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- PDB-6hix: Cryo-EM structure of the Trypanosoma brucei mitochondrial ribosom... -

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Entry
Database: PDB / ID: 6hix
TitleCryo-EM structure of the Trypanosoma brucei mitochondrial ribosome - This entry contains the large mitoribosomal subunit
Components
  • (50S ribosomal protein ...) x 3
  • (Peptidyl-prolyl cis-trans ...) x 2
  • (Ribosomal protein ...) x 3
  • (UNK) x 13
  • (bL12m) x 3
  • 12S rRNAMT-RNR1
  • Chaperone protein DNAj, putative
  • bl19m
  • bl20m
  • bl21m
  • bl27m
  • bl28m
  • bl31m
  • bl32m
  • bl33m
  • bl35m
  • bl36m
  • bl9m
  • mL70
  • ml100
  • ml38
  • ml40
  • ml41
  • ml42
  • ml43
  • ml46
  • ml49
  • ml52
  • ml53
  • ml63
  • ml64
  • ml67
  • ml68
  • ml69
  • ml71
  • ml72
  • ml73
  • ml74
  • ml75
  • ml76
  • ml78
  • ml79
  • ml80
  • ml81
  • ml82
  • ml84
  • ml85
  • ml86
  • ml87
  • ml88
  • ml89
  • ml90
  • ml91
  • ml93
  • ml94
  • ml95
  • ml96
  • ml97
  • ml98
  • ml99
  • ul10m
  • ul15m
  • ul22m
  • ul23m
  • ul24m
  • ul29m
  • ul30m
KeywordsRIBOSOME / mitoribosome / translation / Trypanosoma / large ribosomal subunit / 12S rRNA / ribosomal protein
Function / homologyRibosomal protein L16p/L10e / Ribosomal protein L18e/L15P / Ribosomal protein L20, C-terminal / Alpha/Beta hydrolase fold / Cyclophilin-like domain superfamily / Ribosomal protein L21-like / Ribosomal protein L28/L24 / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / Ribosomal protein L4 domain superfamily / Ribosomal protein L46, N-terminal ...Ribosomal protein L16p/L10e / Ribosomal protein L18e/L15P / Ribosomal protein L20, C-terminal / Alpha/Beta hydrolase fold / Cyclophilin-like domain superfamily / Ribosomal protein L21-like / Ribosomal protein L28/L24 / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / Ribosomal protein L4 domain superfamily / Ribosomal protein L46, N-terminal / Ribosomal protein L11, N-terminal / L21-like superfamily / Ribosomal protein L11, C-terminal / Ribosomal protein L9, N-terminal / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L10e/L16 / Ribosomal protein L30, ferredoxin-like fold domain / NUDIX hydrolase-like domain superfamily / Ribosomal protein L2, domain 2 / Ribosomal protein L25/L23 / 50S ribosomal protein uL4 / Phosphatidylethanolamine-binding protein, eukaryotic / Ribosomal L18e/L15P superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L3 / Ribosomal protein L23 / LIM domain / Ribosomal protein L22p/L17e / DnaJ domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Ribosomal protein L33 superfamily / MRP-L47 superfamily, mitochondrial / Ribosomal protein L28/L24 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Zinc finger C2H2 superfamily / Ribosomal protein L13 superfamily / Rhodanese-like domain superfamily / Chaperone J-domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11, C-terminal domain superfamily / PEBP-like superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein L17 superfamily / Thioredoxin-like superfamily / Ribosomal protein L23/L15e core domain superfamily / Tetratricopeptide-like helical domain superfamily / Ribosomal protein L30p/L7e / Ribosomal protein L9, N-terminal domain / Ribosomal protein L16 / Ribosomal protein L47, mitochondrial / Ribosomal protein L13 / Ribosomal protein L4/L1 family / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal prokaryotic L21 protein / Ribosomal protein L17 / Ribosomal protein L11, N-terminal domain / Ribosomal protein L17 / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Mitochondrial 39-S ribosomal protein L47 (MRP-L47) / 39S mitochondrial ribosomal protein L46 / LIM domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / dnaJ domain profile. / Pentatricopeptide (PPR) repeat profile. / Ribosomal protein L9 / AMP-binding enzyme / Ribosomal protein L3 / Ribosomal protein L4/L1e / Translation protein, beta-barrel domain superfamily / Translation protein SH3-like domain superfamily / Ribosomal protein/NADH dehydrogenase domain / Ribosomal protein L13 / Ribosomal protein L20 / Ribosomal protein L15, bacterial-type / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L24 / AMP-dependent synthetase/ligase / Pentatricopeptide repeat / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Ribosomal protein L21 / Zinc finger, LIM-type / DnaJ domain / Ribosomal protein L22/L17 / Ribosomal protein L11/L12 / Ribosomal protein L11, RNA binding domain / organellar large ribosomal subunit / mitochondrial mRNA editing complex / RNA polyadenylation / mitochondrial RNA processing / mitochondrial ribosome / mitochondrial large ribosomal subunit / mitochondrial translation / posttranscriptional regulation of gene expression / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / catalytic activity / large ribosomal subunit / ribosomal large subunit assembly / protein folding
Function and homology information
Specimen sourceTrypanosoma brucei brucei (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.39 Å resolution
AuthorsRamrath, D.J.F. / Niemann, M. / Leibundgut, M. / Bieri, P. / Prange, C. / Horn, K. / Leitner, A. / Boehringer, D. / Schneider, A. / Ban, N.
CitationJournal: Science / Year: 2018
Title: Evolutionary shift toward protein-based architecture in trypanosomal mitochondrial ribosomes.
Authors: David J F Ramrath / Moritz Niemann / Marc Leibundgut / Philipp Bieri / Céline Prange / Elke K Horn / Alexander Leitner / Daniel Boehringer / André Schneider / Nenad Ban
Abstract: Ribosomal RNA (rRNA) plays key functional and architectural roles in ribosomes. Using electron microscopy, we determined the atomic structure of a highly divergent ribosome found in mitochondria of , ...Ribosomal RNA (rRNA) plays key functional and architectural roles in ribosomes. Using electron microscopy, we determined the atomic structure of a highly divergent ribosome found in mitochondria of , a unicellular parasite that causes sleeping sickness in humans. The trypanosomal mitoribosome features the smallest rRNAs and contains more proteins than all known ribosomes. The structure shows how the proteins have taken over the role of architectural scaffold from the rRNA: They form an autonomous outer shell that surrounds the entire particle and stabilizes and positions the functionally important regions of the rRNA. Our results also reveal the "minimal" set of conserved rRNA and protein components shared by all ribosomes that help us define the most essential functional elements.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 31, 2018 / Release: Sep 26, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Sep 26, 2018Structure modelrepositoryInitial release
1.1Nov 7, 2018Structure modelData collection / Database references / Source and taxonomycitation / entity_src_gen_citation.journal_volume / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_scientific_name

