6QZP

High-resolution cryo-EM structure of the human 80S ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 3.0 of the entry. See complete history


Literature

Visualization of chemical modifications in the human 80S ribosome structure.

Natchiar, S.K.Myasnikov, A.G.Kratzat, H.Hazemann, I.Klaholz, B.P.

(2017) Nature 551: 472-477

  • DOI: 10.1038/nature24482
  • Primary Citation of Related Structures:  
    6QZP

  • PubMed Abstract: 
  • Chemical modifications of human ribosomal RNA (rRNA) are introduced during biogenesis and have been implicated in the dysregulation of protein synthesis, as is found in cancer and other diseases. However, their role in this phenomenon is unknown. Here we visualize more than 130 individual rRNA modifications in the three-dimensional structure of the human ribosome, explaining their structural and functional roles ...

    Chemical modifications of human ribosomal RNA (rRNA) are introduced during biogenesis and have been implicated in the dysregulation of protein synthesis, as is found in cancer and other diseases. However, their role in this phenomenon is unknown. Here we visualize more than 130 individual rRNA modifications in the three-dimensional structure of the human ribosome, explaining their structural and functional roles. In addition to a small number of universally conserved sites, we identify many eukaryote- or human-specific modifications and unique sites that form an extended shell in comparison to bacterial ribosomes, and which stabilize the RNA. Several of the modifications are associated with the binding sites of three ribosome-targeting antibiotics, or are associated with degenerate states in cancer, such as keto alkylations on nucleotide bases reminiscent of specialized ribosomes. This high-resolution structure of the human 80S ribosome paves the way towards understanding the role of epigenetic rRNA modifications in human diseases and suggests new possibilities for designing selective inhibitors and therapeutic drugs.


