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- PDB-7aoi: Trypanosoma brucei mitochondrial ribosome large subunit assembly ... -

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Entry
Database: PDB / ID: 7aoi
TitleTrypanosoma brucei mitochondrial ribosome large subunit assembly intermediate
Components
  • (50S ribosomal protein ...) x 3
  • (Mitochondrial ...) x 2
  • (Peptidyl-prolyl cis-trans ...) x 2
  • (Ribosomal protein ...) x 6
  • Acyl carrier protein
  • Chaperone protein DNAj, putative,mL77,Chaperone protein DNAj, putative
  • Complex1-LYR-like
  • DEAD-box helicase, putative,mt-LAF2
  • GTP-binding protein
  • GTP-binding protein, putative,mt-EngA
  • LIM domain containing protein,mL90
  • Lipase (Class 3)
  • Pseudouridylate synthase, putative
  • RIBOSOMAL_L9 domain-containing protein
  • RNA uridylyltransferase
  • Ribosomal_L18e/L15P domain-containing protein
  • SpoU rRNA Methylase family
  • Tetratricopeptide repeat
  • UNK1
  • UNK10
  • UNK11
  • UNK2
  • UNK3
  • UNK4
  • UNK5
  • UNK6/mt-LAF15_2
  • UNK7
  • UNK8
  • UNK9
  • bL19m
  • bL20m
  • bL28m
  • bL32m
  • bL33m
  • mL100,mL100
  • mL101
  • mL41
  • mL42
  • mL49
  • mL52
  • mL53
  • mL63
  • mL64,mL64
  • mL67
  • mL68,mL68,mL68
  • mL70
  • mL71
  • mL74
  • mL76
  • mL78
  • mL80
  • mL81
  • mL84
  • mL85
  • mL86
  • mL87
  • mL89
  • mL93
  • mL94
  • mL95
  • mL98
  • mL99
  • mt-LAF12
  • mt-LAF14
  • mt-LAF15_1
  • mt-LAF19
  • mt-LAF4
  • mt-LAF7,mt-LAF7
  • mt-LAF8
  • mt-LSU rRNA
  • uL24m
  • uL29m
  • uL30m
KeywordsRIBOSOME / mitochondria / translation / trypanosoma / assembly / evolution / large subunit
Function / homology
Function and homology information


