3JCS

2.8 Angstrom cryo-EM structure of the large ribosomal subunit from the eukaryotic parasite Leishmania


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

2.8- angstrom Cryo-EM Structure of the Large Ribosomal Subunit from the Eukaryotic Parasite Leishmania.

Shalev-Benami, M.Zhang, Y.Matzov, D.Halfon, Y.Zackay, A.Rozenberg, H.Zimmerman, E.Bashan, A.Jaffe, C.L.Yonath, A.Skiniotis, G.

(2016) Cell Rep 16: 288-294

  • DOI: 10.1016/j.celrep.2016.06.014
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Leishmania is a single-cell eukaryotic parasite of the Trypanosomatidae family, whose members cause an array of tropical diseases. The often fatal outcome of infections, lack of effective vaccines, limited selection of therapeutic drugs, and emerging ...

    Leishmania is a single-cell eukaryotic parasite of the Trypanosomatidae family, whose members cause an array of tropical diseases. The often fatal outcome of infections, lack of effective vaccines, limited selection of therapeutic drugs, and emerging resistant strains, underline the need to develop strategies to combat these pathogens. The Trypanosomatid ribosome has recently been highlighted as a promising therapeutic target due to structural features that are distinct from other eukaryotes. Here, we present the 2.8-Å resolution structure of the Leishmania donovani large ribosomal subunit (LSU) derived from a cryo-EM map, further enabling the structural observation of eukaryotic rRNA modifications that play a significant role in ribosome assembly and function. The structure illustrates the unique fragmented nature of leishmanial LSU rRNA and highlights the irregular distribution of rRNA modifications in Leishmania, a characteristic with implications for anti-parasitic drug development.


    Organizational Affiliation

    Life Sciences Institute and Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA. Electronic address: skinioti@umich.edu.



