6AZ1 image
Deposition Date 2017-09-09
Release Date 2017-12-06
Last Version Date 2025-05-28
Entry Detail
PDB ID:
6AZ1
Title:
Cryo-EM structure of the small subunit of Leishmania ribosome bound to paromomycin
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
2.70 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:ribosomal RNA 18S
Chain IDs:HA (auth: 1)
Chain Length:2203
Number of Molecules:1
Biological Source:Leishmania donovani
Polymer Type:polyribonucleotide
Molecule:tRNA-Phe
Chain IDs:IA (auth: 2)
Chain Length:76
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:P-site tRNA
Chain IDs:JA (auth: 3)
Chain Length:77
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:E-site tRNA
Chain IDs:KA (auth: 4)
Chain Length:76
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:LA (auth: 5)
Chain Length:13
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein s1e
Gene (Uniprot):CGC20_0740, CGC20_0745, CGC21_5810, CGC21_5815, LDBPK_350400, LDBPK_350410, LdCL_350009100, LdCL_350009200, LDHU3_35.0560, LDHU3_35.0570
Chain IDs:A
Chain Length:120
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein S2
Chain IDs:B
Chain Length:112
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein S3
Gene (Uniprot):LDBPK_330960
Chain IDs:C
Chain Length:219
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein S4
Chain IDs:D
Chain Length:190
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein S4e
Chain IDs:E
Chain Length:66
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein S5
Chain IDs:F
Chain Length:152
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein S6e
Chain IDs:G
Chain Length:312
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein S7
Chain IDs:H
Chain Length:190
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein S7e
Chain IDs:I
Chain Length:200
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein S8
Gene (Uniprot):CGC20_25145, CGC20_31130, CGC21_28485, LDBPK_111180, LDBPK_291920, LdCL_110017700, LdCL_290024900, LDHU3_11.1430, LDHU3_29.2740
Chain IDs:J
Chain Length:130
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein S8e
Chain IDs:K
Chain Length:220
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein S9
Gene (Uniprot):CGC20_4945, CGC21_31780, CGC21_31785, LDBPK_260840, LDBPK_260850, LdCL_260014100, LdCL_260014200, LDHU3_26.1100
Chain IDs:L
Chain Length:149
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein S10
Chain IDs:M
Chain Length:116
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein S10e
Gene (Uniprot):LDBPK_361040
Chain IDs:N
Chain Length:153
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein S11
Chain IDs:O
Chain Length:144
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein S12
Gene (Uniprot):CGC20_15985, CGC20_22285, CGC20_22290, CGC21_34300, CGC21_34305, LDBPK_211300, LDBPK_211310, LdCL_210018100, LdCL_210018200, LDHU3_21.1530, LDHU3_21.1540
Chain IDs:P
Chain Length:143
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein S12e
Chain IDs:Q
Chain Length:141
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein S13
Gene (Uniprot):LDBPK_360990, LDBPK_361000, LdCL_360015000
Chain IDs:R
Chain Length:153
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein S14
Gene (Uniprot):LDBPK_282360, LDBPK_282650, LdCL_280028700, LdCL_280031600, LDHU3_28.3200, LDHU3_28.3580
Chain IDs:S
Chain Length:57
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein S15
Chain IDs:T
Chain Length:151
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein S17
Chain IDs:U
Chain Length:173
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein S17e
Gene (Uniprot):CGC20_12800, CGC20_12805, CGC21_22780, LDBPK_282750, LDBPK_282760, LdCL_280032600, LdCL_280032700, LDHU3_28.3730, LDHU3_28.3740
Chain IDs:V
Chain Length:143
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein S19
Chain IDs:W
Chain Length:152
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein S19e
Gene (Uniprot):LDBPK_342620
Chain IDs:X
Chain Length:179
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein S21e
Chain IDs:Y
Chain Length:159
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein S24e
Chain IDs:Z
Chain Length:137
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein S25e
Gene (Uniprot):CGC20_2335, CGC20_26645, CGC21_25565, CGC21_8675, LDBPK_251220, LDBPK_340460, LdCL_250018000, LdCL_340009700, LDHU3_25.1560, LDHU3_34.0630
Chain IDs:AA (auth: a)
Chain Length:120
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein S26e
Gene (Uniprot):CGC20_13810, CGC20_6240, CGC21_36310, LDBPK_280570, LDBPK_303240, LdCL_280010400, LdCL_300038000, LDHU3_28.0690, LDHU3_30.4330
Chain IDs:BA (auth: b)
Chain Length:112
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein S27e
Chain IDs:CA (auth: c)
Chain Length:219
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein S28e
Gene (Uniprot):LDBPK_261610, LDBPK_261620, LdCL_260021800, LdCL_260021900, LDHU3_26.2030, LDHU3_26.2040
Chain IDs:DA (auth: d)
Chain Length:190
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein S30e
Gene (Uniprot):LDBPK_300690, LDBPK_300710, LdCL_300012000, LdCL_300012100, LdCL_300012200, LDHU3_30.0880, LDHU3_30.0890, LDHU3_30.0900
Chain IDs:EA (auth: e)
Chain Length:66
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein S31e
Chain IDs:FA (auth: f)
Chain Length:152
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:LACK1
Chain IDs:GA (auth: g)
Chain Length:312
Number of Molecules:1
Biological Source:Leishmania donovani
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
4OC HA C modified residue
5MC HA C modified residue
7MG HA G modified residue
A2M HA A modified residue
MA6 HA A modified residue
MIA IA A modified residue
OMC HA C modified residue
OMG HA G modified residue
OMU HA U modified residue
Primary Citation
Atomic resolution snapshot of Leishmania ribosome inhibition by the aminoglycoside paromomycin.
Nat Commun 8 1589 1589 (2017)
PMID: 29150609 DOI: 10.1038/s41467-017-01664-4

Abstact

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.

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Primary Citation of related structures