4V8M

High-resolution cryo-electron microscopy structure of the Trypanosoma brucei ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.57 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 3.3 of the entry. See complete history


Literature

High-Resolution Cryo-Electron Microscopy Structure of the Trypanosoma Brucei Ribosome.

Hashem, Y.Des Georges, A.Fu, J.Buss, S.N.Jossinet, F.Jobe, A.Zhang, Q.Liao, H.Y.Grassucci, R.A.Bajaj, C.Westhof, E.Madison-Antenucci, S.Frank, J.

(2013) Nature 494: 385

  • DOI: https://doi.org/10.1038/nature11872
  • Primary Citation of Related Structures:  
    4V8M

  • PubMed Abstract: 

    Ribosomes, the protein factories of living cells, translate genetic information carried by messenger RNAs into proteins, and are thus involved in virtually all aspects of cellular development and maintenance. The few available structures of the eukaryotic ribosome reveal that it is more complex than its prokaryotic counterpart, owing mainly to the presence of eukaryote-specific ribosomal proteins and additional ribosomal RNA insertions, called expansion segments. The structures also differ among species, partly in the size and arrangement of these expansion segments. Such differences are extreme in kinetoplastids, unicellular eukaryotic parasites often infectious to humans. Here we present a high-resolution cryo-electron microscopy structure of the ribosome of Trypanosoma brucei, the parasite that is transmitted by the tsetse fly and that causes African sleeping sickness. The atomic model reveals the unique features of this ribosome, characterized mainly by the presence of unusually large expansion segments and ribosomal-protein extensions leading to the formation of four additional inter-subunit bridges. We also find additional rRNA insertions, including one large rRNA domain that is not found in other eukaryotes. Furthermore, the structure reveals the five cleavage sites of the kinetoplastid large ribosomal subunit (LSU) rRNA chain, which is known to be cleaved uniquely into six pieces, and suggests that the cleavage is important for the maintenance of the T. brucei ribosome in the observed structure. We discuss several possible implications of the large rRNA expansion segments for the translation-regulation process. The structure could serve as a basis for future experiments aimed at understanding the functional importance of these kinetoplastid-specific ribosomal features in protein-translation regulation, an essential step towards finding effective and safe kinetoplastid-specific drugs.