    Organizational Affiliation

    Université de Strasbourg, Illkirch, France.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L8D [auth LA]248Homo sapiensMutation(s): 0 
Gene Names: RPL8
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Entity ID: 5
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60S ribosomal protein L3E [auth LB]402Homo sapiensMutation(s): 0 
Gene Names: RPL3OK/SW-cl.32
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Entity ID: 6
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60S ribosomal protein L4F [auth LC]368Homo sapiensMutation(s): 0 
Gene Names: RPL4RPL1
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Entity ID: 7
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60S ribosomal protein L5G [auth LD]293Homo sapiensMutation(s): 0 
Gene Names: RPL5MSTP030
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Entity ID: 8
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60S ribosomal protein L6H [auth LE]236Homo sapiensMutation(s): 0 
Gene Names: RPL6TXREB1
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Entity ID: 9
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60S ribosomal protein L7I [auth LF]225Homo sapiensMutation(s): 0 
Gene Names: RPL7
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60S ribosomal protein L7aJ [auth LG]241Homo sapiensMutation(s): 0 
Gene Names: RPL7ASURF-3SURF3
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Entity ID: 11
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60S ribosomal protein L9K [auth LH]190Homo sapiensMutation(s): 0 
Gene Names: RPL9OK/SW-cl.103RPL9P7RPL9P8RPL9P9
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60S ribosomal protein L10-likeL [auth LI]213Homo sapiensMutation(s): 0 
Gene Names: RPL10L
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60S ribosomal protein L11M [auth LJ]176Homo sapiensMutation(s): 0 
Gene Names: RPL11
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60S ribosomal protein L13N [auth LL]210Homo sapiensMutation(s): 0 
Gene Names: RPL13BBC1OK/SW-cl.46
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60S ribosomal protein L14O [auth LM]139Homo sapiensMutation(s): 0 
Gene Names: RPL14
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Entity ID: 16
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60S ribosomal protein L15P [auth LN]203Homo sapiensMutation(s): 0 
Gene Names: RPL15EC45TCBAP0781
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Entity ID: 17
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60S ribosomal protein L13aQ [auth LO]201Homo sapiensMutation(s): 0 
Gene Names: RPL13A
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60S ribosomal protein L17R [auth LP]153Homo sapiensMutation(s): 0 
Gene Names: RPL17
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60S ribosomal protein L18S [auth LQ]187Homo sapiensMutation(s): 0 
Gene Names: RPL18
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60S ribosomal protein L19T [auth LR]187Homo sapiensMutation(s): 0 
Gene Names: RPL19
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Entity ID: 21
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60S ribosomal protein L18aU [auth LS]175Homo sapiensMutation(s): 0 
Gene Names: RPL18A
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60S ribosomal protein L21V [auth LT]159Homo sapiensMutation(s): 0 
Gene Names: RPL21
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Entity ID: 23
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60S ribosomal protein L22W [auth LU]101Homo sapiensMutation(s): 0 
Gene Names: RPL22
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Entity ID: 24
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60S ribosomal protein L23X [auth LV]131Homo sapiensMutation(s): 0 
Gene Names: RPL23
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Entity ID: 25
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60S ribosomal protein L24Y [auth LW]124Homo sapiensMutation(s): 0 
Gene Names: RPL24
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Entity ID: 26
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60S ribosomal protein L23aZ [auth LX]120Homo sapiensMutation(s): 0 
Gene Names: RPL23A
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Entity ID: 27
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60S ribosomal protein L26AA [auth LY]134Homo sapiensMutation(s): 0 
Gene Names: RPL26
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Entity ID: 28
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60S ribosomal protein L27BA [auth LZ]135Homo sapiensMutation(s): 0 
Gene Names: RPL27
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Entity ID: 29
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60S ribosomal protein L27aCA [auth La]147Homo sapiensMutation(s): 0 
Gene Names: RPL27A
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Entity ID: 30
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60S ribosomal protein L29DA [auth Lb]109Homo sapiensMutation(s): 0 
Gene Names: RPL29
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Entity ID: 31
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60S ribosomal protein L30EA [auth Lc]98Homo sapiensMutation(s): 0 
Gene Names: RPL30
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Entity ID: 32
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60S ribosomal protein L31FA [auth Ld]107Homo sapiensMutation(s): 0 
Gene Names: RPL31
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Entity ID: 33
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60S ribosomal protein L32GA [auth Le]128Homo sapiensMutation(s): 0 
Gene Names: RPL32PP9932
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Entity ID: 34
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60S ribosomal protein L35aHA [auth Lf]109Homo sapiensMutation(s): 0 
Gene Names: RPL35AGIG33
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60S ribosomal protein L34IA [auth Lg]114Homo sapiensMutation(s): 0 
Gene Names: RPL34
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60S ribosomal protein L35JA [auth Lh]122Homo sapiensMutation(s): 0 
Gene Names: RPL35
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60S ribosomal protein L36KA [auth Li]102Homo sapiensMutation(s): 0 
Gene Names: RPL36
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60S ribosomal protein L37LA [auth Lj]86Homo sapiensMutation(s): 0 
Gene Names: RPL37
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60S ribosomal protein L38MA [auth Lk]69Homo sapiensMutation(s): 0 
Gene Names: RPL38
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Entity ID: 40
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60S ribosomal protein L39NA [auth Ll]50Homo sapiensMutation(s): 0 
Gene Names: RPL39
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Entity ID: 41
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Ubiquitin-60S ribosomal protein L40OA [auth Lm]52Homo sapiensMutation(s): 0 
Gene Names: UBA52UBCEP2
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60S ribosomal protein L41PA [auth Ln]24Homo sapiensMutation(s): 0 
Gene Names: RPL41
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60S ribosomal protein L36aQA [auth Lo]105Homo sapiensMutation(s): 0 
Gene Names: RPL36ARPL44GIG15MIG6
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60S ribosomal protein L37aRA [auth Lp]91Homo sapiensMutation(s): 0 
Gene Names: RPL37A
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60S ribosomal protein L28SA [auth Lr]125Homo sapiensMutation(s): 0 
Gene Names: RPL28
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60S ribosomal protein L10aTA [auth Lz]217Homo sapiensMutation(s): 0 
Gene Names: RPL10ANEDD6
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Entity ID: 49
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40S ribosomal protein SAWA [auth SA]221Homo sapiensMutation(s): 0 
Gene Names: RPSALAMBRLAMR1
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40S ribosomal protein S3aXA [auth SB]214Homo sapiensMutation(s): 0 
