3JCS

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.8 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

  • 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

    Department of Microbiology and Molecular Genetics, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem 9112102, Israel.,Life Sciences Institute and Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA. Electronic address: skinioti@umich.edu.,Department of Structural Biology, Faculty of Chemistry, Weizmann Institute of Science, Rehovot 7610001, Israel.,Life Sciences Institute and Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Structural Biology, Faculty of Chemistry, Weizmann Institute of Science, Rehovot 7610001, Israel. Electronic address: ada.yonath@weizmann.ac.il.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L2
A
260N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L3
B
419N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L4
C
373Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BKR3 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BKR3
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L5
D
188Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BFL1 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BFL1
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L6
E
190Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BFB5 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BFB5
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L6e
F
195N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L8e
G
348Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9B949 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9B949
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L13
H
222N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L13e
I
220N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L14
J
139Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BSQ4 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BSQ4
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L14e
K
233Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BG02 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BG02
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L15
L
145Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BSQ2 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BSQ2
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L15e
M
204Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BMB4 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BMB4
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L16
N
213Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9B840 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9B840
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L18
O
305Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BS61 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BS61
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L18e
P
198Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BUI1 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BUI1
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L19e
Q
245Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9B8Q2 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9B8Q2
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L20e
R
179Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BRT7 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BRT7
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L21e
S
159Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BRE2 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BRE2
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L22
T
166Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BGL6 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BGL6
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L22e
U
129Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BU52 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BU52
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L23
V
145Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9B8R9 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9B8R9
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L24
W
143N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L24e
X
124N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L27e
Y
134Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BP34 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BP34
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L28e
Z
147Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BAU9 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BAU9
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L29
a
127Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BIP6 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BIP6
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L29e
b
70Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BU64 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BU64
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L30
c
252Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BI29 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BI29
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L30e
d
104Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BRQ6 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BRQ6
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L31e
e
183Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BSK4 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BSK4
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L32e
f
133Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BFJ5 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BFJ5
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L33e
g
144Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BR22 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BR22
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L34e
h
168Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BUA1 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BUA1
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L36e
i
105Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BF65 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BF65
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L37e
j
83Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BQD7 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BQD7
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L38e
k
83Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9B7P2 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9B7P2
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L39e
l
51Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BCX6 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BCX6
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L43e
m
92Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BFK4 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BFK4
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L44e
n
106Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BBL5 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BBL5
Entity ID: 1
MoleculeChainsLengthOrganism
26S alpha ribosomal RNA11782Leishmania donovani
Entity ID: 2
MoleculeChainsLengthOrganism
26S delta ribosomal RNA21527Leishmania donovani
Entity ID: 3
MoleculeChainsLengthOrganism
26S gamma ribosomal RNA3213Leishmania donovani
Entity ID: 4
MoleculeChainsLengthOrganism
26S delta ribosomal RNA4183Leishmania donovani
Entity ID: 5
MoleculeChainsLengthOrganism
26S epsilon ribosomal RNA5133Leishmania donovani
Entity ID: 6
MoleculeChainsLengthOrganism
26S zeta ribosomal RNA676Leishmania donovani
Entity ID: 7
MoleculeChainsLengthOrganism
5.8S ribosomal RNA7171Leishmania donovani
Entity ID: 8
MoleculeChainsLengthOrganism
5S ribosomal RNA8121Leishmania donovani
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
1, 2, 3, 4, 5, 7, a, C, f, g, h, j, K, M, V
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  5 Unique
IDChainsTypeFormula2D DiagramParent
A2M
Query on A2M
1, 2, 7
RNA LINKINGC11 H16 N5 O7 PA
OMU
Query on OMU
1, 2, 7
RNA LINKINGC10 H15 N2 O9 PU
OMC
Query on OMC
1, 2
RNA LINKINGC10 H16 N3 O8 PC
OMG
Query on OMG
1, 2
RNA LINKINGC11 H16 N5 O8 PG
H2U
Query on H2U
2
RNA LINKINGC9 H15 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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