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- PDB-6az3: Cryo-EM structure of of the large subunit of Leishmania ribosome ... -

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Basic information

Entry
Database: PDB / ID: 6az3
TitleCryo-EM structure of of the large subunit of Leishmania ribosome bound to paromomycin
Components
  • (60S ribosomal protein ...) x 23
  • (Ribosomal protein ...) x 12
  • 60S ribosomal subunit protein L31, putative
  • 60S_ribosomal_protein_L32/GeneDB:LmjF.21.1720
  • 60S_ribosomal_protein_L35_putative/GeneDB:LmjF.26.2330/GeneDB:LmjF.26.2340
  • Probable 60S ribosomal protein L14
  • Ribosomal L27e family protein
  • Ribosomal L38e family protein
  • Ubiquitin-60S ribosomal protein L40
  • rRNA 5.8S
  • rRNA 5S
  • rRNA alpha
  • rRNA beta
  • rRNA delta
  • rRNA epsilon
  • rRNA gamma
  • rRNA zeta
KeywordsRIBOSOME/ANTIBIOTIC / Leishmania / ribosome / aminoglycoside / paromomycin / RIBOSOME-ANTIBIOTIC complex
Function / homology
Function and homology information


maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / large ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / ribosome / rRNA binding / structural constituent of ribosome / translation / ribonucleoprotein complex / RNA binding ...maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / large ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / ribosome / rRNA binding / structural constituent of ribosome / translation / ribonucleoprotein complex / RNA binding / membrane / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L28e / Ribosomal protein L23 / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L38e ...Ribosomal protein L28e / Ribosomal protein L23 / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal L40e family / Ribosomal protein L44e signature. / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L19, eukaryotic / Ribosomal protein L10e / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein L5 eukaryotic, C-terminal / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal L18 C-terminal region / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L30e signature 1. / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / 60S ribosomal protein L19 / 60S ribosomal protein L35 / Ribosomal protein L34Ae / Ribosomal protein L34e / Ribosomal protein L7, eukaryotic / Ribosomal protein L30, N-terminal / Ribosomal L30 N-terminal domain / Ribosomal protein L30/YlxQ / Ribosomal protein L7A/L8 / Ribosomal protein L18e / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L4 C-terminal domain / Ribosomal_L19e / Ribosomal protein L19/L19e / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L19e / Ribosomal protein L36e / Ribosomal protein L37ae / Ribosomal protein L36e domain superfamily / Ribosomal protein L36e / Ribosomal L37ae protein family / Ribosomal protein L14e domain / Ribosomal protein L14 / Ribosomal protein L35A / Ribosomal protein L35Ae / Ribosomal protein L39e / Ribosomal protein L39e domain superfamily / Ribosomal L39 protein / Ribosomal protein L35A superfamily / Ribosomal protein L5 eukaryotic/L18 archaeal / Ribosomal large subunit proteins 60S L5, and 50S L18 / Ribosomal protein L14 / Ribosomal protein L6, conserved site-2 / Ribosomal protein L6 signature 2. / Ribosomal protein L14, KOW motif / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / Ribosomal protein L1e signature. / Ribosomal protein L31e / Ribosomal protein L31e domain superfamily / Ribosomal protein L31e / Ribosomal_L31e / Ribosomal protein L21e / Ribosomal protein L21e, conserved site / Ribosomal protein L21 superfamily / Ribosomal protein L21e / Ribosomal protein L21e signature. / Ribosomal protein L4, eukaryotic and archaeal type / Ribosomal protein L22/L17, eukaryotic/archaeal / Ribosomal protein L7, eukaryotic/archaeal / Ribosomal protein L7/L30 / Ribosomal protein L37e, conserved site / Ribosomal protein L37e signature. / Ribosomal protein L37e / Ribosomal protein L37e / Ribosomal_L15e / Ribosomal protein L15e / Ribosomal protein L15e core domain superfamily / Ribosomal L15 / Ribosomal protein L37ae/L37e / Ribosomal protein L32e
Similarity search - Domain/homology
PAROMOMYCIN / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 60S ribosomal protein L28, putative ...PAROMOMYCIN / : / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 60S ribosomal protein L28, putative / 60S ribosomal protein L39, putative / 60S ribosomal protein L37a / 60S ribosomal protein L21, putative / 60S ribosomal protein L36, putative / 60S ribosomal protein L30 / 60S ribosomal protein L27A/L29, putative / 60S ribosomal protein L34, putative / Ribosomal protein L35Ae family protein / 60S ribosomal protein L23, putative / Ribosomal protein L15 / 60S ribosomal protein L22, putative / 60S ribosomal protein L5, putative / 60S ribosomal subunit protein L31, putative / 60S ribosomal protein L44, putative / Ubiquitin-60S ribosomal