8RXH

CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME WITH A/P/E-site tRNA AND mRNA : PARENTAL STRAIN


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.93 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural and mechanistic insights into the function of Leishmania ribosome lacking a single pseudouridine modification.

Rajan, K.S.Aryal, S.Hiregange, D.G.Bashan, A.Madmoni, H.Olami, M.Doniger, T.Cohen-Chalamish, S.Pescher, P.Taoka, M.Nobe, Y.Fedorenko, A.Bose, T.Zimermann, E.Prina, E.Aharon-Hefetz, N.Pilpel, Y.Isobe, T.Unger, R.Spath, G.F.Yonath, A.Michaeli, S.

(2024) Cell Rep 43: 114203-114203

  • DOI: https://doi.org/10.1016/j.celrep.2024.114203
  • Primary Citation of Related Structures:  
    8A98, 8OVJ, 8RXH, 8RXX

  • PubMed Abstract: 

    Leishmania is the causative agent of cutaneous and visceral diseases affecting millions of individuals worldwide. Pseudouridine (Ψ), the most abundant modification on rRNA, changes during the parasite life cycle. Alterations in the level of a specific Ψ in helix 69 (H69) affected ribosome function. To decipher the molecular mechanism of this phenotype, we determine the structure of ribosomes lacking the single Ψ and its parental strain at ∼2.4-3 Å resolution using cryo-EM. Our findings demonstrate the significance of a single Ψ on H69 to its structure and the importance for its interactions with helix 44 and specific tRNAs. Our study suggests that rRNA modification affects translation of mRNAs carrying codon bias due to selective accommodation of tRNAs by the ribosome. Based on the high-resolution structures, we propose a mechanism explaining how the ribosome selects specific tRNAs.


  • Organizational Affiliation

    Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot 76100001, Israel; The Mina and Everard Goodman Faculty of Life Sciences and Advanced and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 52900, Israel.


Macromolecules

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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L2I [auth LA]260Leishmania major strain FriedlinMutation(s): 0 
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Find proteins for Q4FWX5 (Leishmania major)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosomal protein L3J [auth LB]419Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4Q2Q6 (Leishmania major)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosomal protein L1aK [auth LC]373Leishmania major strain FriedlinMutation(s): 0 
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Find proteins for E9ADW5 (Leishmania major)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11L [auth LD]188Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for P48157 (Leishmania major)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L9M [auth LE]190Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L6N [auth LF]195Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7aO [auth LG]264Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L13aP [auth LH]222Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L13Q [auth LI]220Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L23R [auth LJ]139Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein L14S [auth LK]175Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L27A/L29T [auth LL]145Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L15U [auth LM]204Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L10V [auth LN]213Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L5W [auth LO]305Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18X [auth LP]198Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L19Y [auth LQ]254Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18aZ [auth LR]179Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4Q5J4 (Leishmania major)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L21AA [auth LS]159Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L17BA [auth LT]166Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L22CA [auth LU]129Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L23aDA [auth LV]145Leishmania major strain FriedlinMutation(s): 0 
UniProt
Find proteins for Q4QJ20 (Leishmania major)
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L26EA [auth LW]143Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosomal protein L24FA [auth LX]124Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27GA [auth LY]134Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L28HA [auth LZ]147Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L35IA [auth La]127Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29JA [auth Lb]70Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L7KA [auth Lc]252Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30LA [auth Ld]104Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal subunit protein L31MA [auth Le]188Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32NA [auth Lf]133Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosomal protein l35aOA [auth Lg]144Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L34PA [auth Lh]168Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S Ribosomal protein L36QA [auth Li]105Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L37RA [auth Lj]83Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosomal protein L38SA [auth Lk]83Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L39TA [auth Ll]51Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-60S ribosomal protein L40UA [auth Lm]128Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41VA [auth Ln]34Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37aWA [auth Lo]92Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 60S ribosomal protein L44XA [auth Lp]106Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aDB [auth SA]264Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein SAEB [auth SB]246Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S3FB [auth SC]219Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S9GB [auth SD]190Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4HB [auth SE]273Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2IB [auth SF]265Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6JB [auth SG]249Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S5KB [auth SH]190Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7LB [auth SI]200Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S15AMB [auth SJ]130Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8NB [auth SK]220Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S16OB [auth SL]149Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosomal protein S20PB [auth SM]116Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S10QB [auth SN]168Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14RB [auth SO]144Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S23SB [auth SP]143Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12TB [auth SQ]141Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S18UB [auth SR]153Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ribosomal protein S29VB [auth SS]57Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S13WB [auth ST]151Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S17 family proteinXB [auth SU]173Leishmania major strain FriedlinMutation(s): 0 
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S17YB [auth SV]143Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S15ZB [auth SW]152Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19-like proteinAC [auth SX]161Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 80
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S21BC [auth SY]164Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 81
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24CC [auth SZ]137Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 82
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25DC [auth Sa]120Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 83
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26EC [auth Sb]112Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 84
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S27-1FC [auth Sc]86Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 85
MoleculeChains Sequence LengthOrganismDetailsImage
Putative 40S ribosomal protein S33GC [auth Sd]87Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 86
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30HC [auth Se]66Leishmania major strain FriedlinMutation(s): 0 
UniProt
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Entity ID: 87
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-60S ribosomal protein L40IC [auth Sf]152Leishmania major strain FriedlinMutation(s): 0 
UniProt
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