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 L2
A
260Leishmania donovaniMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L3
B
419Leishmania donovaniMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L4
C
373Leishmania donovaniMutation(s): 0 
Find proteins for E9BKR3 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BKR3

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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L5
D
188Leishmania donovaniMutation(s): 0 
Find proteins for E9BFL1 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BFL1

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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L6
E
190Leishmania donovaniMutation(s): 0 
Find proteins for E9BFB5 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BFB5

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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L6e
F
195Leishmania donovaniMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L8e
G
348Leishmania donovaniMutation(s): 0 
Find proteins for E9B949 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9B949

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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L13
H
222Leishmania donovaniMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L13e
I
220Leishmania donovaniMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L14
J
139Leishmania donovaniMutation(s): 0 
Find proteins for E9BSQ4 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BSQ4

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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L14e
K
233Leishmania donovaniMutation(s): 0 
Find proteins for E9BG02 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BG02

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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L15
L
145Leishmania donovaniMutation(s): 0 
Find proteins for E9BSQ2 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BSQ2

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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L15e
M
204Leishmania donovaniMutation(s): 0 
Find proteins for E9BMB4 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BMB4

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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L16
N
213Leishmania donovaniMutation(s): 0 
Find proteins for E9B840 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9B840

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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L18
O
305Leishmania donovaniMutation(s): 0 
Find proteins for E9BS61 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BS61

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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L18e
P
198Leishmania donovaniMutation(s): 0 
Find proteins for E9BUI1 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BUI1

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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L19e
Q
245Leishmania donovaniMutation(s): 0 
Find proteins for E9B8Q2 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9B8Q2

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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L20e
R
179Leishmania donovaniMutation(s): 1 
Find proteins for E9BRT7 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BRT7

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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L21e
S
159Leishmania donovaniMutation(s): 0 
Find proteins for E9BRE2 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BRE2

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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L22
T
166Leishmania donovaniMutation(s): 0 
Find proteins for E9BGL6 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BGL6

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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L22e
U
129Leishmania donovaniMutation(s): 0 
Find proteins for E9BU52 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BU52

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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L23
V
145Leishmania donovaniMutation(s): 0 
Find proteins for E9B8R9 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9B8R9

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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L24
W
143Leishmania donovaniMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L24e
X
124Leishmania donovaniMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L27e
Y
134Leishmania donovaniMutation(s): 0 
Find proteins for E9BP34 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BP34

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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L28e
Z
147Leishmania donovaniMutation(s): 0 
Find proteins for E9BAU9 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BAU9

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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L29
a
127Leishmania donovaniMutation(s): 0 
Find proteins for E9BIP6 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BIP6

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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L29e
b
70Leishmania donovaniMutation(s): 0 
Find proteins for E9BU64 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BU64

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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L30
c
252Leishmania donovaniMutation(s): 1 
Find proteins for E9BI29 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BI29

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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L30e
d
104Leishmania donovaniMutation(s): 0 
Find proteins for E9BRQ6 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BRQ6

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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L31e
e
183Leishmania donovaniMutation(s): 0 
Find proteins for E9BSK4 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BSK4

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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L32e
f
133Leishmania donovaniMutation(s): 1 
Find proteins for E9BFJ5 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BFJ5

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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L33e
g
144Leishmania donovaniMutation(s): 0 
Find proteins for E9BR22 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BR22

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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L34e
h
168Leishmania donovaniMutation(s): 0 
Find proteins for E9BUA1 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BUA1

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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L36e
i
105Leishmania donovaniMutation(s): 0 
Find proteins for E9BF65 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BF65

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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L37e
j
83Leishmania donovaniMutation(s): 0 
Find proteins for E9BQD7 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BQD7

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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L38e
k
83Leishmania donovaniMutation(s): 0 
Find proteins for E9B7P2 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9B7P2

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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L39e
l
51Leishmania donovaniMutation(s): 0 
Find proteins for E9BCX6 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BCX6

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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L43e
m
92Leishmania donovaniMutation(s): 0 
Find proteins for E9BFK4 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BFK4

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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L44e
n
106Leishmania donovaniMutation(s): 0 
Find proteins for E9BBL5 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BBL5

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Entity ID: 1
MoleculeChainsLengthOrganism
26S alpha ribosomal RNA11782Leishmania donovani

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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
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download CCD File 
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

View Full Validation Report



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