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- PDB-6yxx: State A of the Trypanosoma brucei mitoribosomal large subunit ass... -

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Basic information

Entry
Database: PDB / ID: 6yxx
TitleState A of the Trypanosoma brucei mitoribosomal large subunit assembly intermediate
Components
  • (50S ribosomal protein ...) x 2
  • (Peptidyl-prolyl cis-trans ...) x 2
  • (Ribosomal protein ...) x 3
  • (SpoU_methylase domain-containing ...) x 2
  • (UNK) x 9
  • 12S ribosomal RNA
  • Acyl carrier protein
  • Chaperone protein DNAj, putative
  • DEAD-box helicase, putative
  • DUF4379 domain-containing protein
  • GTP-binding protein, putative
  • KRIPP3
  • KRIPP9
  • L51_S25_CI-B8 domain-containing protein
  • Lipase (Class 3)
  • Pseudouridylate synthase, putative
  • RIBOSOMAL_L9 domain-containing protein
  • Ribosomal_L18e/L15P domain-containing protein
  • Tetratricopeptide repeat
  • bL19m
  • bL20m
  • bL21m
  • bL28m
  • bL32m
  • bL35m
  • mL41
  • mL42
  • mL49
  • mL52
  • mL53
  • mL63
  • mL64
  • mL67
  • mL68
  • mL70
  • mL71
  • mL74
  • mL75
  • mL76
  • mL78
  • mL80
  • mL81
  • mL84
  • mL85
  • mL86
  • mL87
  • mL88
  • mL89
  • mL93
  • mL94
  • mL95
  • mL98
  • mt-EngA
  • mt-LAF12
  • mt-LAF14
  • mt-LAF15a
  • mt-LAF19
  • mt-LAF21
  • mt-LAF23
  • mt-LAF24
  • mt-LAF25
  • mt-LAF27
  • mt-LAF29
  • mt-LAF4
  • mt-LAF7
  • mt-LAF8
  • uL22m
  • uL23m
  • uL24m
  • uL29m
  • uL30m
KeywordsRIBOSOME / mitoribosome / assembly / LSU
Function / homology
Function and homology information


