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- PDB-7aih: The Large subunit of the Kinetoplastid mitochondrial ribosome -

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Basic information

Entry
Database: PDB / ID: 7aih
TitleThe Large subunit of the Kinetoplastid mitochondrial ribosome
Components
  • (Peptidyl-prolyl cis-trans ...) x 2
  • (Putative ribosomal protein ...) x 3
  • 50S ribosomal protein L13-like proteinRibosome
  • C2H2-type domain-containing protein
  • L51_S25_CI-B8 domain-containing protein
  • LIM zinc-binding domain-containing protein
  • MRP-L46 domain-containing protein
  • Putative 50S ribosomal protein L17
  • RIBOSOMAL_L9 domain-containing protein
  • Ribosomal RNA
  • Ribosomal protein L3-like proteinRibosome
  • Ribosomal_L16 domain-containing protein
  • Ribosomal_L18e/L15P domain-containing protein
  • UA
  • UB
  • UC
  • UD
  • bL19m
  • bL20
  • bL21m
  • bL27m
  • bL28m
  • bL31m
  • bL32m
  • bL33m
  • bL35m
  • bL36m
  • mL100
  • mL38
  • mL40
  • mL41
  • mL42
  • mL49
  • mL52,mL52
  • mL53
  • mL54/69
  • 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
  • uL10m
  • uL22m
  • uL23m
  • uL24m
  • uL29m
  • uL30m
  • uL4m
KeywordsRIBOSOME / Mitochondria / Kinetoplastid
Function / homology
Function and homology information


kinetoplast / nuclear lumen / mitochondrial large ribosomal subunit / ciliary plasm / mitochondrial ribosome / cyclosporin A binding / mitochondrial translation / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / large ribosomal subunit rRNA binding ...kinetoplast / nuclear lumen / mitochondrial large ribosomal subunit / ciliary plasm / mitochondrial ribosome / cyclosporin A binding / mitochondrial translation / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / large ribosomal subunit rRNA binding / large ribosomal subunit / protein folding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / mitochondrion / RNA binding / membrane / metal ion binding / nucleus / cytoplasm
Similarity search - Function
PPR repeat family / Pentatricopeptide (PPR) repeat profile. / LIM domain / Pentatricopeptide repeat / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / Ribosomal protein L46, N-terminal / 39S mitochondrial ribosomal protein L46 / LIM domain profile. / 39S ribosomal protein L46, mitochondrial ...PPR repeat family / Pentatricopeptide (PPR) repeat profile. / LIM domain / Pentatricopeptide repeat / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / Ribosomal protein L46, N-terminal / 39S mitochondrial ribosomal protein L46 / LIM domain profile. / 39S ribosomal protein L46, mitochondrial / Ribosomal protein L47, mitochondrial / MRP-L47 superfamily, mitochondrial / 39S ribosomal protein L43/54S ribosomal protein L51 / Mitochondrial 39-S ribosomal protein L47 (MRP-L47) / Phosphatidylethanolamine-binding protein, eukaryotic / PEBP-like superfamily / 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 / AMP-dependent synthetase/ligase / AMP-binding enzyme / Ribosomal protein/NADH dehydrogenase domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Ribosomal protein L11, N-terminal / 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, N-terminal domain / Ribosomal protein L11, RNA binding domain / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / : / Ribosomal protein L16 / 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 L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L10e/L16 / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L16p/L10e / Ribosomal protein L24/L26, conserved site / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein L2 / Tetratricopeptide-like helical domain superfamily / Ribosomal protein L25/L23 / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L14P / Ribosomal protein L14 superfamily / Ribosomal protein L26/L24, KOW domain / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal protein L24 signature. / Ribosomal protein L14p/L23e / Ribosomal protein L22/L17 / Ribosomal protein L22/L17 superfamily / Ribosomal protein L3 / Ribosomal protein L13 / Ribosomal protein L13 / Ribosomal protein L13 superfamily / Ribosomal protein L3 / Ribosomal protein L22p/L17e / Ribosomal protein L4/L1e / Ribosomal protein L4 domain superfamily / Ribosomal protein L18e/L15P / Ribosomal L18e/L15P superfamily / Ribosomal protein L4/L1 family / Alpha/Beta hydrolase fold / Translation protein SH3-like domain superfamily / Ribosomal protein L23/L15e core domain superfamily / Thioredoxin-like superfamily / Translation protein, beta-barrel domain superfamily / Ribosomal protein L2, domain 2 / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Flagellar attachment zone protein 1 / Uncharacterized protein / Ribosomal protein L9 domain-containing protein / Rhodanese domain-containing protein / Large ribosomal subunit protein uL11m ...NICOTINAMIDE-ADENINE-DINUCLEOTIDE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Flagellar attachment zone protein 1 / Uncharacterized protein / Ribosomal protein L9 domain-containing protein / Rhodanese domain-containing protein / Large ribosomal subunit protein uL11m / Uncharacterized protein / Ribosomal protein L3-like protein / C2H2-type domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Large ribosomal subunit protein bL20c / Peptidyl-prolyl cis-trans isomerase / Uncharacterized protein / Putative ribosomal protein L14 / 50S ribosomal protein L13-like protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Phosphatidylethanolamine-binding protein / Uncharacterized protein / 39S ribosomal protein L42, mitochondrial / Large ribosomal subunit protein mL43 / Uncharacterized protein / Uncharacterized protein / 39S ribosomal protein L28, mitochondrial / Uncharacterized protein / AMP-binding domain-containing protein / LIM zinc-binding domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / KOW domain-containing protein / Large ribosomal subunit protein uL23m / Peptidyl-prolyl cis-trans isomerase / Large ribosomal subunit protein uL22c / Mitochondrial RNA binding complex 1 subunit / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Prophage protein / Uncharacterized protein / AB hydrolase-1 domain-containing protein / Putative 50S ribosomal protein L17 / Large ribosomal subunit protein uL15/eL18 domain-containing protein / Ribosomal_L16 domain-containing protein / Large ribosomal subunit protein bL21m / 39S ribosomal protein L16, mitochondrial / Uncharacterized protein / Large ribosomal subunit protein uL4m / Uncharacterized protein / Uncharacterized protein / Putative ribosomal protein L2 / Ribosomal protein L9 domain-containing protein / Uncharacterized protein / Uncharacterized protein / MRP-L46 domain-containing protein / Uncharacterized protein / Ribosomal protein L30 ferredoxin-like fold domain-containing protein / Large ribosomal subunit protein uL29m
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 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
DepositionSep 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release