pseudouridine synthesis / enzyme-directed rRNA pseudouridine synthesis / pseudouridine synthase activity / RNA methyltransferase activity / nuclear lumen / mitochondrial large ribosomal subunit / ciliary plasm / cyclosporin A binding / post-transcriptional regulation of gene expression / mitochondrial translation ...pseudouridine synthesis / enzyme-directed rRNA pseudouridine synthesis / pseudouridine synthase activity / RNA methyltransferase activity / nuclear lumen / mitochondrial large ribosomal subunit / ciliary plasm / cyclosporin A binding / post-transcriptional regulation of gene expression / mitochondrial translation / : / 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 / cytosolic large ribosomal subunit / RNA helicase activity / rRNA binding / hydrolase activity / ribosome / structural constituent of ribosome / mitochondrial matrix / translation / mRNA binding / nucleolus / GTP binding / mitochondrion / RNA binding / ATP binding / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Pseudouridine synthase, TruD / 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 ...Pseudouridine synthase, TruD / 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 / Pseudouridine synthase, catalytic domain superfamily / Protein Iojap/ribosomal silencing factor RsfS / Pentatricopeptide (PPR) repeat profile. / GTP-binding protein, orthogonal bundle domain superfamily / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / Pentatricopeptide repeat / LIM domain profile. / DnaJ domain / 39S ribosomal protein L43/54S ribosomal protein L51 / Ribosomal protein L47, mitochondrial / MRP-L47 superfamily, mitochondrial / 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 / tRNA (guanine-N1-)-methyltransferase, N-terminal / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / 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 domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Complex 1 LYR protein domain / Cyclophilin-like domain superfamily / Complex 1 protein (LYR family) / 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, 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 / Ribosomal protein L28/L24 superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / 50S ribosomal protein L30e-like / Helicase conserved C-terminal domain / Ribosomal protein L22, bacterial/chloroplast-type / 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 / Tetratricopeptide-like helical domain superfamily / Small GTP-binding protein domain / helicase superfamily c-terminal domain / Ribosomal protein L13 / Ribosomal protein L13 / Ribosomal protein L13 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal protein L14P / Ribosomal protein L14 superfamily / Ribosomal protein L14p/L23e / Ribosomal protein L26/L24, KOW domain / Ribosomal protein L22/L17 / Ribosomal protein L22/L17 superfamily / Ribosomal protein L22p/L17e
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / FE2/S2 (INORGANIC) CLUSTER / GUANOSINE-5'-TRIPHOSPHATE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / RNA / RNA (> 10) / RNA (> 100) / Uncharacterized protein / Uncharacterized protein / Peptidyl-prolyl cis-trans isomerase ...ADENOSINE-5'-DIPHOSPHATE / FE2/S2 (INORGANIC) CLUSTER / GUANOSINE-5'-TRIPHOSPHATE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / RNA / RNA (> 10) / RNA (> 100) / Uncharacterized protein / Uncharacterized protein / Peptidyl-prolyl cis-trans isomerase / Uncharacterized protein / Uncharacterized protein / Ribosomal protein L4/L1 family / Uncharacterized protein / Ribosomal protein L23 / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Mitochondrial RNA binding complex 1 subunit / Uncharacterized protein / GTP-binding protein / Uncharacterized protein / Lipase (Class 3) / SpoU rRNA Methylase family / Uncharacterized protein / Replication restart DNA helicase PriA / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Ribosomal protein L22p/L17e / Uncharacterized protein / LIM domain containing protein / Uncharacterized protein / Uncharacterized protein / Ribosomal_L18e/L15P domain-containing protein / Oligomerization domain containing protein / Uncharacterized protein / Complex1-LYR-like / Uncharacterized protein / RIBOSOMAL_L9 domain-containing protein / Ribosomal protein L21 / Tetratricopeptide repeat / 50S ribosomal protein L13 / 50S ribosomal protein L17 / Uncharacterized protein / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / 50S ribosomal protein L14 / Ribosomal protein L11 / KOW domain-containing protein / Uncharacterized protein / Chaperone protein DNAj, putative / GTP-binding protein, putative / Uncharacterized protein / T. brucei spp.-specific protein / Uncharacterized protein / Mitochondrial RNA binding protein / Uncharacterized protein / DEAD-box helicase, putative / Uncharacterized protein / Large ribosomal subunit protein uL29m / Uncharacterized protein / Pseudouridylate synthase, putative / WHIM1 domain-containing protein / Uncharacterized protein / Peptidyl-prolyl cis-trans isomerase / Uncharacterized protein / Acyl carrier protein / Uncharacterized protein / Ribosomal protein L3 mitochondrial, putative
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsTobiasson, V. / Gahura, O. / Aibara, S. / Baradaran, R. / Zikova, A. / Amunts, A.
Funding support Sweden, Czech Republic, 6items
OrganizationGrant numberCountry
The Swedish Foundation for Strategic ResearchFFL15:0325 Sweden
Swedish Research CouncilNT_2015-04107 Sweden
European Research Council (ERC)ERC-2018-StG-805230 Sweden
Knut and Alice Wallenberg Foundation2018.0080 Sweden
European Molecular Biology Organization (EMBO)EMBO Young Investigator Program to A.A Sweden
Czech Science Foundation18-17529S Czech Republic
CitationJournal: EMBO J / Year: 2021
Title: Interconnected assembly factors regulate the biogenesis of mitoribosomal large subunit.
Authors: Victor Tobiasson / Ondřej Gahura / Shintaro Aibara / Rozbeh Baradaran / Alena Zíková / Alexey Amunts /
Abstract: Mitoribosomes consist of ribosomal RNA and protein components, coordinated assembly of which is critical for function. We used mitoribosomes from Trypanosoma brucei with reduced RNA and increased ...Mitoribosomes consist of ribosomal RNA and protein components, coordinated assembly of which is critical for function. We used mitoribosomes from Trypanosoma brucei with reduced RNA and increased protein mass to provide insights into the biogenesis of the mitoribosomal large subunit. Structural characterization of a stable assembly intermediate revealed 22 assembly factors, some of which have orthologues/counterparts/homologues in mammalian genomes. These assembly factors form a protein network that spans a distance of 180 Å, shielding the ribosomal RNA surface. The central protuberance and L7/L12 stalk are not assembled entirely and require removal of assembly factors and remodeling of the mitoribosomal proteins to become functional. The conserved proteins GTPBP7 and mt-EngA are bound together at the subunit interface in proximity to the peptidyl transferase center. A mitochondrial acyl-carrier protein plays a role in docking the L1 stalk, which needs to be repositioned during maturation. Additional enzymatically deactivated factors scaffold the assembly while the exit tunnel is blocked. Together, this extensive network of accessory factors stabilizes the immature sites and connects the functionally important regions of the mitoribosomal large subunit.
History
DepositionOct 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Mar 24, 2021Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-11845
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Structure viewerMolecule:
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Assembly

