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- PDB-7am2: Intermediate assembly of the Large subunit from Leishmania major ... -

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Basic information

Entry
Database: PDB / ID: 7am2
TitleIntermediate assembly of the Large subunit from Leishmania major mitochondrial ribosome
Components
  • (G domain-containing ...) x 2
  • (Peptidyl-prolyl cis-trans ...) x 2
  • (Putative ribosomal protein ...) x 2
  • (mL78) x 2
  • 50S ribosomal protein L13-like protein
  • Acyl carrier protein
  • DEAD/DEAH box helicase-like protein
  • DNAj-like protein
  • GTPase Der
  • L0R8F8
  • L51_S25_CI-B8 domain-containing protein
  • LIM zinc-binding domain-containing protein
  • Pseudouridylate synthase-like protein
  • Putative 50S ribosomal protein L17
  • R1
  • R2
  • R5
  • RIBOSOMAL_L9 domain-containing protein
  • RNA uridylyltransferase
  • Ribosomal RNA
  • Ribosomal protein L3-like protein
  • Ribosomal_L18e/L15P domain-containing protein
  • SpoU_methylase domain-containing protein
  • TRUD domain-containing protein
  • U1
  • U2
  • U3
  • U4
  • U5
  • U6
  • U8
  • UA
  • bL19m
  • bL20m
  • bL21m
  • bL28m
  • bL32m
  • bL35m
  • mL100
  • mL41
  • mL42
  • mL49
  • mL52,mL52
  • mL53
  • mL59/64
  • mL63
  • mL67
  • mL68
  • mL70
  • mL71
  • mL72
  • mL74
  • mL75
  • mL76
  • mL80
  • mL81
  • mL84
  • mL85
  • mL86
  • mL87
  • mL88
  • mL89
  • mL93
  • mL94
  • mL95
  • mL98
  • mL99
  • uL22m
  • uL23m
  • uL24m
  • uL29m
  • uL30m
  • uL4m
KeywordsRIBOSOME / Mitochondria / Kinetoplastid
Function / homology
Function and homology information


