6AZ3

Cryo-EM structure of of the large subunit of Leishmania ribosome bound to paromomycin

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history. 


Literature

Atomic resolution snapshot of Leishmania ribosome inhibition by the aminoglycoside paromomycin.

Shalev-Benami, M., Zhang, Y., Rozenberg, H., Nobe, Y., Taoka, M., Matzov, D., Zimmerman, E., Bashan, A., Isobe, T., Jaffe, C.L., Yonath, A., Skiniotis, G.

(2017) Nat Commun 8: 1589-1589

  • DOI: 10.1038/s41467-017-01664-4
  • Primary Citation of Related Structures:  
    6AZ1, 6AZ3

  • PubMed Abstract: 

    • Leishmania is a single-celled eukaryotic parasite afflicting millions of humans worldwide, with current therapies limited to a poor selection of drugs that mostly target elements in the parasite's cell envelope. Here we determined the atomic resolution electron cryo-microscopy (cryo-EM) structure of the Leishmania ribosome in complex with paromomycin (PAR), a highly potent compound recently approved for treatment of the fatal visceral leishmaniasis (VL) ...

    Leishmania is a single-celled eukaryotic parasite afflicting millions of humans worldwide, with current therapies limited to a poor selection of drugs that mostly target elements in the parasite's cell envelope. Here we determined the atomic resolution electron cryo-microscopy (cryo-EM) structure of the Leishmania ribosome in complex with paromomycin (PAR), a highly potent compound recently approved for treatment of the fatal visceral leishmaniasis (VL). The structure reveals the mechanism by which the drug induces its deleterious effects on the parasite. We further show that PAR interferes with several aspects of cytosolic translation, thus highlighting the cytosolic rather than the mitochondrial ribosome as the primary drug target. The results also highlight unique as well as conserved elements in the PAR-binding pocket that can serve as hotspots for the development of novel therapeutics.

    Organizational Affiliation: 