protein L40 / 60S ribosomal protein L18a / 60S ribosomal protein L11 (L5, L16) / 60S ribosomal protein L10, putative / Ribosomal protein L1a, putative / 60S ribosomal protein L23a, putative / 60S ribosomal protein L17, putative / 60S ribosomal protein L9, putative / 60S ribosomal protein L18, putative / Ribosomal L38e family protein / Ribosomal L27e family protein / 60S ribosomal protein L29 / 60S ribosomal protein L7 family protein / 60S_ribosomal_protein_L35_putative/GeneDB:LmjF.26.2330/GeneDB:LmjF.26.2340 / Ribosomal protein L19e family protein / 60S_ribosomal_protein_L32/GeneDB:LmjF.21.1720 / Ribosomal protein L38, putative / 60S ribosomal protein L10, putative / 60S ribosomal protein L19, putative / 60S ribosomal protein L23a, putative / 60S ribosomal protein L7a / 60S ribosomal protein L28, putative / 60S ribosomal protein L44, putative / 60S ribosomal protein L39, putative / 60S ribosomal protein L36, Putative / 60S ribosomal protein L9, putative / 60S ribosomal protein L32 / 60S ribosomal protein L37a / 60S ribosomal protein L11 (L5, L16) / 60S ribosomal protein L17, putative / 60S ribosomal protein L7, putative / 60S ribosomal protein L35, putative / Ribosomal protein L1a, putative / Ribosomal protein L15 / Ubiquitin-60S ribosomal protein L40 / Ribosomal L27e family protein / Ribosomal protein L35Ae family protein / 60S ribosomal protein L21, putative / 60S ribosomal protein L30 / 60S ribosomal protein L18a / 60S ribosomal protein L5, putative / 60S ribosomal subunit protein L31, putative / 60S ribosomal protein L27A/L29, putative / 60S ribosomal protein L23, putative / Large ribosomal subunit protein eL22 / 60S ribosomal protein L29 / Large ribosomal subunit protein eL34 / 60S ribosomal protein L18, putative / Large ribosomal subunit protein eL37 / Probable 60S ribosomal protein L14
Similarity search - Component
Biological speciesLeishmania donovani (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsShalev-Benami, M. / Zhang, Y. / Rozenberg, H. / Nobe, Y. / Taoka, M. / Matzov, D. / Zimmerman, E. / Bashan, A. / Isobe, T. / Jaffe, C.L. ...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.
CitationJournal: Nat Commun / Year: 2017
Title: Atomic resolution snapshot of Leishmania ribosome inhibition by the aminoglycoside paromomycin.
Authors: Moran Shalev-Benami / Yan Zhang / Haim Rozenberg / Yuko Nobe / Masato Taoka / Donna Matzov / Ella Zimmerman / Anat Bashan / Toshiaki Isobe / Charles L Jaffe / Ada Yonath / Georgios Skiniotis /
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 ...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.
History
DepositionSep 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Apr 13, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / entity / entity_name_com / entity_src_nat / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_mod_residue / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / struct_asym / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _entity_src_nat.strain / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: ribosomal protein uL2
B: ribosomal protein uL3
C: Ribosomal protein L1a, putative
D: 60S ribosomal protein L11 (L5, L16)
E: 60S ribosomal protein L9, putative
F: ribosomal protein eL6
G: 60S ribosomal protein L7a
H: ribosomal protein uL13
I: ribosomal protein eL13
J: 60S ribosomal protein L23, putative
K: Probable 60S ribosomal protein L14
L: 60S ribosomal protein L27A/L29, putative
M: Ribosomal protein L15
N: 60S ribosomal protein L10, putative
O: 60S ribosomal protein L5, putative
P: 60S ribosomal protein L18, putative
Q: Ribosomal protein L19e family protein
R: 60S ribosomal protein L18a
S: 60S ribosomal protein L21, putative
T: 60S ribosomal protein L17, putative
U: 60S ribosomal protein L22, putative
V: 60S ribosomal protein L23a, putative
W: ribosomal protein uL24
X: ribosomal protein eL24
Y: Ribosomal L27e family protein
Z: 60S ribosomal protein L28, putative
a: 60S_ribosomal_protein_L35_putative/GeneDB:LmjF.26.2330/GeneDB:LmjF.26.2340
b: 60S ribosomal protein L29
c: 60S ribosomal protein L7 family protein
d: 60S ribosomal protein L30
e: 60S ribosomal subunit protein L31, putative
f: 60S_ribosomal_protein_L32/GeneDB:LmjF.21.1720
g: Ribosomal protein L35Ae family protein
h: 60S ribosomal protein L34, putative
i: 60S ribosomal protein L36, putative
j: 60S ribosomal protein L37
k: Ribosomal L38e family protein
l: 60S ribosomal protein L39, putative
m: Ubiquitin-60S ribosomal protein L40
n: ribosomal protein eL41
o: 60S ribosomal protein L37a
p: 60S ribosomal protein L44, putative
1: rRNA alpha
2: rRNA beta
3: rRNA gamma
4: rRNA delta
5: rRNA epsilon
6: rRNA zeta
7: rRNA 5.8S
8: rRNA 5S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,119,49094
Polymers2,112,50750
Non-polymers6,98344
Water18,3571019
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area501950 Å2
ΔGint-3861 kcal/mol
Surface area579000 Å2