Gene Names: RPS3AFTE1MFTL
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Entity ID: 51
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40S ribosomal protein S3YA [auth SD]227Homo sapiensMutation(s): 0 
Gene Names: RPS3OK/SW-cl.26
EC: 4.2.99.18
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Entity ID: 52
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40S ribosomal protein S4, X isoformZA [auth SE]262Homo sapiensMutation(s): 0 
Gene Names: RPS4XCCG2RPS4SCAR
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Entity ID: 53
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40S ribosomal protein S5AB [auth SF]189Homo sapiensMutation(s): 0 
Gene Names: RPS5
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Entity ID: 54
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40S ribosomal protein S7BB [auth SH]186Homo sapiensMutation(s): 0 
Gene Names: RPS7
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Entity ID: 55
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40S ribosomal protein S8CB [auth SI]206Homo sapiensMutation(s): 0 
Gene Names: RPS8OK/SW-cl.83
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Entity ID: 56
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40S ribosomal protein S10DB [auth SK]98Homo sapiensMutation(s): 0 
Gene Names: RPS10
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Entity ID: 57
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40S ribosomal protein S11EB [auth SL]153Homo sapiensMutation(s): 0 
Gene Names: RPS11
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S15FB [auth SP]127Homo sapiensMutation(s): 0 
Gene Names: RPS15RIG
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Entity ID: 59
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40S ribosomal protein S16GB [auth SQ]141Homo sapiensMutation(s): 0 
Gene Names: RPS16
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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S17HB [auth SR]135Homo sapiensMutation(s): 0 
Gene Names: RPS17RPS17L
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Entity ID: 61
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40S ribosomal protein S18IB [auth SS]145Homo sapiensMutation(s): 0 
Gene Names: RPS18D6S218E
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Entity ID: 62
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40S ribosomal protein S19JB [auth ST]143Homo sapiensMutation(s): 0 
Gene Names: RPS19
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Entity ID: 63
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40S ribosomal protein S20KB [auth SU]103Homo sapiensMutation(s): 0 
Gene Names: RPS20
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Entity ID: 64
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40S ribosomal protein S21LB [auth SV]83Homo sapiensMutation(s): 0 
Gene Names: RPS21
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Entity ID: 65
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40S ribosomal protein S23MB [auth SX]141Homo sapiensMutation(s): 0 
Gene Names: RPS23
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Entity ID: 66
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40S ribosomal protein S26NB [auth Sa]102Homo sapiensMutation(s): 0 
Gene Names: RPS26
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Entity ID: 67
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40S ribosomal protein S28OB [auth Sc]64Homo sapiensMutation(s): 0 
Gene Names: RPS28
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Entity ID: 68
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40S ribosomal protein S29PB [auth Sd]55Homo sapiensMutation(s): 0 
Gene Names: RPS29
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Entity ID: 69
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Receptor of activated protein C kinase 1QB [auth Sg]313Homo sapiensMutation(s): 0 
Gene Names: RACK1GNB2L1HLC7PIG21
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Entity ID: 70
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40S ribosomal protein S2RB [auth SC]222Homo sapiensMutation(s): 0 
Gene Names: RPS2RPS4
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Entity ID: 71
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S6SB [auth SG]237Homo sapiensMutation(s): 0 
Gene Names: RPS6OK/SW-cl.2
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Entity ID: 72
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40S ribosomal protein S9TB [auth SJ]185Homo sapiensMutation(s): 0 
Gene Names: RPS9
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Entity ID: 73
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40S ribosomal protein S12UB [auth SM]122Homo sapiensMutation(s): 0 
Gene Names: RPS12
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Entity ID: 74
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40S ribosomal protein S13VB [auth SN]150Homo sapiensMutation(s): 0 
Gene Names: RPS13
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Entity ID: 75
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40S ribosomal protein S14WB [auth SO]140Homo sapiensMutation(s): 0 
Gene Names: RPS14PRO2640
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Entity ID: 76
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40S ribosomal protein S15aXB [auth SW]129Homo sapiensMutation(s): 0 
Gene Names: RPS15AOK/SW-cl.82
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Entity ID: 77
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40S ribosomal protein S24YB [auth SY]131Homo sapiensMutation(s): 0 
Gene Names: RPS24
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Entity ID: 78
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40S ribosomal protein S25ZB [auth SZ]75Homo sapiensMutation(s): 0 
Gene Names: RPS25
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Entity ID: 79
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40S ribosomal protein S27AC [auth Sb]83Homo sapiensMutation(s): 0 
Gene Names: RPS27MPS1
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Entity ID: 80
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40S ribosomal protein S30BC [auth Se]58Homo sapiensMutation(s): 0 
Gene Names: FAU
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Entity ID: 81
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Ubiquitin-40S ribosomal protein S27aCC [auth Sf]67Homo sapiensMutation(s): 0 
Gene Names: RPS27AUBA80UBCEP1
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Entity ID: 1
MoleculeChainsLengthOrganismImage
28S rRNA (3773-MER)A [auth L5]3773Homo sapiens
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Entity ID: 2
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5S rRNA (120-MER)B [auth L7]120Homo sapiens
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Entity ID: 3
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5.8S rRNA (156-MER)C [auth L8]156Homo sapiens
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Entity ID: 47
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18S rRNA (1740-MER)UA [auth S2]1740Homo sapiens
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Entity ID: 48
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E site tRNA (75-MER)VA [auth S6]75Homo sapiens
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Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HMT (Subject of Investigation/LOI)
Query on HMT

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QM [auth L5](3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine
C29 H39 N O9
HYFHYPWGAURHIV-JFIAXGOJSA-N
 Ligand Interaction
HYG (Subject of Investigation/LOI)
Query on HYG

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CT [auth S2]HYGROMYCIN B
C20 H37 N3 O13
GRRNUXAQVGOGFE-WRWUMOMGSA-N
 Ligand Interaction
ZN
Query on ZN

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GT [auth Sa], HT [auth Sd], IT [auth Sf], PN [auth Lg], QN [auth Lj], RN [auth Lm], SN [auth Lo], TN [auth Lp]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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