Deposited unit
A1: bL28m
A2: uL29m
A3: uL30m
A5: bL32m
A8: bL33m
AA: mt-LSU rRNA
AE: Ribosomal protein L3 mitochondrial, putative
AF: Ribosomal protein L4/L1 family
AI: RIBOSOMAL_L9 domain-containing protein
AK: Ribosomal protein L11,uL11m
AN: 50S ribosomal protein L13
AP: Ribosomal_L18e/L15P domain-containing protein
AR: 50S ribosomal protein L17
AT: bL19m
AU: bL20m
AV: Ribosomal protein L21
AW: Ribosomal protein L22p/L17e
AX: Ribosomal protein L23
AY: uL24m
Ae: mL41
Af: mL42
Ag: Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain containing protein
Al: mL49
Ao: mL52
Ap: mL53
At: mL63
Av: mL64,mL64
BA: mL67
BB: mL68,mL68,mL68
BD: mL70
BE: mL71
BF: Tetratricopeptide repeat
BH: mL74
BI: Mitochondrial RNA binding complex 1 subunit
BJ: mL76
BK: Chaperone protein DNAj, putative,mL77,Chaperone protein DNAj, putative
BL: mL78
BN: mL80
BO: mL81
BQ: Peptidyl-prolyl cis-trans isomerase
BR: mL84
BS: mL85
BT: mL86
BU: mL87
BW: mL89
BX: LIM domain containing protein,mL90
BZ: Peptidyl-prolyl cis-trans isomerase
Ba: mL93
Bb: mL94
Bc: mL95
Bf: mL98
Bg: mL99
Bh: mL100,mL100
UA: UNK1
UB: UNK2
UC: UNK3
UD: UNK4
UE: UNK5
UF: UNK6/mt-LAF15_2
UG: UNK7
UH: UNK8
UI: UNK9
UJ: UNK10
UK: UNK11
XA: mt-LAF7,mt-LAF7
XB: DEAD-box helicase, putative,mt-LAF2
XC: mt-LAF4
XD: Acyl carrier protein
XE: Acyl carrier protein
XF: mt-LAF15_1
XG: 50S ribosomal protein L14
XH: mt-LAF8
XI: mt-LAF14
XJ: RNA uridylyltransferase
XL: GTP-binding protein, putative,mt-EngA
XM: Complex1-LYR-like
XN: mt-LAF12
XO: SpoU rRNA Methylase family
XP: Pseudouridylate synthase, putative
XQ: GTP-binding protein
XR: Lipase (Class 3)
XS: mL101
XT: mt-LAF19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,333,89493
Polymers2,331,29583
Non-polymers2,59910
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 , 58 types, 59 molecules A1A2A3A5A8AIAPATAUAYAeAfAlAoApAtAvBABBBDBEBFBHBJBKBLBNBOBRBS...

