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- PDB-6yxy: State B of the Trypanosoma brucei mitoribosomal large subunit ass... -

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Basic information

Entry
Database: PDB / ID: 6yxy
TitleState B of the Trypanosoma brucei mitoribosomal large subunit assembly intermediate
Components
  • (UNK) x 6
  • 12S ribosomal RNA
  • L0R8F8
  • MALSU1
  • Mtg1
  • bL17m
  • bL19m
  • bL20m
  • bL21m
  • bL28m
  • bL32m
  • bL35m
  • bL9m
  • mL100
  • mL101
  • mL41
  • mL42
  • mL43
  • mL49
  • mL52
  • mL53
  • mL63
  • mL64Microsoft Macro Assembler
  • mL67
  • mL68
  • mL70
  • mL71
  • mL72
  • mL74
  • mL75
  • mL76
  • mL77
  • mL78
  • mL80
  • mL81
  • mL83
  • mL84
  • mL85
  • mL86
  • mL87
  • mL88
  • mL89
  • mL90
  • mL92
  • mL93
  • mL94
  • mL95
  • mL98
  • mL99
  • mt-ACP
  • mt-EngA
  • mt-EngB
  • mt-LAF12
  • mt-LAF14
  • mt-LAF15a
  • mt-LAF18
  • mt-LAF19
  • mt-LAF2
  • mt-LAF20
  • mt-LAF3
  • mt-LAF4
  • mt-LAF5
  • mt-LAF6
  • mt-LAF7
  • mt-LAF8
  • uL11m
  • uL13m
  • uL14m
  • uL15m
  • uL22m
  • uL23m
  • uL24m
  • uL29m
  • uL30m
  • uL3m
  • uL4m
KeywordsRIBOSOME / mitoribosome / assembly / LSU
Function / homology
Function and homology information