pseudouridine synthesis / pseudouridine synthase activity / negative regulation of ribosome biogenesis / kinetoplast / RNA methyltransferase activity / mitochondrial large ribosomal subunit / ciliary plasm / mitochondrial ribosome / nuclear lumen / mitochondrial translation ...pseudouridine synthesis / pseudouridine synthase activity / negative regulation of ribosome biogenesis / kinetoplast / RNA methyltransferase activity / mitochondrial large ribosomal subunit / ciliary plasm / mitochondrial ribosome / nuclear lumen / mitochondrial translation / cyclosporin A binding / acyl binding / acyl carrier activity / ribosomal large subunit binding / RNA processing / translation initiation factor activity / protein folding chaperone / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / fatty acid biosynthetic process / unfolded protein binding / protein folding / ribosome biogenesis / large ribosomal subunit / protein-folding chaperone binding / large ribosomal subunit rRNA binding / methylation / nucleic acid binding / RNA helicase activity / negative regulation of translation / hydrolase activity / rRNA binding / structural constituent of ribosome / ribosome / translation / mitochondrial matrix / ribonucleoprotein complex / GTPase activity / mRNA binding / GTP binding / nucleolus / mitochondrion / RNA binding / ATP binding / metal ion binding / nucleus / membrane / cytoplasm
Similarity search - Function
: / Pseudouridine synthase, TruD, insertion domain / TRUD domain profile. / Pseudouridine synthase, TruD / Pseudouridine synthase, TruD, catalytic domain / EngB-type guanine nucleotide-binding (G) domain / : / GTP-binding protein EngA / GTPase Der, C-terminal KH-domain-like / KH-domain-like of EngA bacterial GTPase enzymes, C-terminal ...: / Pseudouridine synthase, TruD, insertion domain / TRUD domain profile. / Pseudouridine synthase, TruD / Pseudouridine synthase, TruD, catalytic domain / EngB-type guanine nucleotide-binding (G) domain / : / GTP-binding protein EngA / GTPase Der, C-terminal KH-domain-like / KH-domain-like of EngA bacterial GTPase enzymes, C-terminal / Pseudouridine synthase, RsuA/RluA-like / : / RNA pseudouridylate synthase / PPR repeat family / tRNA/rRNA methyltransferase, SpoU type / SpoU rRNA Methylase family / : / Protein Iojap/ribosomal silencing factor RsfS / Ribosomal silencing factor during starvation / Pseudouridine synthase, catalytic domain superfamily / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / GTP-binding protein, orthogonal bundle domain superfamily / LIM domain profile. / Pentatricopeptide (PPR) repeat profile. / DnaJ domain / Pentatricopeptide repeat / Ribosomal protein L47, mitochondrial / MRP-L47 superfamily, mitochondrial / 39S ribosomal protein L43/54S ribosomal protein L51 / Mitochondrial 39-S ribosomal protein L47 (MRP-L47) / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / 50S ribosome-binding GTPase / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / GTP binding domain / 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 / Acyl carrier protein (ACP) / Nucleotidyltransferase superfamily / Phosphopantetheine attachment site / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / 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 / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / 50S ribosomal protein L30e-like / Helicase conserved C-terminal domain / 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 L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Small GTP-binding protein domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / K homology domain-like, alpha/beta / Tetratricopeptide-like helical domain superfamily / Ribosomal protein L24 signature. / Ribosomal protein L24/L26, conserved site / helicase superfamily c-terminal domain / Ribosomal protein L13 / Ribosomal protein L13 / Ribosomal protein L13 superfamily / Ribosomal protein L25/L23 / Ribosomal protein L30, ferredoxin-like fold domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Flagellar attachment zone protein / Uncharacterized protein / Uncharacterized protein / Pseudouridylate synthase RPUSD4, mitochondrial ...ADENOSINE-5'-TRIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Flagellar attachment zone protein / Uncharacterized protein / Uncharacterized protein / Pseudouridylate synthase RPUSD4, mitochondrial / Ribosomal protein L9 domain-containing protein / Rhodanese domain-containing protein / Putative ribosomal protein L11 / Uncharacterized protein / Acyl carrier protein / Uncharacterized protein / Large ribosomal subunit protein uL3m / tRNA/rRNA methyltransferase SpoU type domain-containing protein / G domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / 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 / G domain-containing protein / Large ribosomal subunit protein mL43 / Uncharacterized protein / Uncharacterized protein / 39S ribosomal protein L28, mitochondrial / Uncharacterized protein / DNAj-like protein / LIM zinc-binding domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / GTPase Der / KOW domain-containing protein / Large ribosomal subunit protein uL23m / Uncharacterized protein / Uncharacterized protein / Peptidyl-prolyl cis-trans isomerase / Ribosomal protein L22p/L17e / Mitochondrial RNA binding complex 1 subunit / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Putative 50S ribosomal protein L17 / Large ribosomal subunit protein uL15/eL18 domain-containing protein / Large ribosomal subunit protein bL21m / Uncharacterized protein / Uncharacterized protein / TRUD domain-containing protein / Large ribosomal subunit protein uL4m / DEAD/DEAH box helicase-like protein / Uncharacterized protein / Ribosomal protein L9 domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein L5213T.03 / Ribosomal protein L30 ferredoxin-like fold domain-containing protein / Large ribosomal subunit protein uL29m
Similarity search - Component
Biological speciesLeishmania tarentolae (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 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 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: 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