organellar large ribosomal subunit / pseudouridine synthesis / pseudouridine synthase activity / kinetoplast / RNA methyltransferase activity / nuclear lumen / mitochondrial large ribosomal subunit / ciliary plasm / mitochondrial ribosome / mitochondrial translation ...organellar large ribosomal subunit / pseudouridine synthesis / pseudouridine synthase activity / kinetoplast / RNA methyltransferase activity / nuclear lumen / mitochondrial large ribosomal subunit / ciliary plasm / mitochondrial ribosome / mitochondrial translation / post-transcriptional regulation of gene expression / cyclosporin A binding / : / acyl binding / acyl carrier activity / RNA processing / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / lipid metabolic process / fatty acid biosynthetic process / large ribosomal subunit / protein folding / large ribosomal subunit rRNA binding / RNA helicase activity / negative regulation of translation / rRNA binding / hydrolase activity / ribosome / structural constituent of ribosome / mitochondrial matrix / ribonucleoprotein complex / translation / GTPase activity / mRNA binding / GTP binding / nucleolus / mitochondrion / RNA binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Pseudouridine synthase, TruD / Pseudouridine synthase, TruD, catalytic domain / : / Probable Zinc-ribbon domain / Probable Zinc-ribbon domain / GTPase Der, C-terminal KH-domain-like / : / KH-domain-like of EngA bacterial GTPase enzymes, C-terminal / Pseudouridine synthase, RsuA/RluA-like ...: / Pseudouridine synthase, TruD / Pseudouridine synthase, TruD, catalytic domain / : / Probable Zinc-ribbon domain / Probable Zinc-ribbon domain / 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 / tRNA/rRNA methyltransferase, SpoU type / SpoU rRNA Methylase family / Fungal lipase-like domain / Lipase (class 3) / Pseudouridine synthase, catalytic domain superfamily / Pentatricopeptide repeat domain / GTP-binding protein, orthogonal bundle domain superfamily / Pentatricopeptide (PPR) repeat profile. / Pentatricopeptide repeat / DnaJ domain / Rhodanese-like domain superfamily / 39S ribosomal protein L43/54S ribosomal protein L51 / Ribosomal protein L47, mitochondrial / MRP-L47 superfamily, mitochondrial / 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 / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / GTP binding domain / 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 / Ribosomal protein/NADH dehydrogenase domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Acyl carrier protein (ACP) / 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, RNA binding domain / Ribosomal protein L11/L12 / ACP-like superfamily / Carrier protein (CP) domain profile. / Ribosomal protein L9 / 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 / K homology domain-like, alpha/beta / Small GTP-binding protein domain / helicase superfamily c-terminal domain / Tetratricopeptide-like helical domain superfamily / Ribosomal protein L13 / Ribosomal protein L13 / Ribosomal protein L13 superfamily / Ribosomal protein L25/L23 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal protein L26/L24, KOW domain / Ribosomal protein L18e/L15P / Ribosomal L18e/L15P superfamily / Ribosomal protein L22/L17 / Ribosomal protein L22/L17 superfamily / Ribosomal protein L22p/L17e / Ribosomal protein L3 / Ribosomal protein L3
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Chem-PM8 / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL4m / Uncharacterized protein ...ADENOSINE-5'-TRIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Chem-PM8 / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL4m / Uncharacterized protein / Lipase (Class 3) / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Tetratricopeptide repeat / KOW domain-containing protein / T. brucei spp.-specific protein / T. brucei spp.-specific protein / Uncharacterized protein / Chaperone protein DNAj, putative / Large ribosomal subunit protein uL22c / Large ribosomal subunit protein bL21m / Probable Zinc-ribbon domain-containing protein / T. brucei spp.-specific protein / Uncharacterized protein / Uncharacterized protein / tRNA/rRNA methyltransferase SpoU type domain-containing protein / Ribosomal protein L30 ferredoxin-like fold domain-containing protein / tRNA/rRNA methyltransferase SpoU type domain-containing protein / Mitochondrial RNA binding complex 1 subunit / Uncharacterized protein / T. brucei spp.-specific protein / T. brucei spp.-specific protein / Uncharacterized protein / Mitochondrial RNA binding protein / T. brucei spp.-specific protein / Uncharacterized protein / T. brucei spp.-specific protein / Uncharacterized protein / DEAD-box helicase, putative / Ribosomal protein S24/S35 mitochondrial conserved domain-containing protein / Large ribosomal subunit protein bL20c / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Peptidyl-prolyl cis-trans isomerase / TRUD domain-containing protein / Large ribosomal subunit protein uL23m / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / GTP-binding protein, putative / Large ribosomal subunit protein uL29m / Rhodanese domain-containing protein / Uncharacterized protein / Pseudouridylate synthase, putative / Uncharacterized protein / Kinetoplast ribosomal PPR-repeat containing protein 3 / GTP-binding protein, putative / Large ribosomal subunit protein uL15/eL18 domain-containing protein / Ribosomal protein L9 domain-containing protein / Peptidyl-prolyl cis-trans isomerase / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Acyl carrier protein / 50S ribosomal protein L17, putative / SAP domain-containing protein / Uncharacterized protein / 50S ribosomal protein L13, putative / Ribosomal protein L3 mitochondrial, putative / Large ribosomal subunit protein mL43 / Uncharacterized protein / Uncharacterized protein / 39S ribosomal protein L28, mitochondrial / Uncharacterized protein / Large ribosomal subunit protein uL11m
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsJaskolowski, M. / Ramrath, D.J.F. / Bieri, P. / Niemann, M. / Mattei, S. / Calderaro, S. / Leibundgut, M.A. / Horn, E.K. / Boehringer, D. / Schneider, A. / Ban, N.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Mol Cell / Year: 2020
Title: Structural Insights into the Mechanism of Mitoribosomal Large Subunit Biogenesis.
Authors: Mateusz Jaskolowski / David J F Ramrath / Philipp Bieri / Moritz Niemann / Simone Mattei / Salvatore Calderaro / Marc Leibundgut / Elke K Horn / Daniel Boehringer / André Schneider / Nenad Ban /
Abstract: In contrast to the bacterial translation machinery, mitoribosomes and mitochondrial translation factors are highly divergent in terms of composition and architecture. There is increasing evidence ...In contrast to the bacterial translation machinery, mitoribosomes and mitochondrial translation factors are highly divergent in terms of composition and architecture. There is increasing evidence that the biogenesis of mitoribosomes is an intricate pathway, involving many assembly factors. To better understand this process, we investigated native assembly intermediates of the mitoribosomal large subunit from the human parasite Trypanosoma brucei using cryo-electron microscopy. We identify 28 assembly factors, 6 of which are homologous to bacterial and eukaryotic ribosome assembly factors. They interact with the partially folded rRNA by specifically recognizing functionally important regions such as the peptidyltransferase center. The architectural and compositional comparison of the assembly intermediates indicates a stepwise modular assembly process, during which the rRNA folds toward its mature state. During the process, several conserved GTPases and a helicase form highly intertwined interaction networks that stabilize distinct assembly intermediates. The presented structures provide general insights into mitoribosomal maturation.
History
DepositionMay 4, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 23, 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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Structure visualization