organellar large ribosomal subunit / pseudouridine synthesis / pseudouridine synthase activity / RNA uridylyltransferase activity / negative regulation of ribosome biogenesis / kinetoplast / RNA methyltransferase activity / nuclear lumen / mitochondrial large ribosomal subunit / ciliary plasm ...organellar large ribosomal subunit / pseudouridine synthesis / pseudouridine synthase activity / RNA uridylyltransferase activity / negative regulation of ribosome biogenesis / kinetoplast / RNA methyltransferase activity / nuclear lumen / mitochondrial large ribosomal subunit / ciliary plasm / acyl binding / mitochondrial ribosome / acyl carrier activity / cyclosporin A binding / mitochondrial translation / post-transcriptional regulation of gene expression / mitochondrial respiratory chain complex I / ribosomal large subunit binding / RNA processing / translation initiation factor activity / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / lipid metabolic process / fatty acid biosynthetic process / large ribosomal subunit rRNA binding / large ribosomal subunit / protein folding / negative regulation of translation / RNA helicase activity / rRNA binding / hydrolase activity / ribosome / mitochondrial matrix / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / GTPase activity / GTP binding / nucleolus / mitochondrion / RNA binding / nucleoplasm / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Pseudouridine synthase, TruD, catalytic domain / EngB-type guanine nucleotide-binding (G) domain profile. / Pseudouridine synthase, TruD / EngB-type guanine nucleotide-binding (G) 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 ...Pseudouridine synthase, TruD, catalytic domain / EngB-type guanine nucleotide-binding (G) domain profile. / Pseudouridine synthase, TruD / EngB-type guanine nucleotide-binding (G) 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) / Ribosomal silencing factor during starvation / Protein Iojap/ribosomal silencing factor RsfS / Pseudouridine synthase, catalytic domain superfamily / Pentatricopeptide (PPR) repeat profile. / LIM domain / GTP-binding protein, orthogonal bundle domain superfamily / Pentatricopeptide repeat / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / DnaJ domain / Ribosomal protein L47, mitochondrial / MRP-L47 superfamily, mitochondrial / 39S ribosomal protein L43/54S ribosomal protein L51 / Mitochondrial 39-S ribosomal protein L47 (MRP-L47) / Rhodanese-like domain superfamily / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / 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 / Complex 1 LYR protein domain / Complex 1 protein (LYR family) / 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 / DEAD/DEAH box helicase domain / Phosphopantetheine attachment site. / Nucleotidyltransferase superfamily / Phosphopantetheine attachment site / 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 / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / 50S ribosomal protein L30e-like / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / 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 / helicase superfamily c-terminal domain / Tetratricopeptide-like helical domain superfamily / Ribosomal protein L25/L23 / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Small GTP-binding protein domain / Ribosomal protein L26/L24, KOW domain / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal protein L22/L17 / Ribosomal protein L22/L17 superfamily / Ribosomal protein L3 / Ribosomal protein L13 / Ribosomal protein L13 / Ribosomal protein L13 superfamily
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Chem-PM8 / SPERMIDINE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) ...ADENOSINE-5'-TRIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Chem-PM8 / SPERMIDINE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Lipase (Class 3) / Replication restart DNA helicase PriA / Uncharacterized protein / Uncharacterized protein / Tetratricopeptide repeat / KOW domain-containing protein / Uncharacterized protein / Importin-beta N-terminal domain-containing protein / Uncharacterized protein / Chaperone protein DNAj, putative / Large ribosomal subunit protein uL22c / Large ribosomal subunit protein bL21m / T. brucei spp.-specific protein / Uncharacterized protein / Uncharacterized protein / SpoU_methylase domain-containing protein / Mitochondrial RNA binding complex 1 subunit / Uncharacterized protein / T. brucei spp.-specific protein / Uncharacterized protein / Uncharacterized protein / T. brucei spp.-specific protein / Uncharacterized protein / DEAD-box helicase, putative / EngB-type G domain-containing protein / Ribosomal protein S24/S35 mitochondrial conserved domain-containing protein / Large ribosomal subunit protein bL20c / Uncharacterized protein / Mitochondrial ribosomal protein L23 / Uncharacterized protein / Peptidyl-prolyl cis-trans isomerase / TRUD domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Large ribosomal subunit protein uL23m / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / SpoU_methylase domain-containing protein / GTP-binding protein, putative / Uncharacterized protein / Large ribosomal subunit protein uL29m / Rhodanese domain-containing protein / Uncharacterized protein / Pseudouridylate synthase, putative / WHIM1 domain-containing protein / Uncharacterized protein / GTP-binding protein, putative / Large ribosomal subunit protein uL15/eL18 domain-containing protein / Ribosomal protein L9 domain-containing protein / Uncharacterized protein / Peptidyl-prolyl cis-trans isomerase / Uncharacterized protein / Uncharacterized protein / Acyl carrier protein / 50S ribosomal protein L17, putative / Uncharacterized protein / Uncharacterized protein / 50S ribosomal protein L13, putative / Ribosomal protein L3 mitochondrial, putative / Large ribosomal subunit protein mL43 / Uncharacterized protein / Uncharacterized protein / LIM zinc-binding domain-containing protein / 39S ribosomal protein L28, mitochondrial / Uncharacterized protein / Large ribosomal subunit protein uL11m / Uncharacterized protein
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 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

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Structure visualization

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Assembly

Deposited unit
A1: bL28m
A2: uL29m
A3: uL30m
A5: bL32m
A8: bL35m
AA: 12S ribosomal RNA
BA: mL67
EA: mt-EngA
BB: mL68
EB: mt-LAF2
EC: mt-LAF3
BD: mL70
ED: mt-LAF4
AE: uL3m
BE: mL71
EE: mt-LAF5
UE: UNK
AF: uL4m
BF: mL72
EF: mt-LAF6
EG: mt-LAF7
BH: mL74
EH: mt-LAF8
AI: bL9m
BI: mL75
EI: MALSU1
UI: UNK
BJ: mL76
EJ: L0R8F8
AK: uL11m
BK: mL77
EK: mt-ACP
UK: UNK
BL: mL78
EL: mt-LAF12
UL: UNK
EM: Mtg1
UM: UNK
AN: uL13m
BN: mL80
EN: mt-LAF14
AO: uL14m
BO: mL81
EO: mt-LAF15a
AP: uL15m
EP: mt-LAF15a
BQ: mL83
EQ: mt-EngB
AR: bL17m
BR: mL84
ER: mt-ACP
BS: mL85
ES: mt-LAF18
AT: bL19m
BT: mL86
ET: mt-LAF19
AU: bL20m
BU: mL87
EU: mt-LAF20
AV: bL21m
BV: mL88
AW: uL22m
BW: mL89
AX: uL23m
BX: mL90
UX: UNK
AY: uL24m
BZ: mL92
Ba: mL93
Bb: mL94
Bc: mL95
Ae: mL41
Af: mL42
Bf: mL98
Ag: mL43
Bg: mL99
Bh: mL100
Bi: mL101
Al: mL49
Ao: mL52
Ap: mL53
At: mL63
Av: mL64
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,253,212131
Polymers3,248,15883
Non-polymers5,05448
Water18010
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 , 76 types, 78 molecules A1A2A3A5A8BAEABBEBECBDEDAEBEEEAFBFEFEGBHEHAIBIEIBJEJAKBKEKER...