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Structure visualization

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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-0231
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Structure viewerMolecule:
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Assembly

Deposited unit
A0: bl27m
A1: bl28m
A2: ul29m
A3: ul30m
A4: bl31m
A5: bl32m
A6: bl33m
A8: bl35m
A9: bl36m
AE: Ribosomal protein L3 mitochondrial, putative
AF: Ribosomal protein L4/L1 family, putative
AI: bl9m
AJ: ul10m
AK: Ribosomal protein L11, putative
AN: 50S ribosomal protein L13, putative
AP: ul15m
AQ: 50S ribosomal protein L16, putative
AR: 50S ribosomal protein L17, putative
AT: bl19m
AU: bl20m
AV: bl21m
AW: ul22m
AX: ul23m
AY: ul24m
Ab: ml38
Ad: ml40
Ae: ml41
Af: ml42
Ag: ml43
Aj: ml46
Al: ml49
Ao: ml52
Ap: ml53
At: ml63
Av: ml64
AB: bL12m
AC: bL12m
AD: bL12m
AG: bL12m
AA: 12S rRNA
BA: ml67
BB: ml68
BC: ml69
BD: mL70
BE: ml71
BF: ml72
BG: ml73
BH: ml74
BI: ml75
BJ: ml76
BK: Chaperone protein DNAj, putative
BL: ml78
BM: ml79
BN: ml80
BO: ml81
BP: ml82
BQ: Peptidyl-prolyl cis-trans isomerase
BR: ml84
BS: ml85
BT: ml86
BU: ml87
BV: ml88
BW: ml89
BX: ml90
BY: ml91
BZ: Peptidyl-prolyl cis-trans isomerase
Ba: ml93
Bb: ml94
Bc: ml95
Bd: ml96
Be: ml97
Bf: ml98
Bg: ml99
Bh: ml100
UA: UNK
UB: UNK
UC: UNK
UD: UNK
UE: UNK
UF: UNK
UG: UNK
UH: UNK
UI: UNK
UK: UNK
UL: UNK
UM: UNK
UN: UNK
UU: UNK
UV: UNK
UW: UNK
UX: UNK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,560,420105
Polyers2,559,19491
Non-polymers1,22614
Water0
1


  • idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein/peptide , 77 types, 82 molecules A0A1A2A3A4A5A6A8A9AIAJAPATAUAVAWAXAYAbAdAeAfAgAjAlAoApAtAvAB...