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  • Deposited structure unit
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
A1: bL28m
E1: mt-LAF21
A2: uL29m
E2: DUF4379 domain-containing protein
A3: uL30m
E3: mt-LAF23
E4: mt-LAF24
A5: bL32m
E5: mt-LAF25
E6: KRIPP3
A8: bL35m
AA: 12S ribosomal RNA
BA: mL67
EA: mt-EngA
UA: UNK
BB: mL68
EB: DEAD-box helicase, putative
EC: Pseudouridylate synthase, putative
BD: mL70
ED: mt-LAF4
AE: Ribosomal protein L3 mitochondrial, putative
BE: mL71
EE: SpoU_methylase domain-containing protein
AF: Ribosomal protein L4/L1 family, putative
BF: Tetratricopeptide repeat
EF: SpoU_methylase domain-containing protein
EG: mt-LAF7
BH: mL74
EH: mt-LAF8
AI: RIBOSOMAL_L9 domain-containing protein
BI: mL75
UI: UNK
BJ: mL76
AK: Ribosomal protein L11, putative
BK: Chaperone protein DNAj, putative
UK: UNK
BL: mL78
EL: mt-LAF12
EM: GTP-binding protein, putative
UM: UNK
AN: 50S ribosomal protein L13, putative
BN: mL80
EN: mt-LAF14
BO: mL81
EO: mt-LAF15a
AP: Ribosomal_L18e/L15P domain-containing protein
EP: mt-LAF15a
BQ: Peptidyl-prolyl cis-trans isomerase
AR: 50S ribosomal protein L17, putative
BR: mL84
ER: Acyl carrier protein
BS: mL85
ES: Lipase (Class 3)
AT: bL19m
BT: mL86
ET: mt-LAF19
AU: bL20m
BU: mL87
AV: bL21m
BV: mL88
AW: uL22m
BW: mL89
AX: uL23m
AY: uL24m
BZ: Peptidyl-prolyl cis-trans isomerase
Ba: mL93
Bb: mL94
Bc: mL95
Ae: mL41
Af: mL42
Bf: mL98
Uf: UNK
Ag: L51_S25_CI-B8 domain-containing protein
E7: mt-LAF27
E8: KRIPP9
E9: mt-LAF29
Al: mL49
Ul: UNK
Um: UNK
Un: UNK
Ao: mL52
Ap: mL53
Up: UNK
Ur: UNK
Us: UNK
At: mL63
Av: mL64
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,478,415118
Polymers3,474,78487
Non-polymers3,63131
Water1448
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 , 68 types, 69 molecules A1E1A2E2A3E3E4A5E5E6A8BAEABBEBECBDEDBEBFEGBHEHAIBIBJBKBLELEM...

