6AZ3 image
Deposition Date 2017-09-09
Release Date 2017-12-06
Last Version Date 2024-10-23
Entry Detail
PDB ID:
6AZ3
Keywords:
RIBOSOME/ANTIBIOTIC
Title:
Cryo-EM structure of of the large subunit of Leishmania ribosome bound to paromomycin
Biological Source:
Source Organism:
Leishmania donovani (Taxon ID: 5661)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
2.50 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
6AZ3 validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:rRNA alpha
Chain IDs:QA (auth: 1)
Chain Length:1778
Number of Molecules:1
Biological Source:Leishmania donovani
Polymer Type:polyribonucleotide
Molecule:rRNA beta
Chain IDs:RA (auth: 2)
Chain Length:1526
Number of Molecules:1
Biological Source:Leishmania donovani
Polymer Type:polyribonucleotide
Molecule:rRNA gamma
Chain IDs:SA (auth: 3)
Chain Length:211
Number of Molecules:1
Biological Source:Leishmania donovani
Polymer Type:polyribonucleotide
Molecule:rRNA delta
Chain IDs:TA (auth: 4)
Chain Length:183
Number of Molecules:1
Biological Source:Leishmania donovani
Polymer Type:polyribonucleotide
Molecule:rRNA epsilon
Chain IDs:UA (auth: 5)
Chain Length:133
Number of Molecules:1
Biological Source:Leishmania donovani
Polymer Type:polyribonucleotide
Molecule:rRNA zeta
Chain IDs:VA (auth: 6)
Chain Length:71
Number of Molecules:1
Biological Source:Leishmania donovani
Polymer Type:polyribonucleotide
Molecule:rRNA 5.8S
Chain IDs:WA (auth: 7)
Chain Length:171
Number of Molecules:1
Biological Source:Leishmania donovani
Polymer Type:polyribonucleotide
Molecule:rRNA 5S
Chain IDs:XA (auth: 8)
Chain Length:118
Number of Molecules:1
Biological Source:Leishmania donovani
Polymer Type:polypeptide(L)
Molecule:ribosomal protein uL2
Chain IDs:A
Chain Length:125
Number of Molecules:1
Biological Source:Leishmania donovani
Polymer Type:polypeptide(L)
Molecule:ribosomal protein uL3
Chain IDs:B
Chain Length:402
Number of Molecules:1
Biological Source:Leishmania donovani
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L1a, putative
Gene (Uniprot):CGC20_25535, CGC20_25540, CGC20_25545, CGC21_28090, CGC21_28095, CGC21_28100, CGC21_28105, LDBPK_291160, LdCL_290016700, LdCL_290016800, LdCL_290016900, LDHU3_29.1610, LDHU3_29.1620, LDHU3_29.1630
Chain IDs:C
Chain Length:227
Number of Molecules:1
Biological Source:Leishmania donovani
UniProt ID:A0A3S5H7L0 Pfam ID:PF00573, PF14374
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L11 (L5, L16)
Gene (Uniprot):CGC20_15690, CGC20_16800, CGC21_2680, CGC21_32945, LDBPK_220004, LdCL_040010100, LdCL_220005300, LDHU3_04.0620, LDHU3_22.0070
Chain IDs:D
Chain Length:92
Number of Molecules:1
Biological Source:Leishmania donovani
UniProt ID:A0A3S5H5A8 Pfam ID:PF00281, PF00673
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L9, putative
Gene (Uniprot):CGC20_6165, CGC21_36380, LdCL_300039500, LDHU3_30.4490
Chain IDs:E
Chain Length:186
Number of Molecules:1
Biological Source:Leishmania donovani
UniProt ID:A0A3S7X3V0 Pfam ID:PF00347
Polymer Type:polypeptide(L)
Molecule:ribosomal protein eL6
Chain IDs:F
Chain Length:130
Number of Molecules:1
Biological Source:Leishmania donovani
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L7a
Gene (Uniprot):LDBPK_070550
Chain IDs:G
Chain Length:348
Number of Molecules:1
Biological Source:Leishmania donovani
UniProt ID:E9B949 Pfam ID:PF01248
Polymer Type:polypeptide(L)
Molecule:ribosomal protein uL13
Chain IDs:H
Chain Length:221
Number of Molecules:1
Biological Source:Leishmania donovani
Polymer Type:polypeptide(L)
Molecule:ribosomal protein eL13
Chain IDs:I
Chain Length:97
Number of Molecules:1
Biological Source:Leishmania donovani
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L23, putative
Gene (Uniprot):CGC20_14830, CGC20_14835, CGC21_7365, CGC21_7370, LDBPK_353840, LdCL_350043400, LdCL_350043500, LDHU3_35.5000, LDHU3_35.5010
Chain IDs:J
Chain Length:134
Number of Molecules:1
Biological Source:Leishmania donovani
UniProt ID:A0A3Q8IIA7 Pfam ID:PF00238
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Probable 60S ribosomal protein L14
Gene (Uniprot):RPL14
Chain IDs:K
Chain Length:76
Number of Molecules:1
Biological Source:Leishmania donovani
UniProt ID:Q25278 Pfam ID:PF00467, PF01929
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L27A/L29, putative
