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: https://doi.org/10.1016/j.celrep.2016.06.014
  • Primary Citation of Related Structures:  
    3JCS

  • 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 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 Structural Biology, Faculty of Chemistry, Weizmann Institute of Science, Rehovot 7610001, Israel.


Macromolecules

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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein L2I [auth A]260Leishmania donovaniMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein L3J [auth B]419Leishmania donovaniMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein L4K [auth C]373Leishmania donovaniMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein L5L [auth D]188Leishmania donovaniMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein L6M [auth E]190Leishmania donovaniMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein L6eN [auth F]195Leishmania donovaniMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein L8eO [auth G]348Leishmania donovaniMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein L13P [auth H]222Leishmania donovaniMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein L13eQ [auth I]220Leishmania donovaniMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein L14R [auth J]139Leishmania donovaniMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein L14eS [auth K]233Leishmania donovaniMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein L15T [auth L]145Leishmania donovaniMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein L15eU [auth M]204Leishmania donovaniMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein L16V [auth N]213Leishmania donovaniMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein L18W [auth O]305Leishmania donovaniMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein L18eX [auth P]198Leishmania donovaniMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein L19eY [auth Q]245Leishmania donovaniMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein L20eZ [auth R]179Leishmania donovaniMutation(s): 1 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein L21eAA [auth S]159Leishmania donovaniMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein L22BA [auth T]166Leishmania donovaniMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein L22eCA [auth U]129Leishmania donovaniMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein L23DA [auth V]145Leishmania donovaniMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein L24EA [auth W]143Leishmania donovaniMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein L24eFA [auth X]124Leishmania donovaniMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein L27eGA [auth Y]134Leishmania donovaniMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein L28eHA [auth Z]147Leishmania donovaniMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein L29IA [auth a]127Leishmania donovaniMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein L29eJA [auth b]70Leishmania donovaniMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein L30KA [auth c]252Leishmania donovaniMutation(s): 1 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein L30eLA [auth d]104Leishmania donovaniMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein L31eMA [auth e]183Leishmania donovaniMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein L32eNA [auth f]133Leishmania donovaniMutation(s): 1 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein L33eOA [auth g]144Leishmania donovaniMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein L34ePA [auth h]168Leishmania donovaniMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein L36eQA [auth i]105Leishmania donovaniMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein L37eRA [auth j]83Leishmania donovaniMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein L38eSA [auth k]83Leishmania donovaniMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein L39eTA [auth l]51Leishmania donovaniMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein L43eUA [auth m]92Leishmania donovaniMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein L44eVA [auth n]106Leishmania donovaniMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
26S alpha ribosomal RNAA [auth 1]1,782Leishmania donovani
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Entity ID: 2
MoleculeChains LengthOrganismImage
26S delta ribosomal RNAB [auth 2]1,527Leishmania donovani
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Entity ID: 3
MoleculeChains LengthOrganismImage
26S gamma ribosomal RNAC [auth 3]213Leishmania donovani
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Entity ID: 4
MoleculeChains LengthOrganismImage
26S delta ribosomal RNAD [auth 4]183Leishmania donovani
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Entity ID: 5
MoleculeChains LengthOrganismImage
26S epsilon ribosomal RNAE [auth 5]133Leishmania donovani
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Entity ID: 6
MoleculeChains LengthOrganismImage
26S zeta ribosomal RNAF [auth 6]76Leishmania donovani
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Entity ID: 7
MoleculeChains LengthOrganismImage
5.8S ribosomal RNAG [auth 7]171Leishmania donovani
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Entity ID: 8
MoleculeChains LengthOrganismImage
5S ribosomal RNAH [auth 8]121Leishmania donovani
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth 1]
AC [auth 1]
AD [auth 2]
AE [auth 5]
AF [auth j]
AB [auth 1],
AC [auth 1],
AD [auth 2],
AE [auth 5],
AF [auth j],
BB [auth 1],
BC [auth 1],
BD [auth 2],
BE [auth 5],
CB [auth 1],
CC [auth 1],
CD [auth 2],
CE [auth 5],
DB [auth 1],
DC [auth 1],
DD [auth 2],
DE [auth 7],
EB [auth 1],
EC [auth 1],
ED [auth 2],
EE [auth 7],
FB [auth 1],
FC [auth 1],
FD [auth 2],
FE [auth 7],
GB [auth 1],
GC [auth 1],
GD [auth 2],
GE [auth 7],
HB [auth 1],
HC [auth 1],
HD [auth 2],
HE [auth 7],
IB [auth 1],
IC [auth 1],
ID [auth 2],
IE [auth 7],
JB [auth 1],
JC [auth 1],
JD [auth 2],
JE [auth 7],
KB [auth 1],
KC [auth 1],
KD [auth 2],
KE [auth 7],
LB [auth 1],
LC [auth 1],
LD [auth 2],
LE [auth 7],
MB [auth 1],
MC [auth 1],
MD [auth 2],
ME [auth C],
NB [auth 1],
NC [auth 1],
ND [auth 2],
NE [auth K],
OB [auth 1],
OC [auth 1],
OD [auth 2],
OE [auth M],
PB [auth 1],
PC [auth 1],
PD [auth 2],
PE [auth M],
QB [auth 1],
QC [auth 1],
QD [auth 2],
QE [auth M],
RB [auth 1],
RC [auth 1],
RD [auth 2],
RE [auth V],
SB [auth 1],
SC [auth 1],
SD [auth 2],
SE [auth a],
TB [auth 1],
TC [auth 1],
TD [auth 2],
TE [auth f],
UB [auth 1],
UC [auth 1],
UD [auth 3],
UE [auth f],
VB [auth 1],
VC [auth 2],
VD [auth 3],
VE [auth g],
WA [auth 1],
WB [auth 1],
WC [auth 2],
WD [auth 3],
WE [auth h],
XA [auth 1],
XB [auth 1],
XC [auth 2],
XD [auth 4],
XE [auth j],
YA [auth 1],
YB [auth 1],
YC [auth 2],
YD [auth 4],
YE [auth j],
ZA [auth 1],
ZB [auth 1],
ZC [auth 2],
ZD [auth 5],
ZE [auth j]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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