#1: Protein bL28m


Mass: 28051.373 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q586A2
#2: Protein mt-LAF21


Mass: 56574.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q57WG6
#3: Protein uL29m


Mass: 54045.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q38EM7
#4: Protein DUF4379 domain-containing protein


Mass: 63645.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: C9ZTN9
#5: Protein uL30m


Mass: 25218.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: C9ZY77
#6: Protein mt-LAF23


Mass: 63989.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: D0A795
#7: Protein mt-LAF24


Mass: 49278.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q585A0
#8: Protein bL32m


Mass: 9745.710 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q584F4
#9: Protein mt-LAF25


Mass: 32017.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote)
#10: Protein KRIPP3


Mass: 58601.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q4GZA2
#11: Protein bL35m


Mass: 21661.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: D0A1K1
#13: Protein mL67


Mass: 93569.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: D0A5V6
#14: Protein mt-EngA


Mass: 65528.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q57TZ4
#16: Protein mL68


Mass: 62806.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: D0A135
#17: Protein DEAD-box helicase, putative


Mass: 85715.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: D0A9G9
#18: Protein Pseudouridylate synthase, putative


Mass: 46374.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q38FJ3
#19: Protein mL70


Mass: 62442.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote)
#20: Protein mt-LAF4


Mass: 69432.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q385G9
#22: Protein mL71


Mass: 50313.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q57WG1
#25: Protein Tetratricopeptide repeat


Mass: 49407.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: A0A3L6LA84
#27: Protein mt-LAF7


Mass: 18645.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q387S8
#28: Protein mL74


Mass: 39765.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q38AM5
#29: Protein mt-LAF8


Mass: 68904.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: A0A1G4IEQ9
#30: Protein RIBOSOMAL_L9 domain-containing protein


Mass: 30729.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q57UC5
#31: Protein mL75


Mass: 39770.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: D0A108
#33: Protein mL76


Mass: 39638.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q383M2
#35: Protein Chaperone protein DNAj, putative


Mass: 43754.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: C9ZQR6
#37: Protein mL78


Mass: 35104.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: D0A4P5
#38: Protein mt-LAF12


Mass: 77908.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: C9ZVC0
#39: Protein GTP-binding protein, putative


Mass: 50416.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q38E75
#42: Protein mL80


Mass: 34883.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: C9ZQF0
#43: Protein mt-LAF14


Mass: 82108.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: C9ZPS0
#44: Protein mL81


Mass: 29284.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: D0A755
#45: Protein mt-LAF15a


Mass: 34621.383 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: C9ZMA6
#46: Protein Ribosomal_L18e/L15P domain-containing protein


Mass: 43780.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q57U68
#49: Protein mL84


Mass: 24773.643 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q586A6
#50: Protein Acyl carrier protein


Mass: 16550.807 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q57WW9
#51: Protein mL85


Mass: 22657.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q38FG8
#52: Protein Lipase (Class 3)


Mass: 58830.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: A0A3L6L1Y4
#53: Protein bL19m


Mass: 16931.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q4GZ98
#54: Protein mL86


Mass: 22376.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: A0A3L6L8W0
#55: Protein mt-LAF19


Mass: 12076.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q383S4
#56: Protein bL20m


Mass: 24393.943 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q383R2
#57: Protein mL87


Mass: 22337.521 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: D0A7Z9
#58: Protein bL21m


Mass: 20895.268 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: C9ZT11
#59: Protein mL88


Mass: 22255.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: C9ZUW3
#60: Protein uL22m


Mass: 32083.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: C9ZSI8
#61: Protein mL89


Mass: 22213.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q57WW5
#62: Protein uL23m


Mass: 28847.963 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q387G3
#63: Protein uL24m


Mass: 43999.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: C9ZK52
#65: Protein mL93


Mass: 18929.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: D0A4T0
#66: Protein mL94


Mass: 17830.959 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q38EP7
#67: Protein mL95