#1: Protein/peptide bl27m


Mass: 21793.092 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: TEOVI_000532300 / Production host: Trypanosoma brucei brucei (eukaryote) / References: UniProt: A0A1G4I8T3
#2: Protein/peptide bl28m


Mass: 28051.373 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: Tb927.6.4040 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: Q586A2
#3: Protein/peptide ul29m


Mass: 54045.367 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: Tb09.160.5240 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: Q38EM7
#4: Protein/peptide ul30m


Mass: 25204.334 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: TbgDal_IX4520 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: C9ZY77
#5: Protein/peptide bl31m


Mass: 21083.229 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: Tb10.6k15.1920 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: Q38AB0
#6: Protein/peptide bl32m


Mass: 9745.710 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: Tb927.4.2330 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: Q584F4
#7: Protein/peptide bl33m


Mass: 13042.740 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: Tb927.4.1810 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: Q581Q0
#8: Protein/peptide bl35m


Mass: 21661.453 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: TbgDal_X2260 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: D0A1K1
#9: Protein/peptide bl36m


Mass: 21795.227 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: TbgDal_IV4820 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: C9ZMA9
#12: Protein/peptide bl9m


Mass: 31032.697 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: Tb927.5.3410 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: Q57UC5
#13: Protein/peptide ul10m


Mass: 20283.566 Da / Num. of mol.: 1 / Details: residues 106-129 built as polyalanines / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: TbgDal_V3970 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: C9ZPD1
#16: Protein/peptide ul15m


Mass: 43780.016 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: Tb927.5.3980 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: Q57U68
#19: Protein/peptide bl19m


Mass: 16931.455 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: TB927.1.1210 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: Q4GZ98
#20: Protein/peptide bl20m


Mass: 24393.943 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: Tb11.01.1930 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: Q383R2
#21: Protein/peptide bl21m


Mass: 20895.268 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: TbgDal_VII4650 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: C9ZT11
#22: Protein/peptide ul22m


Mass: 32083.285 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: TbgDal_VII3160 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: C9ZSI8
#23: Protein/peptide ul23m


Mass: 28822.936 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: Tb11.03.0260 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: Q387G3
#24: Protein/peptide ul24m


Mass: 43999.047 Da / Num. of mol.: 1 / Details: residues 313-340 built as polyalanines / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: TbgDal_III1550 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: C9ZK52
#25: Protein/peptide ml38


Mass: 58437.895 Da / Num. of mol.: 1 / Details: residues 41-53 and 294-311 built as polyalanines / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: Tb11.01.6620 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: Q381T7
#26: Protein/peptide ml40


Mass: 33646.066 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: TbgDal_X14530 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: D0A511
#27: Protein/peptide ml41


Mass: 22556.877 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: TbgDal_XI11060 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: D0A8I6
#28: Protein/peptide ml42


Mass: 21602.639 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: Tb11.01.1840 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: Q383S1
#29: Protein/peptide ml43


Mass: 31300.406 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: Tb927.4.4600 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: Q583E5
#30: Protein/peptide ml46


Mass: 33984.199 Da / Num. of mol.: 1 / Details: residues 149-159 built as polyalanines / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: TbgDal_VII5370 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: C9ZT91
#31: Protein/peptide ml49


Mass: 24501.486 Da / Num. of mol.: 1 / Details: residues 102-109 built as polyalanines / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: Tb927.5.3110 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: Q57Z82
#32: Protein/peptide ml52


Mass: 29175.984 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: Tb11.02.2250 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: Q385V2
#33: Protein/peptide ml53


Mass: 35656.383 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: Tb927.7.2990, Tb927.7.3030 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: Q57YA9
#34: Protein/peptide ml63


Mass: 18213.924 Da / Num. of mol.: 1 / Details: residues 64-73 built as polyalanines / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: TbgDal_VII8230 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: C9ZU82
#35: Protein/peptide ml64


Mass: 28545.977 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: Tb11.01.3500 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: Q383B7
#36: Protein/peptide bL12m