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Assembly

Deposited unit
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: bL20
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,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: mL54/69
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: Ribosomal RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,045,00178
Polymers5,043,94571
Non-polymers1,0567
Water0
1


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

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Components

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Protein , 65 types, 65 molecules ABCDFGHIJKLMNOPQRSTUVWXYZBAUABBAwBj...

#1: Protein Ribosomal protein L3-like protein / Ribosome


Mass: 54025.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: E9ADK5
#2: Protein uL4m


Mass: 50000.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QGU6
#3: Protein RIBOSOMAL_L9 domain-containing protein


Mass: 30510.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QIE5
#4: 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
#6: Protein 50S ribosomal protein L13-like protein / Ribosome


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


Mass: 43567.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QF19
#8: Protein Ribosomal_L16 domain-containing protein


Mass: 19130.045 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QFP0
#9: Protein Putative 50S ribosomal protein L17 /


Mass: 35830.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QF04
#10: Protein bL19m


Mass: 16695.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QCY7
#11: Protein bL20


Mass: 22442.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q192
#12: Protein bL21m


Mass: 21037.311 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QFQ5
#13: Protein uL22m


Mass: 32278.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QBR0
#14: Protein uL23m


Mass: 28838.916 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QA05
#15: Protein uL24m


Mass: 53621.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q9S7
#16: Protein bL27m


Mass: 21610.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QG34
#17: Protein bL28m


Mass: 27222.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q719
#18: Protein uL29m


Mass: 54235.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q9XZY7
#19: Protein uL30m


Mass: 45564.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q9U0Z7
#20: Protein bL32m


Mass: 9865.692 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q2W9
#21: Protein bL33m


Mass: 13473.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q2Q8
#22: Protein bL35m


Mass: 18393.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QCK6
#23: Protein bL36m


Mass: 21851.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q6A3
#24: Protein mL38


Mass: 58116.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q5A3
#25: 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
#26: 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
#27: 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
#28: Protein UA


Mass: 17294.268 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote)
#29: 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
#30: 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
#31: 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
#32: 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
#33: 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
#35: 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
#36: 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
#37: 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
#38: 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
#39: 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
#40: 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
#41: 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
#42: 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
#43: 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
#44: 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
#45: 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
#46: 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
#48: 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
#49: 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
#50: 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
#51: 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
#52: Protein mL52,mL52


Mass: 29196.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4QGE0
#53: 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
#54: 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
#55: 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
#56: 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
#57: 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
#58: 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
#59: 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
#60: 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
#61: 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
#62: 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
#63: Protein mL54/69


Mass: 28602.615 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: Q4Q829
#64: 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
#67: Protein mL100


Mass: 146807.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: A0A504WW14
#68: Protein UB


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


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


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

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

#5: Protein Putative ribosomal protein L11 /


Mass: 40274.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote) / References: UniProt: E9ACT9
#65: 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
#66: 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

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

#34: Protein Peptidyl-prolyl cis-trans isomerase / Prolyl 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
#47: Protein Peptidyl-prolyl cis-trans isomerase / Prolyl 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

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RNA chain , 1 types, 1 molecules 1

#71: RNA chain Ribosomal RNA /


Mass: 2895416.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania major (eukaryote)

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Non-polymers , 2 types, 7 molecules

#72: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#73: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM

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Details

Has ligand of interestY

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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 mitochondrial ribosome / Type: RIBOSOME / Entity ID: #1-#71 / Source: NATURAL
Source (natural)Organism: Leishmania tarentolae (eukaryote)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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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 FIELDBright-field microscopy
Image recordingElectron dose: 60 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameCategory
2EPUimage acquisition
4GctfCTF correction
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 82060 / Symmetry type: POINT

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