  • Organizational Affiliation

    Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN S3A, PUTATIVEA [auth A0]256Trypanosoma brucei brucei TREU927Mutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN S4, PUTATIVEB [auth A1]273Trypanosoma brucei brucei TREU927Mutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN S5, PUTATIVEC [auth A2]190Trypanosoma brucei brucei TREU927Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN S6D [auth A3]250Trypanosoma brucei brucei TREU927Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S7, PUTATIVEE [auth A4]202Trypanosoma brucei brucei TREU927Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN S8F [auth A5]220Trypanosoma brucei brucei TREU927Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN S9, PUTATIVEG [auth A6]190Trypanosoma brucei brucei TREU927Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
GUANINE NUCLEOTIDE-BINDING PROTEIN BETA SUBUNIT-LIKE PROTEINH [auth A7]318Trypanosoma brucei brucei TREU927Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S29, PUTATIVEI [auth A8]57Trypanosoma brucei brucei TREU927Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
UBIQUITIN/RIBOSOMAL PROTEIN S27A, PUTATIVEJ [auth A9]153Trypanosoma brucei brucei TREU927Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN SA, PUTATIVEK [auth AC]277Trypanosoma brucei brucei TREU927Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN S10, PUTATIVEL [auth AD]172Trypanosoma brucei brucei TREU927Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEINS S11, PUTATIVEM [auth AE]174Trypanosoma brucei brucei TREU927Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN S12N [auth AF]144Trypanosoma brucei brucei TREU927Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN S13, PUTATIVEO [auth AG]151Trypanosoma brucei brucei TREU927Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN S14P [auth AH]144Trypanosoma brucei brucei TREU927Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN S15, PUTATIVEQ [auth AI]152Trypanosoma brucei brucei TREU927Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN S15A, PUTATIVER [auth AJ]130Trypanosoma brucei brucei TREU927Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN S16, PUTATIVES [auth AK]149Trypanosoma brucei brucei TREU927Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN S17, PUTATIVET [auth AL]142Trypanosoma brucei brucei TREU927Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN S18, PUTATIVEU [auth AM]153Trypanosoma brucei brucei TREU927Mutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S19, PUTATIVEV [auth AO]167Trypanosoma brucei brucei TREU927Mutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN S2, PUTATIVEW [auth AP]266Trypanosoma brucei brucei TREU927Mutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S20, PUTATIVEX [auth AQ]117Trypanosoma brucei brucei TREU927Mutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN S21, PUTATIVEY [auth AR]194Trypanosoma brucei brucei TREU927Mutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN S23, PUTATIVEZ [auth AS]143Trypanosoma brucei brucei TREU927Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN S24AA [auth AT]137Trypanosoma brucei brucei TREU927Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN S25, PUTATIVEBA [auth AU]113Trypanosoma brucei brucei TREU927Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S26, PUTATIVECA [auth AV]111Trypanosoma brucei brucei TREU927Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN S27, PUTATIVEDA [auth AW]86Trypanosoma brucei brucei TREU927Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN S3, PUTATIVEEA [auth AX]214Trypanosoma brucei brucei TREU927Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN S30, PUTATIVEFA [auth AY]66Trypanosoma brucei brucei TREU927Mutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN S33, PUTATIVEGA [auth AZ]103Trypanosoma brucei brucei TREU927Mutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L18PA [auth BI]193Trypanosoma brucei brucei TREU927Mutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEINQA [auth BJ]214Trypanosoma brucei brucei TREU927Mutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L10, PUTATIVERA [auth BK]213Trypanosoma brucei brucei TREU927Mutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L11, PUTATIVESA [auth BL]194Trypanosoma brucei brucei TREU927Mutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L12, PUTATIVETA [auth BM]164Trypanosoma brucei brucei TREU927Mutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L13UA [auth BN]218Trypanosoma brucei brucei TREU927Mutation(s): 0 
UniProt
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L13A, PUTATIVEVA [auth BO]222Trypanosoma brucei brucei TREU927Mutation(s): 0 
UniProt
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
PROBABLE 60S RIBOSOMAL PROTEIN L14WA [auth BP]189Trypanosoma brucei brucei TREU927Mutation(s): 0 
UniProt
Find proteins for P55842 (Trypanosoma brucei brucei)
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L15XA [auth BQ]221Trypanosoma brucei brucei TREU927Mutation(s): 0 
UniProt
Find proteins for Q38CY7 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L17, PUTATIVEYA [auth BR]166Trypanosoma brucei brucei TREU927Mutation(s): 0 
UniProt
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L18AZA [auth BS]179Trypanosoma brucei brucei TREU927Mutation(s): 0 
UniProt
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L19, PUTATIVEAB [auth BT]260Trypanosoma brucei brucei TREU927Mutation(s): 0 
UniProt
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L21E, PUTATIVEBB [auth BU]159Trypanosoma brucei brucei TREU927Mutation(s): 0 
UniProt
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L22, PUTATIVECB [auth BV]130Trypanosoma brucei brucei TREU927Mutation(s): 0 
UniProt
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L23, PUTATIVEDB [auth BW]139Trypanosoma brucei brucei TREU927Mutation(s): 0 
UniProt
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L23AEB [auth BX]164Trypanosoma brucei brucei TREU927Mutation(s): 0 
UniProt
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L24, PUTATIVEFB [auth BY]125Trypanosoma brucei brucei TREU927Mutation(s): 0 
UniProt
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L26, PUTATIVEGB [auth BZ]143Trypanosoma brucei brucei TREU927Mutation(s): 0 
UniProt
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L27, PUTATIVEHB [auth Ba]133Trypanosoma brucei brucei TREU927Mutation(s): 0 
UniProt
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L27AIB [auth Bb]145Trypanosoma brucei brucei TREU927Mutation(s): 0 
UniProt
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L28, PUTATIVEJB [auth Bc]146Trypanosoma brucei brucei TREU927Mutation(s): 0 
UniProt
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L29, PUTATIVEKB [auth Bd]71Trypanosoma brucei brucei TREU927Mutation(s): 0 
UniProt
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L2, PUTATIVELB [auth Be]260Trypanosoma brucei brucei TREU927Mutation(s): 0 
UniProt
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L3, MITOCHONDRIAL, PUTATIVEMB [auth Bf]429Trypanosoma brucei brucei TREU927Mutation(s): 0 
UniProt
Find proteins for Q581Q1 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L30NB [auth Bg]105Trypanosoma brucei brucei TREU927Mutation(s): 0 
UniProt
Find proteins for Q38BI9 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL SUBUNIT PROTEIN L31, PUTATIVEOB [auth Bh]188Trypanosoma brucei brucei TREU927Mutation(s): 0 
UniProt
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L32, PUTATIVEPB [auth Bi]132Trypanosoma brucei brucei TREU927Mutation(s): 0 
UniProt
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L34, PUTATIVEQB [auth Bj]170Trypanosoma brucei brucei TREU927Mutation(s): 0 
UniProt
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L35, PUTATIVERB [auth Bk]127Trypanosoma brucei brucei TREU927Mutation(s): 0 
UniProt
Find proteins for Q38FW8 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L35A, PUTATIVESB [auth Bl]149Trypanosoma brucei brucei TREU927Mutation(s): 0 
UniProt
Find proteins for Q584G9 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L36, PUTATIVETB [auth Bm]109Trypanosoma brucei brucei TREU927Mutation(s): 0 
UniProt
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L37UB [auth Bn]84Trypanosoma brucei brucei TREU927Mutation(s): 0 
UniProt
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L37A, PUTATIVEVB [auth Bo]93Trypanosoma brucei brucei TREU927Mutation(s): 0 
UniProt
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L38, PUTATIVEWB [auth Bp]82Trypanosoma brucei brucei TREU927Mutation(s): 0 
UniProt
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L39, PUTATIVEXB [auth Bq]51Trypanosoma brucei brucei TREU927Mutation(s): 0 
UniProt
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L4YB [auth Br]374Trypanosoma brucei brucei TREU927Mutation(s): 0 
UniProt
Find proteins for Q582N2 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
UBIQUITIN-60S RIBOSOMAL PROTEIN L40ZB [auth Bs]128Trypanosoma brucei brucei TREU927Mutation(s): 0 
UniProt
Find proteins for P21899 (Trypanosoma brucei brucei)
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L44AC [auth Bt]106Trypanosoma brucei brucei TREU927Mutation(s): 0 
UniProt
Find proteins for D7SG81 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 80
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L5, PUTATIVEBC [auth Bu]308Trypanosoma brucei brucei TREU927Mutation(s): 0 
UniProt
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Entity ID: 81
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L6, PUTATIVECC [auth Bv]192Trypanosoma brucei brucei TREU927Mutation(s): 0 
UniProt
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Entity ID: 82
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L7, PUTATIVEDC [auth Bw]257Trypanosoma brucei brucei TREU927Mutation(s): 0 
UniProt
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