Gene (Uniprot):CGC20_14840, CGC20_14850, CGC21_7350, CGC21_7360, LDBPK_353810, LdCL_350043100, LdCL_350043300, LDHU3_35.4970, LDHU3_35.4990
Chain IDs:L
Chain Length:50
Number of Molecules:1
Biological Source:Leishmania donovani
UniProt ID:A0A3Q8IGI9 Pfam ID:PF00828
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L15
Chain IDs:M
Chain Length:50
Number of Molecules:1
Biological Source:Leishmania donovani
UniProt ID:E9BMB4 Pfam ID:PF00827
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L10, putative
Gene (Uniprot):CGC20_9400, CGC20_9495, CGC21_2805, CGC21_2905, LDBPK_040750, LdCL_040013100, LdCL_040015100, LDHU3_04.0970, LDHU3_04.1190
Chain IDs:N
Chain Length:33
Number of Molecules:1
Biological Source:Leishmania donovani
UniProt ID:A0A3S5H5C4 Pfam ID:PF00252
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L5, putative
Gene (Uniprot):CGC20_0095, CGC20_0100, CGC20_0105, CGC20_0110, CGC21_6440, CGC21_6445, CGC21_6450, CGC21_6455, CGC21_6460, LDBPK_351870, LdCL_350023600, LdCL_350023700, LdCL_350023800, LdCL_350023900, LdCL_350024000, LDHU3_35.2440, LDHU3_35.2450, LDHU3_35.2460, LDHU3_35.2470, LDHU3_35.2480
Chain IDs:O
Chain Length:90
Number of Molecules:1
Biological Source:Leishmania donovani
UniProt ID:A0A3Q8IJC5 Pfam ID:PF17144, PF14204
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18, putative
Gene (Uniprot):CGC20_27670, CGC21_14640, CGC21_33175, LDBPK_364730, LdCL_130009900, LdCL_360054400, LDHU3_13.0620, LDHU3_36.6360
Chain IDs:P
Chain Length:197
Number of Molecules:1
Biological Source:Leishmania donovani
UniProt ID:A0A3S7XBN1 Pfam ID:PF17135
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L19e family protein
Gene (Uniprot):CGC20_20145
Chain IDs:Q
Chain Length:189
Number of Molecules:1
Biological Source:Leishmania donovani
UniProt ID:A0A504XXD2 Pfam ID:PF01280
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18a
Gene (Uniprot):CGC20_0675, CGC20_33790, CGC21_20030, LdCL_320014900, LDHU3_32.1220, LDHU3_35.0740
Chain IDs:R
Chain Length:178
Number of Molecules:1
Biological Source:Leishmania donovani
UniProt ID:A0A3Q8IT55 Pfam ID:PF01775
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L21, putative
Gene (Uniprot):CGC20_20775, CGC20_36460, CGC21_25130, CGC21_27025, LDBPK_343440, LdCL_160009600, LdCL_340043800, LDHU3_16.0550, LDHU3_34.5670
Chain IDs:S
Chain Length:154
Number of Molecules:1
Biological Source:Leishmania donovani
UniProt ID:A0A3Q8ICH0 Pfam ID:PF01157
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L17, putative
Gene (Uniprot):CGC20_11495, CGC21_15705, LDBPK_240040, LdCL_240005300, LDHU3_24.0060
Chain IDs:T
Chain Length:154
Number of Molecules:1
Biological Source:Leishmania donovani
UniProt ID:A0A3S7WY02 Pfam ID:PF00237
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L22, putative
Gene (Uniprot):CGC20_28260, CGC21_14000, LDBPK_363430, LdCL_360041100, LDHU3_36.4690
Chain IDs:U
Chain Length:121
Number of Molecules:1
Biological Source:Leishmania donovani
UniProt ID:A0A3Q8IJA8 Pfam ID:PF01776
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L23a, putative
Chain IDs:V
Chain Length:118
Number of Molecules:1
Biological Source:Leishmania donovani
UniProt ID:E9B8R9 Pfam ID:PF00276
Polymer Type:polypeptide(L)
Molecule:ribosomal protein uL24
Chain IDs:W
Chain Length:121
Number of Molecules:1
Biological Source:Leishmania donovani
Polymer Type:polypeptide(L)
Molecule:ribosomal protein eL24
Chain IDs:X
Chain Length:65
Number of Molecules:1
Biological Source:Leishmania donovani
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal L27e family protein
Gene (Uniprot):CGC20_34730
Chain IDs:Y
Chain Length:132
Number of Molecules:1
Biological Source:Leishmania donovani
UniProt ID:A0A504XEJ0 Pfam ID:PF01777
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L28, putative
Gene (Uniprot):CGC20_31100, CGC20_31110, CGC21_0695, CGC21_0705, LDBPK_111110, LdCL_110017100, LDHU3_11.1330, LDHU3_11.1350, LDHU3_11.1370
Chain IDs:Z
Chain Length:140
Number of Molecules:1
Biological Source:Leishmania donovani
UniProt ID:A0A3Q8I959 Pfam ID:PF01778
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S_ribosomal_protein_L35_putative/GeneDB:LmjF.26.2330/GeneDB:LmjF.26.2340
Chain IDs:AA (auth: a)
Chain Length:125
Number of Molecules:1