Macromolecules

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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L2A260Leishmania donovaniMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L3B419Leishmania donovaniMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L4C373Leishmania donovaniMutation(s): 0 
Find proteins for E9BKR3 (Leishmania donovani (strain BPK282A1))
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Go to UniProtKB:  E9BKR3
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L5D188Leishmania donovaniMutation(s): 0 
Find proteins for E9BFL1 (Leishmania donovani (strain BPK282A1))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L6E190Leishmania donovaniMutation(s): 0 
Find proteins for E9BFB5 (Leishmania donovani (strain BPK282A1))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L6eF195Leishmania donovaniMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L8eG348Leishmania donovaniMutation(s): 0 
Find proteins for E9B949 (Leishmania donovani (strain BPK282A1))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L13H222Leishmania donovaniMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L13eI220Leishmania donovaniMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L14J139Leishmania donovaniMutation(s): 0 
Find proteins for E9BSQ4 (Leishmania donovani (strain BPK282A1))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L14eK233Leishmania donovaniMutation(s): 0 
Find proteins for E9BG02 (Leishmania donovani (strain BPK282A1))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L15L145Leishmania donovaniMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L15eM204Leishmania donovaniMutation(s): 0 
Find proteins for E9BMB4 (Leishmania donovani (strain BPK282A1))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L16N213Leishmania donovaniMutation(s): 0 
Find proteins for E9B840 (Leishmania donovani (strain BPK282A1))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L18O305Leishmania donovaniMutation(s): 0 
Find proteins for E9BS61 (Leishmania donovani (strain BPK282A1))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L18eP198Leishmania donovaniMutation(s): 0 
Find proteins for E9BUI1 (Leishmania donovani (strain BPK282A1))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L19eQ245Leishmania donovaniMutation(s): 0 
Find proteins for E9B8Q2 (Leishmania donovani (strain BPK282A1))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L20eR179Leishmania donovaniMutation(s): 1 
Find proteins for E9BRT7 (Leishmania donovani (strain BPK282A1))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L21eS159Leishmania donovaniMutation(s): 0 
Find proteins for E9BRE2 (Leishmania donovani (strain BPK282A1))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L22T166Leishmania donovaniMutation(s): 0 
Find proteins for E9BGL6 (Leishmania donovani (strain BPK282A1))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L22eU129Leishmania donovaniMutation(s): 0 
Find proteins for E9BU52 (Leishmania donovani (strain BPK282A1))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L23V145Leishmania donovaniMutation(s): 0 
Find proteins for E9B8R9 (Leishmania donovani (strain BPK282A1))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L24W143Leishmania donovaniMutation(s): 0 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L24eX124Leishmania donovaniMutation(s): 0 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L27eY134Leishmania donovaniMutation(s): 0 
Find proteins for E9BP34 (Leishmania donovani (strain BPK282A1))
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L28eZ147Leishmania donovaniMutation(s): 0 
Find proteins for E9BAU9 (Leishmania donovani (strain BPK282A1))
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L29a127Leishmania donovaniMutation(s): 0 
Find proteins for E9BIP6 (Leishmania donovani (strain BPK282A1))
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L30c252Leishmania donovaniMutation(s): 1 
Find proteins for E9BI29 (Leishmania donovani (strain BPK282A1))
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L30ed104Leishmania donovaniMutation(s): 0 
Find proteins for E9BRQ6 (Leishmania donovani (strain BPK282A1))
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L31ee183Leishmania donovaniMutation(s): 0 
Find proteins for E9BSK4 (Leishmania donovani (strain BPK282A1))
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L32ef133Leishmania donovaniMutation(s): 1 
Find proteins for E9BFJ5 (Leishmania donovani (strain BPK282A1))
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L34eh168Leishmania donovaniMutation(s): 0 
Find proteins for E9BUA1 (Leishmania donovani (strain BPK282A1))
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L36ei105Leishmania donovaniMutation(s): 0 
Find proteins for E9BF65 (Leishmania donovani (strain BPK282A1))
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L37ej83Leishmania donovaniMutation(s): 0 
Gene Names: RPL37
Find proteins for P62885 (Leishmania donovani)
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Go to UniProtKB:  P62885
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L39el51Leishmania donovaniMutation(s): 0 
Find proteins for E9BCX6 (Leishmania donovani (strain BPK282A1))
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L43em92Leishmania donovaniMutation(s): 0 
Find proteins for E9BFK4 (Leishmania donovani (strain BPK282A1))
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L44en106Leishmania donovaniMutation(s): 0 
Find proteins for E9BBL5 (Leishmania donovani (strain BPK282A1))
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L29eb70Leishmania donovaniMutation(s): 0 
Find proteins for E9BU64 (Leishmania donovani (strain BPK282A1))
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L33eg144Leishmania donovaniMutation(s): 0 
Find proteins for E9BR22 (Leishmania donovani (strain BPK282A1))
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L38ek83Leishmania donovaniMutation(s): 0 
Find proteins for E9B7P2 (Leishmania donovani (strain BPK282A1))
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Entity ID: 2
MoleculeChainsLengthOrganism
26S delta ribosomal RNA21527Leishmania donovani

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Entity ID: 3
MoleculeChainsLengthOrganism
26S gamma ribosomal RNA3213Leishmania donovani

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Entity ID: 4
MoleculeChainsLengthOrganism
26S delta ribosomal RNA4183Leishmania donovani

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Entity ID: 5
MoleculeChainsLengthOrganism
26S epsilon ribosomal RNA5133Leishmania donovani

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Entity ID: 6
MoleculeChainsLengthOrganism
26S zeta ribosomal RNA676Leishmania donovani

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Entity ID: 7
MoleculeChainsLengthOrganism
5.8S ribosomal RNA7171Leishmania donovani

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Entity ID: 8
MoleculeChainsLengthOrganism
5S ribosomal RNA8121Leishmania donovani

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Entity ID: 1
MoleculeChainsLengthOrganism
26S alpha ribosomal RNA11782Leishmania donovani
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

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1, 2, 3, 4, 5, 7, C, K, M, V, a, f, g, h, j
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-07-20
    Type: Initial release
  • Version 1.1: 2016-07-27
    Changes: Database references
  • Version 1.2: 2018-07-18
    Changes: Data collection