#1: Protein bL28m


Mass: 25444.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6L6A9
#2: Protein uL29m


Mass: 53072.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q38EM7
#3: Protein uL30m


Mass: 17508.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6L456
#4: Protein bL32m


Mass: 6931.294 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6LD92
#5: Protein bL33m


Mass: 17173.025 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6L070
#9: Protein RIBOSOMAL_L9 domain-containing protein


Mass: 25387.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6L8Y1
#12: Protein Ribosomal_L18e/L15P domain-containing protein


Mass: 41643.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6L758
#14: Protein bL19m


Mass: 16154.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6LD66
#15: Protein bL20m


Mass: 22376.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6KV21
#19: Protein uL24m


Mass: 39724.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: C9ZK52
#20: Protein mL41


Mass: 13153.083 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6KTI0
#21: Protein mL42


Mass: 15185.235 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6KXE9
#23: Protein mL49


Mass: 20508.795 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6L7H5
#24: Protein mL52


Mass: 14975.835 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6KS48
#25: Protein mL53


Mass: 33284.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6L3K9
#26: Protein mL63


Mass: 17103.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: C9ZU82
#27: Protein mL64,mL64


Mass: 23722.240 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6KTC7
#28: Protein mL67


Mass: 89787.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: D0A5V6
#29: Protein mL68,mL68,mL68


Mass: 40602.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6KX69
#30: Protein mL70


Mass: 47556.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6L6S3
#31: Protein mL71


Mass: 49032.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: C9ZSQ8
#32: Protein Tetratricopeptide repeat


Mass: 48742.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6LA84
#33: Protein mL74


Mass: 25893.432 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6KXN2
#35: Protein mL76


Mass: 18931.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6KX00
#36: Protein Chaperone protein DNAj, putative,mL77,Chaperone protein DNAj, putative


Mass: 30694.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: C9ZQR6
#37: Protein mL78


Mass: 31316.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6L166
#38: Protein mL80


Mass: 25435.553 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: C9ZQF0
#39: Protein mL81


Mass: 25450.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6KS29
#41: Protein mL84


Mass: 23419.980 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6L538
#42: Protein mL85


Mass: 16955.400 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q38FG8
#43: Protein mL86


Mass: 19667.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6L8W0
#44: Protein mL87


Mass: 9886.448 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6KX50
#45: Protein mL89


Mass: 22082.209 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q57WW5
#46: Protein LIM domain containing protein,mL90


Mass: 13189.013 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6L637
#48: Protein mL93


Mass: 16882.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: D0A4T0
#49: Protein mL94


Mass: 11446.005 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6L3K4
#50: Protein mL95


Mass: 16813.174 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6L276
#51: Protein mL98


Mass: 10096.247 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6L4A5
#52: Protein mL99


Mass: 9313.546 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6LDF0
#53: Protein mL100,mL100


Mass: 10554.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6L2V1
#59: Protein UNK6/mt-LAF15_2


Mass: 9897.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote)
#65: Protein mt-LAF7,mt-LAF7


Mass: 18502.107 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q387S8
#66: Protein DEAD-box helicase, putative,mt-LAF2


Mass: 76345.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: D0A9G9
#67: Protein mt-LAF4


Mass: 69432.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: D0A7A5
#68: Protein Acyl carrier protein


Mass: 9779.900 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q57WW9
#69: Protein mt-LAF15_1


Mass: 21686.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6LB16
#71: Protein mt-LAF8


Mass: 58945.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote)
#72: Protein mt-LAF14


Mass: 78937.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q57U79
#73: Protein RNA uridylyltransferase