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Components

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Ribosomal protein ... , 12 types, 12 molecules ABCFHIMQWXgn

#1: Protein ribosomal protein uL2 /


Mass: 27520.994 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote)
#2: Protein ribosomal protein uL3 /


Mass: 45741.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote)
#3: Protein Ribosomal protein L1a, putative / Ribosome / Ribosomal protein L4/L1 family protein / Ribosomal_protein_L1a_putative/GeneDB:LmjF.29.107 0/GeneDB: ...Ribosomal protein L4/L1 family protein / Ribosomal_protein_L1a_putative/GeneDB:LmjF.29.107 0/GeneDB:LmjF.29.1090


Mass: 40523.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: A0A3S5H7L0, UniProt: E9BKR3*PLUS
#6: Protein ribosomal protein eL6 /


Mass: 21208.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote)
#8: Protein ribosomal protein uL13 /


Mass: 25346.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote)
#9: Protein ribosomal protein eL13 /


Mass: 23897.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote)
#13: Protein Ribosomal protein L15 /


Mass: 24366.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: A0A3Q8IIZ6, UniProt: E9BMB4*PLUS
#17: Protein Ribosomal protein L19e family protein / Ribosome


Mass: 22901.018 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: A0A504XXD2, UniProt: E9B8Q2*PLUS
#23: Protein ribosomal protein uL24 /


Mass: 13874.408 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote)
#24: Protein ribosomal protein eL24 /


