P61927 (Homo sapiens)
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GTEx:  ENSG00000145592 
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38TB [auth Ck]70Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000172809 
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39UB [auth Cl]51Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198918 
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4VB [auth CC]427Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174444 
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L40WB [auth Cm]52Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000221983 
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41XB [auth Cn]25Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000229117 
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37aYB [auth Cp]92Homo sapiensMutation(s): 0 
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PHAROS:  P61513
GTEx:  ENSG00000197756 
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36aZB [auth Co]106Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000241343 
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11AC [auth CJ]178Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142676 
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Entity ID: 80
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9BC [auth CH]192Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163682 
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Entity ID: 81
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6CC [auth CE]288Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000089009 
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Entity ID: 82
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7aDC [auth CG]266Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000148303 
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Entity ID: 83
MoleculeChains Sequence LengthOrganismDetailsImage
60S acidic ribosomal protein P1EC [auth Cs],
FC [auth Ct]		114Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000137818 
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Entity ID: 84
MoleculeChains Sequence LengthOrganismDetailsImage
60S acidic ribosomal protein P2GC [auth Cu],
HC [auth Cv]		115Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000177600 
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Entity ID: 36
MoleculeChains LengthOrganismImage
18S ribosomal RNAJA [auth B2]1,869Homo sapiens
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Entity ID: 37
MoleculeChains LengthOrganismImage
E-tRNAKA [auth BC]75Homo sapiens
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Entity ID: 85
MoleculeChains LengthOrganismImage
28S ribosomal RNAIC [auth A5]5,070Homo sapiens
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Entity ID: 86
MoleculeChains LengthOrganismImage
5S ribosomal RNAJC [auth A7]121Homo sapiens
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Entity ID: 87
MoleculeChains LengthOrganismImage
5.8S ribosomal RNAKC [auth A8]157Homo sapiens
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONSPIDER

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
  • Version 1.5: 2023-02-01
    Changes: Database references
  • Version 1.6: 2024-11-06
    Changes: Data collection, Structure summary