    Departments of Molecular and Cellular Physiology, and Structural Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA. yiorgo@stanford.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein uL2A254Leishmania donovaniMutation(s): 0 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein uL3B402Leishmania donovaniMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L1a, putativeC366Leishmania donovaniMutation(s): 0 
Gene Names: 
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Find proteins for A0A3S5H7L0 (Leishmania donovani)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L11 (L5, L16)D168Leishmania donovaniMutation(s): 0 
Gene Names: CGC20_15690, CGC20_16800, CGC21_2680, CGC21_32945, LdCL_040010100, LdCL_220005300, LDHU3_04.0620, LDHU3_22.0070
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Find proteins for A0A3S5H5A8 (Leishmania donovani)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L9, putativeE186Leishmania donovaniMutation(s): 0 
Gene Names: CGC20_6165, CGC21_36380, LdCL_300039500, LDHU3_30.4490
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein eL6F195Leishmania donovaniMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L7aG348Leishmania donovaniMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein uL13H221Leishmania donovaniMutation(s): 0 
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Entity ID: 9
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ribosomal protein eL13I212Leishmania donovaniMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L23, putativeJ134Leishmania donovaniMutation(s): 0 
Gene Names: CGC20_14830, CGC20_14835, CGC21_7365, CGC21_7370, LdCL_350043400, LdCL_350043500, LDHU3_35.5000, LDHU3_35.5010
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Find proteins for A0A3Q8IIA7 (Leishmania donovani)
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Probable 60S ribosomal protein L14K149Leishmania donovaniMutation(s): 0 
Gene Names: RPL14, LPD23
UniProt
Find proteins for Q25278 (Leishmania donovani)
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Entity ID: 12
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60S ribosomal protein L27A/L29, putativeL144Leishmania donovaniMutation(s): 0 
Gene Names: CGC20_14840, CGC20_14850, CGC21_7350, CGC21_7360, LdCL_350043100, LdCL_350043300, LDHU3_35.4970, LDHU3_35.4990
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Find proteins for A0A3Q8IGI9 (Leishmania donovani)
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Entity ID: 13
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Ribosomal protein L15M203Leishmania donovaniMutation(s): 0 
Gene Names: CGC20_0090, CGC20_6005, CGC21_36545, CGC21_6465, LdCL_300042500, LdCL_350024100, LDHU3_30.4940
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Find proteins for A0A3Q8IIZ6 (Leishmania donovani)
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Entity ID: 14
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60S ribosomal protein L10, putativeN213Leishmania donovaniMutation(s): 0 
Gene Names: CGC20_9400, CGC20_9495, CGC21_2805, CGC21_2905, LdCL_040013100, LdCL_040015100, LDHU3_04.0970, LDHU3_04.1190
UniProt
Find proteins for A0A3S5H5C4 (Leishmania donovani)
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Entity ID: 15
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60S ribosomal protein L5, putativeO305Leishmania donovaniMutation(s): 0 
Gene Names: 
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Find proteins for A0A3Q8IJC5 (Leishmania donovani)
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Entity ID: 16
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60S ribosomal protein L18, putativeP197Leishmania donovaniMutation(s): 0 
Gene Names: CGC20_27670, CGC21_14640, CGC21_33175, LdCL_130009900, LdCL_360054400, LDHU3_13.0620, LDHU3_36.6360
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Find proteins for A0A3S7XBN1 (Leishmania donovani)
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L19e family proteinQ189Leishmania donovaniMutation(s): 0 
Gene Names: CGC20_20145
UniProt
Find proteins for A0A504XXD2 (Leishmania donovani)
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L18aR178Leishmania donovaniMutation(s): 0 
Gene Names: CGC20_0675, CGC20_33790, CGC21_20030, LdCL_320014900, LDHU3_32.1220, LDHU3_35.0740
UniProt
Find proteins for A0A3Q8IT55 (Leishmania donovani)
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Entity ID: 19
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60S ribosomal protein L21, putativeS154Leishmania donovaniMutation(s): 0 
Gene Names: CGC20_20775, CGC20_36460, CGC21_25130, CGC21_27025, LdCL_160009600, LdCL_340043800, LDHU3_16.0550, LDHU3_34.5670
UniProt
Find proteins for A0A3Q8ICH0 (Leishmania donovani)
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L17, putativeT154Leishmania donovaniMutation(s): 0 
Gene Names: CGC20_11495, CGC21_15705, LdCL_240005300, LDHU3_24.0060
UniProt
Find proteins for A0A3S7WY02 (Leishmania donovani)
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L22, putativeU121Leishmania donovaniMutation(s): 0 
Gene Names: CGC20_28260, CGC21_14000, LdCL_360041100, LDHU3_36.4690
UniProt
Find proteins for A0A3Q8IJA8 (Leishmania donovani)
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L23a, putativeV118Leishmania donovaniMutation(s): 0 
Gene Names: CGC20_20065, CGC20_20070, CGC21_24275, CGC21_24280, LdCL_060011000, LdCL_060011100, LDHU3_06.0690, LDHU3_06.0700
UniProt
Find proteins for A0A3S7WPH7 (Leishmania donovani)
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein uL24W121Leishmania donovaniMutation(s): 0 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein eL24X65Leishmania donovaniMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal L27e family proteinY132Leishmania donovaniMutation(s): 0 
Gene Names: CGC20_34730
UniProt
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L28, putativeZ140Leishmania donovaniMutation(s): 0 
Gene Names: CGC20_31100, CGC20_31110, CGC21_0695, CGC21_0705, LdCL_110017100, LDHU3_11.1330, LDHU3_11.1350, LDHU3_11.1370
UniProt
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
60S_ribosomal_protein_L35_putative/GeneDB:LmjF.26.2330/GeneDB:LmjF.26.2340AA [auth a]125Leishmania donovaniMutation(s): 0 
Gene Names: CGC20_5605, CGC20_5610, CGC21_32450, CGC21_32455, LDHU3_26.3070, LDHU3_26.3080
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Find proteins for A0A504XWA8 (Leishmania donovani)
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Entity ID: 28