Mass: 7988.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote)
#33: Protein Ribosomal protein L35Ae family protein / Ribosome / Ribosomal protein l35a / putative / Ribosomal_protein_l35a_putative/GeneDB:LmjF.10.00 70/GeneDB:LmjF.34.2470


Mass: 14336.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: A0A3Q8II82, UniProt: E9BR22*PLUS
#40: Protein/peptide ribosomal protein eL41 /


Mass: 4259.300 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote)

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60S ribosomal protein ... , 23 types, 23 molecules DEGJLNOPRSTUVZbcdhijlop

#4: Protein 60S ribosomal protein L11 (L5, L16) / Ribosome / 60S_ribosomal_protein_L11_(L5_L16)/GeneDB:LmjF.04.0470/GeneDB:LmjF.22.0030 / ADP-ribosylation_ ...60S_ribosomal_protein_L11_(L5_L16)/GeneDB:LmjF.04.0470/GeneDB:LmjF.22.0030 / ADP-ribosylation_factor_putative/GeneDB:LmjF.04.0 480 / Ribosomal L5P C-terminus family protein


Mass: 19245.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: A0A3S5H5A8, UniProt: E9BFL1*PLUS
#5: Protein 60S ribosomal protein L9, putative / Ribosome / 60S_ribosomal_protein_L9_putative/GeneDB:LmjF.21. 1050/GeneDB:LmjF.30.3340 / Ribosomal protein L6 ...60S_ribosomal_protein_L9_putative/GeneDB:LmjF.21. 1050/GeneDB:LmjF.30.3340 / Ribosomal protein L6 family protein


Mass: 21118.717 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: A0A3S7X3V0, UniProt: E9BFB5*PLUS
#7: Protein 60S ribosomal protein L7a /


Mass: 39175.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / Strain: BPK282A1 / References: UniProt: E9B949
#10: Protein 60S ribosomal protein L23, putative / Ribosome / 60S_ribosomal_protein_L23_putative/GeneDB:LmjF.35.3790/GeneDB:LmjF.35.3800 / Ribosomal protein ...60S_ribosomal_protein_L23_putative/GeneDB:LmjF.35.3790/GeneDB:LmjF.35.3800 / Ribosomal protein L14p/L23e family protein


Mass: 14421.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: A0A3Q8IIA7, UniProt: E9BSQ4*PLUS
#12: Protein 60S ribosomal protein L27A/L29, putative / Ribosome / 60S_ribosomal_protein_L27A/L29_putative/GeneDB:Lm jF.35.3760/GeneDB:LmjF.35.3780 / Ribosomal ...60S_ribosomal_protein_L27A/L29_putative/GeneDB:Lm jF.35.3760/GeneDB:LmjF.35.3780 / Ribosomal protein L18e/L15 family protein


Mass: 16034.684 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: A0A3Q8IGI9, UniProt: E9BSQ2*PLUS
#14: Protein 60S ribosomal protein L10, putative / Ribosome / 60S_ribosomal_protein_L10_putative/GeneDB:LmjF.04.0750/GeneDB:LmjF.04.0950 / Hypothetical_protein / ...60S_ribosomal_protein_L10_putative/GeneDB:LmjF.04.0750/GeneDB:LmjF.04.0950 / Hypothetical_protein / Ribosomal protein L10.e


Mass: 24607.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: A0A3S5H5C4, UniProt: E9B840*PLUS
#15: Protein 60S ribosomal protein L5, putative / Ribosome / 60S_ribosomal_protein_L5_putative/GeneDB:LmjF.35. 1880/GeneDB:LmjF.35.1890/GeneDB:LmjF.35.1900 / ...60S_ribosomal_protein_L5_putative/GeneDB:LmjF.35. 1880/GeneDB:LmjF.35.1890/GeneDB:LmjF.35.1900 / Ribosomal L18p/L5e family protein