Mass: 17803.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q389K3
#68: Protein mL41


Mass: 22610.928 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q383U6
#69: Protein mL42


Mass: 21602.639 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q383S1
#70: Protein mL98


Mass: 12968.644 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q388M2
#71: Protein L51_S25_CI-B8 domain-containing protein


Mass: 31300.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q583E5
#72: Protein mt-LAF27


Mass: 11609.306 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote)
#73: Protein KRIPP9


Mass: 89421.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q57YZ6
#74: Protein mt-LAF29


Mass: 38525.980 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: A0A3L6L206
#75: Protein mL49


Mass: 24501.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q57Z82
#76: Protein UNK


Mass: 20272.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote)
#79: Protein mL52


Mass: 167692.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote)
#80: Protein mL53


Mass: 35656.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: A0A3L6L3K9
#81: Protein UNK


Mass: 7422.140 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote)
#82: Protein UNK


Mass: 6741.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote)
#83: Protein mL63


Mass: 18213.924 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: C9ZU82
#84: Protein mL64


Mass: 28545.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: D0A934

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RNA chain , 1 types, 1 molecules AA

#12: RNA chain 12S ribosomal RNA


Mass: 365178.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote)

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Protein/peptide , 6 types, 8 molecules UAUfUIUrUKUMUmUn

#15: Protein/peptide UNK


Mass: 869.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote)
#32: Protein/peptide UNK


Mass: 1805.216 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote)
#36: Protein/peptide UNK


Mass: 2145.636 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote)
#40: Protein/peptide UNK


Mass: 698.854 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote)
#77: Protein/peptide UNK


Mass: 2315.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote)
#78: Protein/peptide UNK


Mass: 2400.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote)

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Ribosomal protein ... , 3 types, 3 molecules AEAFAK

#21: Protein Ribosomal protein L3 mitochondrial, putative


Mass: 55073.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q580R4
#24: Protein Ribosomal protein L4/L1 family, putative


Mass: 53156.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: A0A1G4HYD1
#34: Protein Ribosomal protein L11, putative


Mass: 40266.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q586R9

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SpoU methylase domain-containing ... , 2 types, 2 molecules EEEF

#23: Protein SpoU_methylase domain-containing protein


Mass: 67167.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: C9ZZ65
#26: Protein SpoU_methylase domain-containing protein


Mass: 40223.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: C9ZWD9

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50S ribosomal protein ... , 2 types, 2 molecules ANAR

#41: Protein 50S ribosomal protein L13, putative


Mass: 24341.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q580D5
#48: Protein 50S ribosomal protein L17, putative


Mass: 35117.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q57YI7

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

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


Mass: 25579.004 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q57WF8, peptidylprolyl isomerase
#64: Protein Peptidyl-prolyl cis-trans isomerase / PPIase


Mass: 20542.291 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q383Y4, peptidylprolyl isomerase

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Non-polymers , 8 types, 39 molecules

#85: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#86: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Mg
#87: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#88: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#89: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#90: Chemical ChemComp-PM8 / S-(2-{[N-(2-HYDROXY-4-{[HYDROXY(OXIDO)PHOSPHINO]OXY}-3,3-DIMETHYLBUTANOYL)-BETA-ALANYL]AMINO}ETHYL) DECANETHIOATE


Mass: 496.598 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H41N2O7PS
#91: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#92: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

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Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: State B of the Trypanosoma brucei mitoribosomal large subunit assembly intermediate
Type: RIBOSOME / Entity ID: #1-#84 / Source: NATURAL
Source (natural)Organism: Trypanosoma brucei brucei (eukaryote) / Strain: 427
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277 K
Details: 3.5 uL of the sample was blotted for 7-9 sec before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 75 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM softwareName: RELION / Version: 3 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16215 / Symmetry type: POINT
Atomic model buildingDetails: Initial models of ribosomal proteins of the T. brucei mitochondrial ribosomal large subunit were taken from PDB 6HIX. Assembly factors of the mitoribosomal large subunit were built de novo.

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