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Assembly

Deposited unit
A: Ribosomal protein L3-like protein
B: uL4m
C: RIBOSOMAL_L9 domain-containing protein
E: Putative ribosomal protein L11
F: 50S ribosomal protein L13-like protein
G: Ribosomal_L18e/L15P domain-containing protein
I: Putative 50S ribosomal protein L17
J: bL19m
K: bL20m
L: bL21m
M: uL22m
N: uL23m
O: uL24m
Q: bL28m
R: uL29m
S: uL30m
T: bL32m
V: bL35m
Z: mL41
BA: mL94
CA: TRUD domain-containing protein
UA: UA
BB: mL95
CB: RNA uridylyltransferase
BK: mL67
BQ: mL71
BN: mL81
BE: mL98
BO: Putative ribosomal protein L14
At: mL86
Au: mL87
Ae: mL53
Af: mL63
Ah: mL68
Ap: mL80
Al: mL74
Ab: L51_S25_CI-B8 domain-containing protein
Aa: mL42
BP: mL52,mL52
Az: mL93
Am: mL75
As: mL85
BG: mL100
Ad: mL49
Aw: mL89
BH: Peptidyl-prolyl cis-trans isomerase
Aj: mL72
Ar: mL84
An: mL76
BF: mL99
Av: mL88
BM: mL70
Ag: mL59/64
Bl: Peptidyl-prolyl cis-trans isomerase
Ax: LIM zinc-binding domain-containing protein
BS: DNAj-like protein
BY: SpoU_methylase domain-containing protein
BX: SpoU_methylase domain-containing protein
BZ: Pseudouridylate synthase-like protein
CC: Acyl carrier protein
CD: L0R8F8
BT: G domain-containing protein
BU: GTPase Der
BW: DEAD/DEAH box helicase-like protein
BV: G domain-containing protein
U7: mL78
U6: U6
U1: U1
U3: U3
U4: U4
U5: U5
BR: mL78
U2: U2
1: Ribosomal RNA
R1: R1
R2: R2
R5: R5
U8: U8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,589,49080
Polymers8,588,46078
Non-polymers1,0302
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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Protein , 64 types, 65 molecules ABCFGIJKLMNOQRSTVZBACAUABBCBBKBQBNBEAtAuAe...

#1: Protein Ribosomal protein L3-like protein


Mass: 54025.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (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 tarentolae (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 tarentolae (eukaryote) / References: UniProt: Q4QIE5
#5: 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 tarentolae (eukaryote) / References: UniProt: Q4Q2H6
#6: 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 tarentolae (eukaryote) / References: UniProt: Q4QF19
#7: Protein Putative 50S ribosomal protein L17


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


Mass: 16695.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: Q4QCY7
#9: Protein bL20m


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


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


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


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


Mass: 53621.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: Q4Q9S7
#14: Protein bL28m


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


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


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


Mass: 9865.692 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: Q4Q2W9
#18: Protein bL35m


Mass: 18393.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: Q4QCK6
#19: Protein mL41


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


Mass: 17885.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: E9ACP5
#21: Protein TRUD domain-containing protein


Mass: 68396.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: Q4QGU5
#22: Protein UA


Mass: 14446.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote)
#23: Protein mL95


Mass: 18694.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: Q4Q4D6
#24: Protein RNA uridylyltransferase


Mass: 23355.764 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: Q9NE59, RNA uridylyltransferase
#25: Protein mL67


Mass: 97698.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: E9AD80
#26: Protein mL71


Mass: 49368.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: Q4QBK0
#27: Protein mL81


Mass: 37743.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: Q4QAP7
#28: Protein mL98


Mass: 13262.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: Q4QE16
#30: Protein mL86


Mass: 21071.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: Q4Q4L5
#31: Protein mL87


Mass: 22265.654 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: Q4Q8J6
#32: Protein mL53


Mass: 35479.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: E9ACG2
#33: Protein mL63


Mass: 18099.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: Q4QJB6
#34: Protein mL68


Mass: 65792.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: Q4QC45
#35: Protein mL80


Mass: 27945.424 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: Q4Q7V3
#36: Protein mL74