Mass: 34100.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: A0A3Q8IJC5, UniProt: E9BS61*PLUS
#16: Protein 60S ribosomal protein L18, putative / Ribosome / 60S_ribosomal_protein_L18_putative/GeneDB:LmjF.13.0560/GeneDB:LmjF.36.4510 / Ribosomal protein ...60S_ribosomal_protein_L18_putative/GeneDB:LmjF.13.0560/GeneDB:LmjF.36.4510 / Ribosomal protein L18e/L15 family protein


Mass: 21939.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: A0A3S7XBN1, UniProt: E9BUI1*PLUS
#18: Protein 60S ribosomal protein L18a /


Mass: 20703.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: A0A3Q8IT55, UniProt: E9BRT7*PLUS
#19: Protein 60S ribosomal protein L21, putative / Ribosome / 60S_ribosomal_protein_L21_putative/GeneDB:LmjF.16.0460/GeneDB:LmjF.34.3650 / Ribosomal protein L21e ...60S_ribosomal_protein_L21_putative/GeneDB:LmjF.16.0460/GeneDB:LmjF.34.3650 / Ribosomal protein L21e family protein


Mass: 17437.443 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: A0A3Q8ICH0, UniProt: E9BRE2*PLUS
#20: Protein 60S ribosomal protein L17, putative / Ribosome / Ribosomal protein L22 / Ribosomal_protein_L22p/L17e_putative/Pfam:PF00237


Mass: 17828.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: A0A3S7WY02, UniProt: E9BGL6*PLUS
#21: Protein 60S ribosomal protein L22, putative / Ribosome / 60S_ribosomal_protein_L22_putative/GeneDB:LmjF.36.3270/GeneDB:LmjF.36.4420 / Ribosomal L22e family protein


Mass: 14042.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: A0A3Q8IJA8, UniProt: E9BU52*PLUS
#22: Protein 60S ribosomal protein L23a, putative / Ribosome / 60S_ribosomal_protein_L23a_putative/GeneDB:LmjF.0 6.0570/GeneDB:LmjF.06.0580 / Archaeal ribosomal protein L23


Mass: 13461.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: A0A3S7WPH7, UniProt: E9B8R9*PLUS
#26: Protein 60S ribosomal protein L28, putative / Ribosome / 60S_ribosomal_protein_L28_putative/GeneDB:LmjF.11.1110/GeneDB:LmjF.11.1130 / Ribosomal L28e family protein


Mass: 15525.923 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: A0A3Q8I959, UniProt: E9BAU9*PLUS
#28: Protein 60S ribosomal protein L29 /


Mass: 7788.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: A0A504XJE6, UniProt: E9BU64*PLUS
#29: Protein 60S ribosomal protein L7 family protein / Ribosome


Mass: 26313.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: A0A504XVT8, UniProt: E9BI29*PLUS
#30: Protein 60S ribosomal protein L30 / / 60S_ribosomal_protein_L30/GeneDB:LmjF.35.0240 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family protein


Mass: 10122.675 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: A0A3Q8IET6, UniProt: E9BRQ6*PLUS
#34: Protein 60S ribosomal protein L34, putative / Ribosome / 60S_ribosomal_protein_L34_putative/GeneDB:LmjF.18.1400


Mass: 14640.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: A0A3Q8IHK2, UniProt: E9BUA1*PLUS
#35: Protein 60S ribosomal protein L36, putative / Ribosome / 60S_ribosomal_protein_L36_putative/GeneDB:LmjF.21.0730 / Ribosomal protein L36e family protein


Mass: 11050.092 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: A0A3Q8IDW6, UniProt: E9BF65*PLUS
#36: Protein 60S ribosomal protein L37 /


Mass: 9531.135 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: P62885
#38: Protein/peptide 60S ribosomal protein L39, putative / Ribosome / 60S_ribosomal_protein_L39_putative/GeneDB:LmjF.16.1170/GeneDB:LmjF.29.2370


Mass: 6373.649 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: A0A3Q8IAG7, UniProt: E9BCX6*PLUS
#41: Protein 60S ribosomal protein L37a / / 60S_ribosomal_protein_L37a/GeneDB:LmjF.36.1925


Mass: 10092.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: A0A3Q8IC65, UniProt: E9BFK4*PLUS
#42: Protein 60S ribosomal protein L44, putative / Ribosome / 60S_ribosomal_protein_L44_putative/GeneDB:LmjF.13.1670 / Ribosomal protein L44 family protein


Mass: 11141.353 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: A0A3Q8IKJ4, UniProt: E9BBL5*PLUS

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Protein , 6 types, 6 molecules KYaefk

#11: Protein Probable 60S ribosomal protein L14 / 23 kDa cell surface protein / LDP 23


Mass: 17038.955 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: Q25278
#25: Protein Ribosomal L27e family protein


Mass: 15223.005 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: A0A504XEJ0, UniProt: E9BP34*PLUS
#27: Protein 60S_ribosomal_protein_L35_putative/GeneDB:LmjF.26.2330/GeneDB:LmjF.26.2340 / Ribosomal L29 family protein


Mass: 14987.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: A0A504XWA8, UniProt: E9BIP6*PLUS
#31: Protein 60S ribosomal subunit protein L31, putative / / 60S_ribosomal_subunit_protein_L31_putative/GeneDB:LmjF.35.3280/GeneDB:LmjF.35.3290 / Ribosomal ...60S_ribosomal_subunit_protein_L31_putative/GeneDB:LmjF.35.3280/GeneDB:LmjF.35.3290 / Ribosomal protein L31e family protein


Mass: 13503.024 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: A0A3Q8IJL7, UniProt: E9BSK4*PLUS
#32: Protein 60S_ribosomal_protein_L32/GeneDB:LmjF.21.1720 / Ribosomal protein L32 family protein


Mass: 15029.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: A0A504XZK6, UniProt: E9BFJ5*PLUS
#37: Protein Ribosomal L38e family protein


Mass: 8761.474 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: A0A504WZU0, UniProt: E9B7P2*PLUS

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Protein/peptide , 1 types, 1 molecules m

#39: Protein/peptide Ubiquitin-60S ribosomal protein L40


Mass: 5912.278 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: UniProt: A0A3Q8ISR1, UniProt: E9BMW6*PLUS

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RNA chain , 8 types, 8 molecules 12345678

#43: RNA chain rRNA alpha


Mass: 575707.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: GenBank: 322500086
#44: RNA chain rRNA beta


Mass: 492460.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: GenBank: 322500086
#45: RNA chain rRNA gamma


Mass: 67568.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: GenBank: 322500086
#46: RNA chain rRNA delta


Mass: 59144.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: GenBank: 5019758
#47: RNA chain rRNA epsilon


Mass: 42869.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: GenBank: 5019758
#48: RNA chain rRNA zeta


Mass: 22725.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: GenBank: 5019758
#49: RNA chain rRNA 5.8S


Mass: 54989.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: GenBank: 1229082208
#50: RNA chain rRNA 5S


Mass: 37923.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) / References: GenBank: 1229082190

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Non-polymers , 3 types, 1063 molecules

#51: Chemical
ChemComp-PAR / PAROMOMYCIN / PAROMOMYCIN I / AMMINOSIDIN / CATENULIN / CRESTOMYCIN / MONOMYCIN A / NEOMYCIN E / Paromomycin


Mass: 615.628 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C23H45N5O14 / Comment: Antimicrobial, medication*YM
#52: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 34 / Source method: obtained synthetically / Formula: Mg
#53: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1019 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Leishmania donovani 91S ribosome LSU / Type: RIBOSOME / Entity ID: #1-#50 / Source: NATURAL
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Leishmania donovani (eukaryote)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 1 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 141028 / Symmetry type: POINT

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