Mass: 17337.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6L766, RNA uridylyltransferase
#74: Protein GTP-binding protein, putative,mt-EngA


Mass: 60253.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: C9ZS56
#75: Protein Complex1-LYR-like


Mass: 10607.263 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6L7X4
#76: Protein mt-LAF12


Mass: 70343.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q57YY3
#77: Protein SpoU rRNA Methylase family


Mass: 48529.980 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6L241
#78: Protein Pseudouridylate synthase, putative


Mass: 42582.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q38FJ3
#79: Protein GTP-binding protein


Mass: 33914.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6L0D5
#80: Protein Lipase (Class 3)


Mass: 18808.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6L1Y4
#81: Protein mL101


Mass: 21799.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q4GZ80
#82: Protein mt-LAF19


Mass: 11412.251 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6KWY9

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RNA chain , 1 types, 1 molecules AA

#6: RNA chain mt-LSU rRNA


Mass: 242538.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote)

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Ribosomal protein ... , 6 types, 6 molecules AEAFAKAVAWAX

#7: Protein Ribosomal protein L3 mitochondrial, putative


Mass: 42538.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q580R4
#8: Protein Ribosomal protein L4/L1 family


Mass: 51178.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6KTM7
#10: Protein Ribosomal protein L11,uL11m


Mass: 29590.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6LEQ0
#16: Protein Ribosomal protein L21


Mass: 20182.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6LA68
#17: Protein Ribosomal protein L22p/L17e


Mass: 31952.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6L4Z4
#18: Protein Ribosomal protein L23


Mass: 19685.502 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6KW11

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50S ribosomal protein ... , 3 types, 3 molecules ANARXG

#11: Protein 50S ribosomal protein L13


Mass: 20327.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6LAE5
#13: Protein 50S ribosomal protein L17


Mass: 30480.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6LAG5
#70: Protein 50S ribosomal protein L14


Mass: 19559.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6LE16

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Mitochondrial ... , 2 types, 2 molecules AgBI

#22: Protein Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain containing protein


Mass: 22110.842 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6LCE5
#34: Protein Mitochondrial RNA binding complex 1 subunit


Mass: 37503.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6KZH2

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

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


Mass: 20286.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q57WF8, peptidylprolyl isomerase
#47: Protein Peptidyl-prolyl cis-trans isomerase / PPIase


Mass: 20411.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6KTB1, peptidylprolyl isomerase

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Protein/peptide , 10 types, 10 molecules UAUBUCUDUEUGUHUIUJUK

#54: Protein/peptide UNK1


Mass: 3287.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote)
#55: Protein/peptide UNK2


Mass: 657.715 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote)
#56: Protein/peptide UNK3


Mass: 1013.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote)
#57: Protein/peptide UNK4


Mass: 586.638 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote)
#58: Protein/peptide UNK5


Mass: 870.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote)
#60: Protein/peptide UNK7


Mass: 1368.494 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote)
#61: Protein/peptide UNK8


Mass: 1226.338 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote)
#62: Protein/peptide UNK9


Mass: 2790.050 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote)
#63: Protein/peptide UNK10


Mass: 1794.960 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote)
#64: Protein/peptide UNK11


Mass: 3358.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote)

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Non-polymers , 6 types, 10 molecules

#83: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#84: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


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


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#86: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#87: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#88: 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

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Details

Has ligand of interestN

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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: Trypanosoma brucei mitochondrial ribosome large subunit assembly intermediate
Type: RIBOSOME / Entity ID: #1-#82 / Source: NATURAL
Molecular weightValue: 2.23 MDa / Experimental value: YES
Source (natural)Organism: Trypanosoma brucei (eukaryote) / Cellular location: Mitochondrial Matrix / Organelle: Mitochondrion
Buffer solutionpH: 7.45
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 %

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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
Image recordingElectron dose: 35 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 32300 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT

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