#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 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
#3: 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: Q38ED8
#4: 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
#5: 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
#7: 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: Q386Z1
#8: 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
#9: 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
#10: Protein mt-LAF2


Mass: 85715.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: D0A9G9
#11: Protein mt-LAF3


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


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


Mass: 69460.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q385G9
#14: Protein uL3m


Mass: 55073.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q580R4
#15: 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
#16: Protein mt-LAF5


Mass: 67167.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q38DC9
#18: Protein uL4m


Mass: 53156.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: D0A7A6
#19: Protein mL72


Mass: 49407.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: A0A3L6LA84
#20: Protein mt-LAF6


Mass: 40106.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: C9ZWD9
#21: 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
#22: 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
#23: 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: Q57ZS6
#24: Protein bL9m


Mass: 30729.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q57UC5
#25: 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
#26: Protein MALSU1


Mass: 39553.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q584Y2
#28: 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
#29: Protein L0R8F8


Mass: 13444.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q57UQ1
#30: Protein uL11m


Mass: 40266.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q586R9
#31: Protein mL77


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


Mass: 16550.807 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q57WW9
#34: 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: Q389N4
#35: 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
#36: Protein UNK


Mass: 6145.567 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote)
#37: Protein Mtg1


Mass: 50416.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q38E75
#39: Protein uL13m


Mass: 24341.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q580D5
#40: 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
#41: 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
#42: Protein uL14m


Mass: 25133.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote)
#43: 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: Q385L5
#44: 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
#45: Protein uL15m


Mass: 43780.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q57U68
#46: Protein mL83 / 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
#47: Protein mt-EngB


Mass: 71472.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q380Y8
#48: Protein bL17m


Mass: 35117.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q57YI7
#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 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
#51: Protein mt-LAF18


Mass: 58830.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: A0A3L6L1Y4
#52: 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
#53: 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
#54: 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
#55: 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
#56: 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
#57: Protein mt-LAF20


Mass: 6939.401 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote)
#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 mL90


Mass: 22123.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q585P1
#64: Protein UNK


Mass: 15336.877 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote)
#65: 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
#66: Protein mL92 / 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
#67: 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
#68: 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
#69: 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
#70: 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
#71: 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
#72: 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
#73: Protein mL43


Mass: 31300.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q583E5
#74: Protein mL99


Mass: 12334.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q587H8
#75: Protein mL100


Mass: 10600.362 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: A0A3L6L2V1
#76: Protein mL101


Mass: 28455.811 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q4GZ80
#77: 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
#78: Protein mL52


Mass: 167692.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q385V2
#79: 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
#80: 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
#81: Protein mL64 / Microsoft Macro Assembler


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

#6: RNA chain 12S ribosomal RNA /


Mass: 373911.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: GenBank: 343546

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Protein/peptide , 4 types, 4 molecules UEUIUKUM

#17: Protein/peptide UNK


Mass: 2826.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote)
#27: Protein/peptide UNK


Mass: 1975.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote)
#33: Protein/peptide UNK


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


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

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Non-polymers , 9 types, 58 molecules

#82: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#83: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: Mg
#84: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34) / Spermidine


Mass: 145.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H19N3
#85: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#86: Chemical ChemComp-NA / SODIUM ION


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


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#88: 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.: 2 / Source method: obtained synthetically / Formula: C21H41N2O7PS
#89: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


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


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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-#81 / 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 FIELDBright-field microscopy / 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: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 98508 / 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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