Biological Source:Leishmania donovani
UniProt ID:E9BIP6 Pfam ID:PF00831
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L29
Gene (Uniprot):CGC20_28200, CGC21_14070
Chain IDs:BA (auth: b)
Chain Length:402
Number of Molecules:1
Biological Source:Leishmania donovani
UniProt ID:A0A504XJE6 Pfam ID:PF01779
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L7 family protein
Gene (Uniprot):CGC20_4660
Chain IDs:CA (auth: c)
Chain Length:227
Number of Molecules:1
Biological Source:Leishmania donovani
UniProt ID:A0A504XVT8 Pfam ID:PF08079, PF00327
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L30
Gene (Uniprot):CGC20_0820, CGC21_5735, LDBPK_350240, LdCL_350007400, LDHU3_35.0330
Chain IDs:DA (auth: d)
Chain Length:92
Number of Molecules:1
Biological Source:Leishmania donovani
UniProt ID:A0A3Q8IET6 Pfam ID:PF01248
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal subunit protein L31, putative
Gene (Uniprot):CGC20_15065, CGC20_15070, CGC21_7135, CGC21_7140, LdCL_350038300, LdCL_350038400, LDHU3_35.4380, LDHU3_35.4390
Chain IDs:EA (auth: e)
Chain Length:186
Number of Molecules:1
Biological Source:Leishmania donovani
UniProt ID:A0A3Q8IJL7 Pfam ID:PF01198
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S_ribosomal_protein_L32/GeneDB:LmjF.21.1720
Gene (Uniprot):CGC20_21925, LDHU3_21.2480
Chain IDs:FA (auth: f)
Chain Length:130
Number of Molecules:1
Biological Source:Leishmania donovani
UniProt ID:A0A504XZK6 Pfam ID:PF01655
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L35Ae family protein
Gene (Uniprot):CGC20_21340, CGC20_35910, CGC21_23885, CGC21_26415, LDBPK_342240, LdCL_100005700, LdCL_340030100, LDHU3_10.0110, LDHU3_34.3730
Chain IDs:GA (auth: g)
Chain Length:348
Number of Molecules:1
Biological Source:Leishmania donovani
UniProt ID:A0A3Q8II82 Pfam ID:PF01247
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L34, putative
Gene (Uniprot):LDBPK_363930, LdCL_180019100, LdCL_360046300, LDHU3_18.1760, LDHU3_36.5270
Chain IDs:HA (auth: h)
Chain Length:221
Number of Molecules:1
Biological Source:Leishmania donovani
UniProt ID:A0A3Q8IHK2 Pfam ID:PF01199
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L36, putative
Gene (Uniprot):CGC21_34065, LDBPK_210800, LdCL_210012900, LDHU3_21.0900
Chain IDs:IA (auth: i)
Chain Length:97
Number of Molecules:1
Biological Source:Leishmania donovani
UniProt ID:A0A3Q8IDW6 Pfam ID:PF01158
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L37
Gene (Uniprot):RPL37
Chain IDs:JA (auth: j)
Chain Length:134
Number of Molecules:1
Biological Source:Leishmania donovani
UniProt ID:P62885 Pfam ID:PF01907
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal L38e family protein
Gene (Uniprot):CGC21_32395
Chain IDs:KA (auth: k)
Chain Length:76
Number of Molecules:1
Biological Source:Leishmania donovani
UniProt ID:A0A504WZU0 Pfam ID:PF01781
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L39, putative
Chain IDs:LA (auth: l)
Chain Length:50
Number of Molecules:1
Biological Source:Leishmania donovani
UniProt ID:E9BCX6 Pfam ID:PF00832
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ubiquitin-60S ribosomal protein L40
Gene (Uniprot):CGC20_3125, CGC20_3180, CGC21_11230, CGC21_11280, CGC21_36880, LDBPK_311930, LdCL_090014900, LdCL_310027200, LdCL_310028700, LDHU3_31.3500, LDHU3_31.3730
Chain IDs:MA (auth: m)
Chain Length:50
Number of Molecules:1
Biological Source:Leishmania donovani
UniProt ID:A0A3Q8ISR1 Pfam ID:PF01020
Polymer Type:polypeptide(L)
Molecule:ribosomal protein eL41
Chain IDs:NA (auth: n)
Chain Length:33
Number of Molecules:1
Biological Source:Leishmania donovani
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L37a
Chain IDs:OA (auth: o)
Chain Length:90
Number of Molecules:1
Biological Source:Leishmania donovani
UniProt ID:E9BFK4 Pfam ID:PF01780
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L44, putative
Chain IDs:PA (auth: p)
Chain Length:197
Number of Molecules:1
Biological Source:Leishmania donovani
UniProt ID:E9BBL5 Pfam ID:PF00935
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
A2M QA A modified residue
OMC QA C modified residue
OMG QA G modified residue
OMU QA U modified residue
Ligand Molecules
MG
PAR
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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
6AZ1