Mass: 39392.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: Q4Q1C8
#37: 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 tarentolae (eukaryote) / References: UniProt: Q4Q6A7
#38: Protein mL42


Mass: 22170.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: Q4Q183
#39: Protein mL52,mL52


Mass: 29196.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: Q4QGE0
#40: Protein mL93


Mass: 18858.525 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: Q4Q4D9
#41: Protein mL75


Mass: 39654.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: Q4QC22
#42: Protein mL85


Mass: 27526.311 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: E9ABZ5
#43: Protein mL100


Mass: 146807.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A504WW14
#44: Protein mL49


Mass: 26212.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: Q4QIB3
#45: Protein mL89


Mass: 21557.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: E9AD00
#47: Protein mL72


Mass: 56554.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: Q4Q728
#48: Protein mL84


Mass: 24621.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: Q4Q712
#49: Protein mL76


Mass: 38656.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: Q4Q0F5
#50: Protein mL99


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


Mass: 22340.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: Q4QIT7
#52: Protein mL70


Mass: 50752.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: Q4Q703
#53: Protein mL59/64


Mass: 28602.615 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: Q4Q829
#55: 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 tarentolae (eukaryote) / References: UniProt: Q4Q7T1
#56: Protein DNAj-like protein


Mass: 45397.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: Q4Q7K0
#57: Protein SpoU_methylase domain-containing protein


Mass: 63872.289 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: E9AFB3
#58: Protein Pseudouridylate synthase-like protein


Mass: 47450.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: E9AC17
#59: Protein Acyl carrier protein


Mass: 16629.881 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: E9AD06
#60: Protein L0R8F8


Mass: 14783.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: Q4QFS7
#62: Protein GTPase Der


Mass: 56550.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: Q4Q9G4
#63: Protein DEAD/DEAH box helicase-like protein


Mass: 87394.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: Q4QHU1
#66: Protein U6


Mass: 13309.536 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote)
#68: Protein U3


Mass: 5348.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote)
#69: Protein U4


Mass: 9684.576 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote)
#70: Protein U5


Mass: 6699.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote)
#71: Protein mL78


Mass: 33017.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A504XZ90
#77: Protein U8


Mass: 4211.603 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote)

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Putative ribosomal protein ... , 2 types, 2 molecules EBO

#4: Protein Putative ribosomal protein L11


Mass: 40274.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: E9ACT9
#29: Protein Putative ribosomal protein L14


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

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

#46: 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 tarentolae (eukaryote) / References: UniProt: Q4QBK2, peptidylprolyl isomerase
#54: 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 tarentolae (eukaryote) / References: UniProt: Q4Q1A6, peptidylprolyl isomerase

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G domain-containing ... , 2 types, 2 molecules BTBV

#61: Protein G domain-containing protein


Mass: 51661.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: E9AFZ4
#64: Protein G domain-containing protein


Mass: 86927.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: Q4Q4X0

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Protein/peptide , 3 types, 3 molecules U7U1U2

#65: Protein/peptide mL78


Mass: 3422.209 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote)
#67: Protein/peptide U1


Mass: 3287.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote)
#72: Protein/peptide U2


Mass: 2647.894 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote)

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RNA chain , 4 types, 4 molecules 1R1R2R5

#73: RNA chain Ribosomal RNA


Mass: 6061920.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote)
#74: RNA chain R1


Mass: 896.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote)
#75: RNA chain R2


Mass: 10670.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote)
#76: RNA chain R5


Mass: 1485.872 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote)

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Non-polymers , 2 types, 2 molecules

#78: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#79: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM

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Details

Has ligand of interestY
Has protein modificationY

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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, #10-#19, #2, #20-#29, #3, #30-#39, #4, #40-#49, #5, #50-#59, #6, #60-#69, #7, #70-#77, #8-#9
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 type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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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 FIELD
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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 59200 / Symmetry type: POINT

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