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60S ribosomal protein L29BA [auth b]68Leishmania donovaniMutation(s): 0 
Gene Names: CGC20_28200, CGC21_14070
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Entity ID: 29
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60S ribosomal protein L7 family proteinCA [auth c]227Leishmania donovaniMutation(s): 0 
Gene Names: CGC20_4660
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Entity ID: 30
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60S ribosomal protein L30DA [auth d]92Leishmania donovaniMutation(s): 0 
Gene Names: CGC20_0820, CGC21_5735, LdCL_350007400, LDHU3_35.0330
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Find proteins for A0A3Q8IET6 (Leishmania donovani)
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Entity ID: 31
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60S ribosomal subunit protein L31, putativeEA [auth e]119Leishmania donovaniMutation(s): 0 
Gene Names: CGC20_15065, CGC20_15070, CGC21_7135, CGC21_7140, LdCL_350038300, LdCL_350038400, LDHU3_35.4380, LDHU3_35.4390
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
60S_ribosomal_protein_L32/GeneDB:LmjF.21.1720FA [auth f]130Leishmania donovaniMutation(s): 0 
Gene Names: CGC20_21925, LDHU3_21.2480
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L35Ae family proteinGA [auth g]125Leishmania donovaniMutation(s): 0 
Gene Names: CGC20_21340, CGC20_35910, CGC21_23885, CGC21_26415, LdCL_100005700, LdCL_340030100, LDHU3_10.0110, LDHU3_34.3730
UniProt
Find proteins for A0A3Q8II82 (Leishmania donovani)
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Entity ID: 34
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60S ribosomal protein L34, putativeHA [auth h]125Leishmania donovaniMutation(s): 0 
Gene Names: LdCL_180019100, LdCL_360046300, LDHU3_18.1760, LDHU3_36.5270
UniProt
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Entity ID: 35
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60S ribosomal protein L36, putativeIA [auth i]97Leishmania donovaniMutation(s): 0 
Gene Names: CGC21_34065, LdCL_210012900, LDHU3_21.0900
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Find proteins for A0A3Q8IDW6 (Leishmania donovani)
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L37JA [auth j]80Leishmania donovaniMutation(s): 0 
Gene Names: RPL37
UniProt
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Entity ID: 37
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Ribosomal L38e family proteinKA [auth k]76Leishmania donovaniMutation(s): 0 
Gene Names: CGC21_32395
UniProt
Find proteins for A0A504WZU0 (Leishmania donovani)
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Entity ID: 38
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60S ribosomal protein L39, putativeLA [auth l]50Leishmania donovaniMutation(s): 0 
Gene Names: LdCL_160017400, LdCL_290030800, LDHU3_16.1490, LDHU3_29.3680
UniProt
Find proteins for A0A3Q8IAG7 (Leishmania donovani)
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UniProt GroupA0A3Q8IAG7
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-60S ribosomal protein L40MA [auth m]50Leishmania donovaniMutation(s): 0 
Gene Names: CGC20_3125, CGC20_3180, CGC21_11230, CGC21_11280, CGC21_36880, LdCL_090014900, LdCL_310027200, LdCL_310028700, LDHU3_31.3500, LDHU3_31.3730
UniProt
Find proteins for A0A3Q8ISR1 (Leishmania donovani)
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UniProt GroupA0A3Q8ISR1
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein eL41NA [auth n]33Leishmania donovaniMutation(s): 0 
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L37aOA [auth o]90Leishmania donovaniMutation(s): 0 
Gene Names: LdCL_210027600, LdCL_360025700, LDHU3_21.2600, LDHU3_36.2630
UniProt
Find proteins for A0A3Q8IC65 (Leishmania donovani)
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L44, putativePA [auth p]96Leishmania donovaniMutation(s): 0 
Gene Names: CGC20_16835, CGC20_9735, CGC21_33710, CGC21_5530, LdCL_130021400, LdCL_330041500, LDHU3_13.1930, LDHU3_33.4890
UniProt
Find proteins for A0A3Q8IKJ4 (Leishmania donovani)
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Entity ID: 43
MoleculeChainsLengthOrganismImage
rRNA alphaQA [auth 1]1,778Leishmania donovani
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Entity ID: 44
MoleculeChainsLengthOrganismImage
rRNA betaRA [auth 2]1,526Leishmania donovani
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Entity ID: 45
MoleculeChainsLengthOrganismImage
rRNA gammaSA [auth 3]211Leishmania donovani
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Entity ID: 46
MoleculeChainsLengthOrganismImage
rRNA deltaTA [auth 4]183Leishmania donovani
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Entity ID: 47
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rRNA epsilonUA [auth 5]133Leishmania donovani
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Entity ID: 48
MoleculeChainsLengthOrganismImage
rRNA zetaVA [auth 6]71Leishmania donovani
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Entity ID: 49
MoleculeChainsLengthOrganismImage
rRNA 5.8SWA [auth 7]171Leishmania donovani
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Entity ID: 50
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rRNA 5SXA [auth 8]118Leishmania donovani
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PAR
Query on PAR
Download Ideal Coordinates CCD File 
AB [auth 1],
AC [auth 2],
BB [auth 1],
BC [auth 2],
CB [auth 1],
AB [auth 1],
AC [auth 2],
BB [auth 1],
BC [auth 2],
CB [auth 1],
CC [auth 2],
NC [auth 7],
YA [auth 1],
ZA [auth 1],
ZB [auth 2]
PAROMOMYCIN
C23 H45 N5 O14
UOZODPSAJZTQNH-LSWIJEOBSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
DB [auth 1],
DC [auth 2],
EB [auth 1],
EC [auth 2],
FB [auth 1],
DB [auth 1],
DC [auth 2],
EB [auth 1],
EC [auth 2],
FB [auth 1],
FC [auth 2],
GB [auth 1],
GC [auth 2],
HB [auth 1],
HC [auth 2],
IB [auth 1],
IC [auth 2],
JB [auth 1],
JC [auth 2],
KB [auth 1],
KC [auth 3],
LB [auth 1],
LC [auth 4],
MB [auth 1],
MC [auth 5],
NB [auth 1],
OB [auth 1],
OC [auth 7],
PB [auth 1],
PC [auth 7],
QB [auth 1],
RB [auth 1],
SB [auth 1],
TB [auth 1],
UB [auth 1],
VB [auth 1],
WB [auth 1],
XB [auth 1],
YB [auth 2]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-06
    Type: Initial release
  • Version 1.1: 2017-12-13
    Changes: Database references
  • Version 2.0: 2022-04-13
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary