3JCS image
Deposition Date 2016-01-21
Release Date 2016-07-20
Last Version Date 2025-06-11
Entry Detail
PDB ID:
3JCS
Keywords:
Title:
2.8 Angstrom cryo-EM structure of the large ribosomal subunit from the eukaryotic parasite Leishmania
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
2.80 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:26S alpha ribosomal RNA
Chain IDs:A (auth: 1)
Chain Length:1782
Number of Molecules:1
Biological Source:Leishmania donovani
Polymer Type:polyribonucleotide
Molecule:26S delta ribosomal RNA
Chain IDs:B (auth: 2)
Chain Length:1527
Number of Molecules:1
Biological Source:Leishmania donovani
Polymer Type:polyribonucleotide
Molecule:26S gamma ribosomal RNA
Chain IDs:C (auth: 3)
Chain Length:213
Number of Molecules:1
Biological Source:Leishmania donovani
Polymer Type:polyribonucleotide
Molecule:26S delta ribosomal RNA
Chain IDs:D (auth: 4)
Chain Length:183
Number of Molecules:1
Biological Source:Leishmania donovani
Polymer Type:polyribonucleotide
Molecule:26S epsilon ribosomal RNA
Chain IDs:E (auth: 5)
Chain Length:133
Number of Molecules:1
Biological Source:Leishmania donovani
Polymer Type:polyribonucleotide
Molecule:26S zeta ribosomal RNA
Chain IDs:F (auth: 6)
Chain Length:76
Number of Molecules:1
Biological Source:Leishmania donovani
Polymer Type:polyribonucleotide
Molecule:5.8S ribosomal RNA
Chain IDs:G (auth: 7)
Chain Length:171
Number of Molecules:1
Biological Source:Leishmania donovani
Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:H (auth: 8)
Chain Length:121
Number of Molecules:1
Biological Source:Leishmania donovani
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L2
Chain IDs:I (auth: A)
Chain Length:127
Number of Molecules:1
Biological Source:Leishmania donovani
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L3
Chain IDs:J (auth: B)
Chain Length:419
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L4
Chain IDs:K (auth: C)
Chain Length:373
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L5
Chain IDs:L (auth: D)
Chain Length:104
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L6
Chain IDs:M (auth: E)
Chain Length:190
Number of Molecules:1
Biological Source:Leishmania donovani
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L6e
Chain IDs:N (auth: F)
Chain Length:133
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L8e
Gene (Uniprot):LDBPK_070550
Chain IDs:O (auth: G)
Chain Length:144
Number of Molecules:1
Biological Source:Leishmania donovani
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L13
Chain IDs:P (auth: H)
Chain Length:222
Number of Molecules:1
Biological Source:Leishmania donovani
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L13e
Chain IDs:Q (auth: I)
Chain Length:105
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L14
Chain IDs:R (auth: J)
Chain Length:83
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L14e
Gene (Uniprot):LDBPK_221370
Chain IDs:S (auth: K)
Chain Length:233
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L15
Chain IDs:T (auth: L)
Chain Length:51
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L15e
Gene (Uniprot):CGC20_0090, CGC20_6005, CGC21_36545, CGC21_6465, LDBPK_303710, LDBPK_351890, LdCL_300042500, LdCL_350024100, LDHU3_30.4940
Chain IDs:U (auth: M)
Chain Length:204
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L16
Chain IDs:V (auth: N)
Chain Length:213
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L18
Chain IDs:W (auth: O)
Chain Length:305
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L18e
Chain IDs:X (auth: P)
Chain Length:198
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L19e
Gene (Uniprot):CGC21_24350, LDBPK_060410
Chain IDs:Y (auth: Q)
Chain Length:245
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L20e
Chain IDs:Z (auth: R)
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 L21e
Chain IDs:AA (auth: S)
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 L22
Chain IDs:BA (auth: T)
Chain Length:166
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L22e
Chain IDs:CA (auth: U)
Chain Length:129
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L23
Gene (Uniprot):CGC20_20065, CGC20_20070, CGC21_24275, CGC21_24280, LDBPK_060590, LDBPK_060600, LdCL_060011000, LdCL_060011100, LDHU3_06.0690, LDHU3_06.0700
Chain IDs:DA (auth: V)
Chain Length:145
Number of Molecules:1
Biological Source:Leishmania donovani
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L24
Chain IDs:EA (auth: W)
Chain Length:143
Number of Molecules:1
Biological Source:Leishmania donovani
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L24e
Chain IDs:FA (auth: X)
Chain Length:124
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L27e
Gene (Uniprot):CGC20_34735, CGC21_20965, LDBPK_322830, LDBPK_322850, LdCL_320034200, LdCL_320034400, LDHU3_32.3590, LDHU3_32.3610
Chain IDs:GA (auth: Y)
Chain Length:134
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L28e
Chain IDs:HA (auth: Z)
Chain Length:147
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L29
Gene (Uniprot):CGC20_5605, CGC20_5610, CGC21_32450, CGC21_32455, LDBPK_262350, LDBPK_262360, LDHU3_26.3070, LDHU3_26.3080
Chain IDs:IA (auth: a)
Chain Length:127
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L29e
Gene (Uniprot):LDBPK_363550, LDBPK_363560, LdCL_360042500, LdCL_360042600, LDHU3_36.4830
Chain IDs:JA (auth: b)
Chain Length:419
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L30
Gene (Uniprot):LDBPK_260160
Chain IDs:KA (auth: c)
Chain Length:373
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L30e
Chain IDs:LA (auth: d)
Chain Length:104
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L31e
Gene (Uniprot):LDBPK_353330, LDBPK_353340
Chain IDs:MA (auth: e)
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 L32e
Chain IDs:NA (auth: f)
Chain Length:133
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L33e
Chain IDs:OA (auth: g)
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 L34e
Chain IDs:PA (auth: h)
Chain Length:222
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L36e
Chain IDs:QA (auth: i)
Chain Length:105
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L37e
Chain IDs:RA (auth: j)
Chain Length:83
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L38e
Gene (Uniprot):LDBPK_030240, LDBPK_262230, LdCL_030007400, LdCL_260028000, LDHU3_03.0250, LDHU3_26.2920
Chain IDs:SA (auth: k)
Chain Length:233
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L39e
Gene (Uniprot):LDBPK_161220, LDBPK_292480, LdCL_160017400, LdCL_290030800, LDHU3_16.1490, LDHU3_29.3680
Chain IDs:TA (auth: l)
Chain Length:51
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L43e
Gene (Uniprot):LDBPK_212190, LDBPK_362020, LdCL_210027600, LdCL_360025700, LDHU3_21.2600, LDHU3_36.2630
Chain IDs:UA (auth: m)
Chain Length:204
Number of Molecules:1
Biological Source:Leishmania donovani
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ribosomal protein L44e
Gene (Uniprot):CGC20_16835, CGC20_9735, CGC21_33710, CGC21_5530, LDBPK_131410, LDBPK_333380, LdCL_130021400, LdCL_330041500, LDHU3_13.1930, LDHU3_33.4890
Chain IDs:VA (auth: n)
Chain Length:213
Number of Molecules:1
Biological Source:Leishmania donovani
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
A2M A A ?
H2U B U 5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE
OMC A C O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE
OMG A G O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE
OMU A U O2'-METHYLURIDINE 5'-MONOPHOSPHATE
Ligand Molecules
Primary Citation
2.8- angstrom Cryo-EM Structure of the Large Ribosomal Subunit from the Eukaryotic Parasite Leishmania.
Cell Rep 16 288 294 (2016)
PMID: 27373148 DOI: 10.1016/j.celrep.2016.06.014

Abstact

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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures