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- PDB-7ane: Leishmania Major mitochondrial ribosome -

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Basic information

Entry
Database: PDB / ID: 7ane
TitleLeishmania Major mitochondrial ribosome
Components
  • (Peptidyl-prolyl cis-trans ...) x 2
  • (Putative ribosomal protein ...) x 3
  • 30S Ribosomal protein S17-like protein
  • 50S ribosomal protein L13-like protein
  • AKAP7_NLS domain-containing protein
  • C2H2-type domain-containing protein
  • Excreted/secreted protein 15
  • L51_S25_CI-B8 domain-containing protein
  • LIM zinc-binding domain-containing protein
  • Large ribosomal RNA
  • MRP-L46 domain-containing protein
  • Protein FYV4, mitochondrial
  • Putative 50S ribosomal protein L17
  • Putative superoxide dismutase
  • RIBOSOMAL_L9 domain-containing protein
  • Rhodanese domain-containing protein
  • Ribosomal protein L3-like protein
  • Ribosomal_L16 domain-containing protein
  • Ribosomal_L18e/L15P domain-containing protein
  • Ribosomal_S5_C domain-containing protein
  • UA
  • UB
  • UC
  • UD
  • Ubiquitin-like domain-containing protein
  • bL19m
  • bL20m
  • bL21m
  • bL27m
  • bL28m
  • bL31m
  • bL32m
  • bL33m
  • bL35m
  • bL36m
  • bS16m
  • bS18m
  • bS21m
  • bS6m
  • mL100
  • mL38
  • mL40
  • mL41
  • mL42
  • mL49
  • mL52
  • mL53
  • mL59/64
  • mL63
  • mL68
  • mL69
  • mL70
  • mL72
  • mL73
  • mL74
  • mL75
  • mL76
  • mL79
  • mL80
  • mL82
  • mL84
  • mL85
  • mL86
  • mL87
  • mL88
  • mL89
  • mL93
  • mL94
  • mL95
  • mL96
  • mL97
  • mL98
  • mL99
  • mS22
  • mS23
  • mS26
  • mS29
  • mS33
  • mS34
  • mS35
  • mS37
  • mS43
  • mS47
  • mS48
  • mS49
  • mS50
  • mS51
  • mS52
  • mS53
  • mS55
  • mS56
  • mS57
  • mS58
  • mS59
  • mS60
  • mS61
  • mS62
  • mS63
  • mS65
  • mS66
  • mS69
  • mS70
  • mS71
  • mS72
  • mS73
  • uL10m
  • uL22m
  • uL23m
  • uL24m
  • uL29m
  • uL30m
  • uL4m
  • uS10m
  • uS11m
  • uS14m
  • uS15m
  • uS19m
  • uS3m
  • uS8m
  • uS9m
KeywordsRIBOSOME / Mitochondria / Kinetoplastid
Function / homology
Function and homology information


medium-chain fatty acid-CoA ligase activity / kinetoplast / thiosulfate-cyanide sulfurtransferase activity / ciliary plasm / mitochondrial large ribosomal subunit / nuclear lumen / mRNA stabilization / mitochondrial ribosome / mitochondrial small ribosomal subunit / mitochondrial translation ...medium-chain fatty acid-CoA ligase activity / kinetoplast / thiosulfate-cyanide sulfurtransferase activity / ciliary plasm / mitochondrial large ribosomal subunit / nuclear lumen / mRNA stabilization / mitochondrial ribosome / mitochondrial small ribosomal subunit / mitochondrial translation / cyclosporin A binding / superoxide dismutase / fatty acid beta-oxidation / protein kinase A regulatory subunit binding / superoxide dismutase activity / RNA processing / removal of superoxide radicals / peptidyl-prolyl cis-trans isomerase activity / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / fatty acid metabolic process / mitochondrion organization / peptidylprolyl isomerase / protein folding / large ribosomal subunit / large ribosomal subunit rRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / mitochondrion / RNA binding / nucleoplasm / metal ion binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Nucleoid-associated protein YbaB-like domain superfamily / : / Protein kinase A anchor protein, nuclear localisation signal domain / AKAP7 2'5' RNA ligase-like domain / Probable Zinc-ribbon domain / Probable Treble clef zinc finger domain / : / Small ribosomal subunit protein mS41 SAM domain / PPR repeat family / Enoyl-CoA hydratase/isomerase domain ...Nucleoid-associated protein YbaB-like domain superfamily / : / Protein kinase A anchor protein, nuclear localisation signal domain / AKAP7 2'5' RNA ligase-like domain / Probable Zinc-ribbon domain / Probable Treble clef zinc finger domain / : / Small ribosomal subunit protein mS41 SAM domain / PPR repeat family / Enoyl-CoA hydratase/isomerase domain / Enoyl-CoA hydratase/isomerase / Protein Fyv4 / IGR protein motif / IGR / Cyclic phosphodiesterase / Rhodanese Homology Domain / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / Pentatricopeptide (PPR) repeat profile. / Ribosomal protein S23/S29, mitochondrial / Mitochondrial ribosomal death-associated protein 3 / Pentatricopeptide repeat / Ribosomal protein L46, N-terminal / Rhodanese-like domain / 39S mitochondrial ribosomal protein L46 / 39S ribosomal protein L46, mitochondrial / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / LysM domain / Manganese/iron superoxide dismutase, C-terminal / Manganese/iron superoxide dismutase, C-terminal domain superfamily / Manganese/iron superoxide dismutase, N-terminal domain superfamily / 39S ribosomal protein L43/54S ribosomal protein L51 / Iron/manganese superoxide dismutases, C-terminal domain / Ribosomal protein L47, mitochondrial / MRP-L47 superfamily, mitochondrial / Mitochondrial 39-S ribosomal protein L47 (MRP-L47) / Phosphatidylethanolamine-binding protein, eukaryotic / PEBP-like superfamily / LysM domain / AMP-dependent synthetase/ligase / AMP-binding enzyme / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Ribosomal protein/NADH dehydrogenase domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / ClpP/crotonase-like domain superfamily / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, RNA binding domain / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L33 superfamily / Ribosomal protein L16 / Ribosomal protein L28/L24 / : / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal protein L24 / Ribosomal protein S18 superfamily / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / Ribosomal protein S6 superfamily / 50S ribosomal protein uL4 / Translation elongation factor EF1B/ribosomal protein S6 / : / Ribosomal protein L10e/L16 / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L16p/L10e / Ribosomal protein S5, N-terminal / Ribosomal protein S5, C-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Uncharacterized protein / Ribosomal protein L9 domain-containing protein / Uncharacterized protein / Rhodanese domain-containing protein ...NICOTINAMIDE-ADENINE-DINUCLEOTIDE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Uncharacterized protein / Ribosomal protein L9 domain-containing protein / Uncharacterized protein / Rhodanese domain-containing protein / Putative ribosomal protein L11 / Uncharacterized protein / Uncharacterized protein / Mitochondrial SSU ribosomal protein / Uncharacterized protein / Large ribosomal subunit protein uL3m / C2H2-type domain-containing protein / Pentacotripeptide-repeat region of PRORP domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / 30S Ribosomal protein S17-like protein / Chromosome passenger complex (CPC) protein INCENP N terminal / Excreted/secreted protein 15 / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Enoyl-CoA hydratase/isomerase domain-containing protein / Uncharacterized protein / Peptidyl-prolyl cis-trans isomerase / Uncharacterized protein / Mitochondrial ribosomal protein S18 / Uncharacterized protein / Putative ribosomal protein L14 / 50S ribosomal protein L13-like protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Ribosomal protein S6 / Mitochondrial RNA binding complex 1 subunit / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Small ribosomal subunit protein mS41 / Uncharacterized protein / LysM domain-containing protein / Uncharacterized protein / Phosphatidylethanolamine-binding protein / Uncharacterized protein / A-kinase anchor protein 7-like phosphoesterase domain-containing protein / 39S ribosomal protein L36, mitochondrial / Large ribosomal subunit protein mL43 / Rhodanese domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Putative superoxide dismutase / 39S ribosomal protein L28, mitochondrial / Uncharacterized protein / Uncharacterized protein / AMP-dependent synthetase/ligase domain-containing protein / Uncharacterized protein / LIM zinc-binding domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Ubiquitin-like domain-containing protein / KOW domain-containing protein / Large ribosomal subunit protein uL23m / Uncharacterized protein / Ribosomal protein S9 / Peptidyl-prolyl cis-trans isomerase / Uncharacterized protein / Uncharacterized protein / Ribosomal protein L22p/L17e / Uncharacterized protein / Mitochondrial RNA binding complex 1 subunit / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Ribosomal protein S8 / Treble clef zinc finger domain-containing protein / Uncharacterized protein / Uncharacterized protein / AB hydrolase-1 domain-containing protein / Uncharacterized protein / Putative 50S ribosomal protein L17 / Large ribosomal subunit protein uL15/eL18 domain-containing protein / Uncharacterized protein / Uncharacterized protein
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsSoufari, H. / Waltz, F. / Parrot, C. / Bochler, A. / Hashem, Y.
Funding support France, 1items
OrganizationGrant numberCountry
European Research Council (ERC) France
CitationJournal: Proc Natl Acad Sci U S A / Year: 2020
Title: Structure of the mature kinetoplastids mitoribosome and insights into its large subunit biogenesis.
Authors: Heddy Soufari / Florent Waltz / Camila Parrot / Stéphanie Durrieu-Gaillard / Anthony Bochler / Lauriane Kuhn / Marie Sissler / Yaser Hashem /
Abstract: Kinetoplastids are unicellular eukaryotic parasites responsible for such human pathologies as Chagas disease, sleeping sickness, and leishmaniasis. They have a single large mitochondrion, essential ...Kinetoplastids are unicellular eukaryotic parasites responsible for such human pathologies as Chagas disease, sleeping sickness, and leishmaniasis. They have a single large mitochondrion, essential for the parasite survival. In kinetoplastid mitochondria, most of the molecular machineries and gene expression processes have significantly diverged and specialized, with an extreme example being their mitochondrial ribosomes. These large complexes are in charge of translating the few essential mRNAs encoded by mitochondrial genomes. Structural studies performed in already highlighted the numerous peculiarities of these mitoribosomes and the maturation of their small subunit. However, several important aspects mainly related to the large subunit (LSU) remain elusive, such as the structure and maturation of its ribosomal RNA. Here we present a cryo-electron microscopy study of the protozoans and mitoribosomes. For both species, we obtained the structure of their mature mitoribosomes, complete rRNA of the LSU, as well as previously unidentified ribosomal proteins. In addition, we introduce the structure of an LSU assembly intermediate in the presence of 16 identified maturation factors. These maturation factors act on both the intersubunit and the solvent sides of the LSU, where they refold and chemically modify the rRNA and prevent early translation before full maturation of the LSU.
History
DepositionOct 11, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.0Jun 23, 2021Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 23, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 23, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.1Apr 9, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: database_2 / em_admin / Data content type: EM metadata / EM metadata / EM metadata
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update

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Structure visualization

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Assembly

Deposited unit
2: Large ribosomal RNA
h: uS14m
aw: mS69
m: bS18m
f: uS11m
s: mS33
au: Rhodanese domain-containing protein
am: mS59
n: uS19m
ae: mS53
ay: mS71
ag: mS55
aj: mS57
e: uS10m
d: uS9m
az: mS72
ax: mS70
r: mS29
af: Excreted/secreted protein 15
u: mS35
aa: mS48
ab: mS49
ak: mS58
ac: mS50
ad: mS51
an: mS60
ao: mS61
ap: mS62
aq: mS63
as: mS65
at: mS66
y: mS43
w: Protein FYV4, mitochondrial
v: mS37
t: mS34
p: mS23
j: bS16m
l: mS52
ar: AKAP7_NLS domain-containing protein
av: Ubiquitin-like domain-containing protein
ai: mS56
x: Putative superoxide dismutase
i: uS15m
g: bS21m
o: mS22
c: uS8m
k: 30S Ribosomal protein S17-like protein
q: mS26
b: bS6m
a: Ribosomal_S5_C domain-containing protein
ba: mS73
z: mS47
bd: uS3m
A: Ribosomal protein L3-like protein
B: uL4m
C: RIBOSOMAL_L9 domain-containing protein
D: uL10m
E: Putative ribosomal protein L11
F: 50S ribosomal protein L13-like protein
G: Ribosomal_L18e/L15P domain-containing protein
H: Ribosomal_L16 domain-containing protein
I: Putative 50S ribosomal protein L17
J: bL19m
K: bL20m
L: bL21m
M: uL22m
N: uL23m
O: uL24m
P: bL27m
Q: bL28m
R: uL29m
S: uL30m
T: bL32m
U: bL33m
V: bL35m
W: bL36m
X: mL38
Y: mL40
Z: mL41
BA: mL94
UA: UA
BB: mL95
Aw: mL89
Bj: bL31m
An: mL76
Al: mL74
BI: Peptidyl-prolyl cis-trans isomerase
Az: mL93
At: mL86
BC: mL96
Ab: L51_S25_CI-B8 domain-containing protein
Ai: mL69
Ap: mL80
Au: mL87
Aa: mL42
Ao: mL79
BM: mL70
Ar: mL84
Aj: mL72
BH: Peptidyl-prolyl cis-trans isomerase
Am: mL75
Aq: mL82
BE: mL98
Ak: mL73
BP: mL52
Ad: mL49
BF: mL99
Av: mL88
Af: mL63
As: mL85
Ae: mL53
Ac: MRP-L46 domain-containing protein
Ah: mL68
BD: mL97
Ay: C2H2-type domain-containing protein
Ag: mL59/64
Ax: LIM zinc-binding domain-containing protein
BL: Putative ribosomal protein L2
BO: Putative ribosomal protein L14
BG: mL100
UB: UB
UC: UC
UD: UD
1: Large ribosomal RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,803,411133
Polymers16,802,306124
Non-polymers1,1049
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 1 types, 2 molecules 21

#1: RNA chain Large ribosomal RNA


Mass: 6061246.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: GenBank: 1756572068

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Protein , 117 types, 117 molecules hawmfsauamnaeayagajedazaxrafuaaabakacadanaoapaqasat...

#2: Protein uS14m


Mass: 19553.537 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QIP8
#3: Protein mS69


Mass: 16298.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QHA2
#4: Protein bS18m


Mass: 37786.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q1J0
#5: Protein uS11m


Mass: 40966.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QJG8
#6: Protein mS33


Mass: 20892.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: E9ACZ5
#7: Protein Rhodanese domain-containing protein


Mass: 30144.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q6T5
#8: Protein mS59


Mass: 35759.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote)
#9: Protein uS19m


Mass: 19609.830 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q7N2
#10: Protein mS53


Mass: 72161.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QFA7
#11: Protein mS71


Mass: 19874.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q7W4
#12: Protein mS55


Mass: 65155.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: E9ADP4
#13: Protein mS57


Mass: 45727.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q7Q8
#14: Protein uS10m


Mass: 92510.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q4M2
#15: Protein uS9m


Mass: 39580.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QB37
#16: Protein mS72


Mass: 19487.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QBM5
#17: Protein mS70


Mass: 21523.709 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q103
#18: Protein mS29


Mass: 54251.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QGU0
#19: Protein Excreted/secreted protein 15


Mass: 92396.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q1X7J7
#20: Protein mS35


Mass: 99579.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: E9AD40
#21: Protein mS48


Mass: 199814.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QEP4
#22: Protein mS49


Mass: 133168.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: E9ADG8
#23: Protein mS58


Mass: 36065.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: E9ACK8
#24: Protein mS50


Mass: 139232.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QBP8
#25: Protein mS51


Mass: 94543.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QAQ0
#26: Protein mS60


Mass: 35159.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QBR4
#27: Protein mS61


Mass: 33399.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: E9AF47
#28: Protein mS62


Mass: 27471.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q847
#29: Protein mS63


Mass: 33830.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QF40
#30: Protein mS65


Mass: 30295.689 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QIF7
#31: Protein mS66


Mass: 44353.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QE10
#32: Protein mS43


Mass: 51476.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q3D4
#33: Protein Protein FYV4, mitochondrial


Mass: 22242.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q4E6
#34: Protein mS37


Mass: 24315.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QCC8
#35: Protein mS34


Mass: 29272.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q8W5
#36: Protein mS23


Mass: 36807.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QFH6
#37: Protein bS16m


Mass: 22466.064 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q8H5
#38: Protein mS52


Mass: 75466.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q3T6
#39: Protein AKAP7_NLS domain-containing protein


Mass: 31464.025 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q5L8
#40: Protein Ubiquitin-like domain-containing protein


Mass: 27343.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q9M1
#41: Protein mS56


Mass: 43583.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q6W8
#42: Protein Putative superoxide dismutase


Mass: 30365.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q716, superoxide dismutase
#43: Protein uS15m


Mass: 50375.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QCY9
#44: Protein bS21m


Mass: 22841.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: E9AE13
#45: Protein mS22


Mass: 73146.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: E9AFL9
#46: Protein uS8m


Mass: 35099.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QDW2
#47: Protein 30S Ribosomal protein S17-like protein


Mass: 36019.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: E9AFK9
#48: Protein mS26


Mass: 49494.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: E9AFH3
#49: Protein bS6m


Mass: 18824.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q3G8
#50: Protein Ribosomal_S5_C domain-containing protein


Mass: 49346.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q1N8
#51: Protein mS73


Mass: 11375.776 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q6W6
#52: Protein mS47


Mass: 131570.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q190
#53: Protein uS3m


Mass: 10675.792 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote)
#54: Protein Ribosomal protein L3-like protein


Mass: 53894.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: E9ADK5
#55: Protein uL4m


Mass: 49869.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QGU6
#56: Protein RIBOSOMAL_L9 domain-containing protein


Mass: 30379.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QIE5
#57: Protein uL10m


Mass: 22169.115 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QI77
#59: Protein 50S ribosomal protein L13-like protein


Mass: 20500.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q2H6
#60: Protein Ribosomal_L18e/L15P domain-containing protein


Mass: 43436.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QF19
#61: Protein Ribosomal_L16 domain-containing protein


Mass: 18998.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QFP0
#62: Protein Putative 50S ribosomal protein L17


Mass: 35699.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QF04
#63: Protein bL19m


Mass: 16564.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QCY7
#64: Protein bL20m


Mass: 22311.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q192
#65: Protein bL21m


Mass: 20906.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QFQ5
#66: Protein uL22m


Mass: 32147.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QBR0
#67: Protein uL23m


Mass: 28707.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QA05
#68: Protein uL24m


Mass: 53490.598 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q9S7
#69: Protein bL27m


Mass: 21479.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QG34
#70: Protein bL28m


Mass: 27091.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q719
#71: Protein uL29m


Mass: 54104.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q9XZY7
#72: Protein uL30m


Mass: 45433.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q9U0Z7
#73: Protein bL32m


Mass: 9734.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q2W9
#74: Protein bL33m


Mass: 13341.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q2Q8
#75: Protein bL35m


Mass: 18262.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QCK6
#76: Protein bL36m


Mass: 21719.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q6A3
#77: Protein mL38


Mass: 57985.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q5A3
#78: Protein mL40


Mass: 33207.035 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q448
#79: Protein mL41


Mass: 22673.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q152
#80: Protein mL94


Mass: 17885.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: E9ACP5
#81: Protein UA


Mass: 17294.268 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote)
#82: Protein mL95


Mass: 18694.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q4D6
#83: Protein mL89


Mass: 21557.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: E9AD00
#84: Protein bL31m


Mass: 21261.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q0E1
#85: Protein mL76


Mass: 38656.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q0F5
#86: Protein mL74


Mass: 39392.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q1C8
#88: Protein mL93


Mass: 18858.525 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q4D9
#89: Protein mL86


Mass: 21071.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q4L5
#90: Protein mL96


Mass: 16713.799 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q5D8
#91: Protein L51_S25_CI-B8 domain-containing protein


Mass: 31231.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q6A7
#92: Protein mL69


Mass: 54183.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q7P8
#93: Protein mL80


Mass: 27945.424 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q7V3
#94: Protein mL87


Mass: 22265.654 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q8J6
#95: Protein mL42


Mass: 22170.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q183
#96: Protein mL79


Mass: 33388.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q547
#97: Protein mL70


Mass: 50752.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q703
#98: Protein mL84


Mass: 24621.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q712
#99: Protein mL72


Mass: 56554.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q728
#101: Protein mL75


Mass: 39654.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QC22
#102: Protein mL82


Mass: 37905.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QD92
#103: Protein mL98


Mass: 13262.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QE16
#104: Protein mL73


Mass: 36084.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QEC8
#105: Protein mL52


Mass: 29196.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote)
#106: Protein mL49


Mass: 26212.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QIB3
#107: Protein mL99


Mass: 13048.815 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QIQ1
#108: Protein mL88


Mass: 22340.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QIT7
#109: Protein mL63


Mass: 18099.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QJB6
#110: Protein mL85


Mass: 27526.311 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: E9ABZ5
#111: Protein mL53


Mass: 35479.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: E9ACG2
#112: Protein MRP-L46 domain-containing protein


Mass: 33348.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QJ75
#113: Protein mL68


Mass: 65792.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QC45
#114: Protein mL97


Mass: 12078.795 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QE11
#115: Protein C2H2-type domain-containing protein


Mass: 20926.838 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: E9ADN7
#116: Protein mL59/64


Mass: 28602.615 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q829
#117: Protein LIM zinc-binding domain-containing protein


Mass: 25173.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q7T1
#120: Protein mL100


Mass: 146807.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote)
#121: Protein UB


Mass: 5720.042 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote)
#122: Protein UC


Mass: 12273.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote)
#123: Protein UD


Mass: 8102.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote)

-
Putative ribosomal protein ... , 3 types, 3 molecules EBLBO

#58: Protein Putative ribosomal protein L11


Mass: 40143.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: E9ACT9
#118: Protein Putative ribosomal protein L2


Mass: 43379.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QIE1
#119: Protein Putative ribosomal protein L14


Mass: 21633.137 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q2G1

-
Peptidyl-prolyl cis-trans ... , 2 types, 2 molecules BIBH

#87: Protein Peptidyl-prolyl cis-trans isomerase / PPIase


Mass: 28924.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q1A6, peptidylprolyl isomerase
#100: Protein Peptidyl-prolyl cis-trans isomerase / PPIase


Mass: 25314.658 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QBK2, peptidylprolyl isomerase

-
Non-polymers , 3 types, 9 molecules

#124: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#125: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#126: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Leishmania major mitochondrial riobosome / Type: RIBOSOME / Entity ID: #1-#123 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Leishmania major (eukaryote)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/2
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 82060 / Symmetry type: POINT

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