Mass: 3998.370 Da / Num. of mol.: 1 / Details: residues built as UNK / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427
#37: Protein/peptide bL12m


Mass: 2008.194 Da / Num. of mol.: 2 / Details: residues built as UNK / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427
#38: Protein/peptide bL12m


Mass: 1937.116 Da / Num. of mol.: 1 / Details: residues built as UNK / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427
#40: Protein/peptide ml67


Mass: 93569.273 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: TbgDal_XI1730 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: D0A5V6
#41: Protein/peptide ml68


Mass: 62806.293 Da / Num. of mol.: 1 / Details: residues 264-343 built as polyalanines / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: TbgDal_X580 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: D0A135
#42: Protein/peptide ml69


Mass: 59010.855 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: Tb927.6.2010 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: Q584V5
#43: Protein/peptide mL70


Mass: 62442.410 Da / Num. of mol.: 1 / Details: residues built as polyalanines / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427
#44: Protein/peptide ml71


Mass: 50313.797 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: Tb927.7.3460 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: Q57WG1
#45: Protein/peptide ml72


Mass: 49407.000 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: TbgDal_VI3710 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: C9ZR63
#46: Protein/peptide ml73


Mass: 41857.875 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: Tb927.7.6800 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: Q57Y49
#47: Protein/peptide ml74


Mass: 39765.176 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: Tb10.6k15.3290 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: Q38AM5
#48: Protein/peptide ml75


Mass: 39841.617 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: Tb10.70.7960 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: Q38CK0
#49: Protein/peptide ml76


Mass: 39638.914 Da / Num. of mol.: 1 / Details: residues 168-176 built as polyalanines / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: Tb11.01.2340 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: Q383M2
#50: Protein/peptide Chaperone protein DNAj, putative /


Mass: 43819.699 Da / Num. of mol.: 1 / Details: residues 248-281 built as polyalanines / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: TbgDal_VI2240 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: C9ZQR6
#51: Protein/peptide ml78


Mass: 35104.535 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: TbgDal_X13360 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: D0A4P5
#52: Protein/peptide ml79


Mass: 33079.617 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: Tb11.01.7140 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: Q381N5
#53: Protein/peptide ml80


Mass: 34883.273 Da / Num. of mol.: 1 / Details: residues 145-174 built as polyalanines / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: Tb927.6.1440 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: Q585A3
#54: Protein/peptide ml81


Mass: 29284.467 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: TbgDal_XI6240 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: D0A755
#55: Protein/peptide ml82


Mass: 29283.676 Da / Num. of mol.: 1 / Details: residues 153-162 built as polyalanines / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: TbgDal_X19420 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: D0A0S6
#57: Protein/peptide ml84


Mass: 24773.643 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: Tb927.6.4080 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: Q586A6
#58: Protein/peptide ml85


Mass: 22657.951 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: Tb09.160.2250 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: Q38FG8
#59: Protein/peptide ml86


Mass: 22376.191 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: TbgDal_V5660 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: C9ZPU8
#60: Protein/peptide ml87


Mass: 22337.521 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: TbgDal_XI9190 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: D0A7Z9
#61: Protein/peptide ml88


Mass: 22255.590 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: TbgDal_VIII1510 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: C9ZUW3
#62: Protein/peptide ml89


Mass: 22213.406 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: Tb927.3.820 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: Q57WW5
#63: Protein/peptide ml90


Mass: 22123.414 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: Tb927.6.1700 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: Q585P1
#64: Protein/peptide ml91


Mass: 20618.520 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: Tb927.3.5300 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: Q580U5
#66: Protein/peptide ml93


Mass: 18929.691 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: TbgDal_X13710 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: D0A4T0
#67: Protein/peptide ml94


Mass: 17830.959 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: Tb09.160.5050 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: Q38EP7
#68: Protein/peptide ml95


Mass: 17803.377 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: Tb10.26.0585 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: Q389K3
#69: Protein/peptide ml96


Mass: 16387.654 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: Tb11.01.6285 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: Q381W9
#70: Protein/peptide ml97


Mass: 12974.785 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: Tb10.61.3115 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: Q388L8
#71: Protein/peptide ml98


Mass: 12968.644 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: Tb10.61.3155 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: Q388M2
#72: Protein/peptide ml99


Mass: 12334.969 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: Tb927.2.2590 / Production host: Trypanosoma brucei brucei (eukaryote) / References: UniProt: Q587H8
#73: Protein/peptide ml100


Mass: 10600.362 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: TEOVI_000790200 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: A0A1G4HYZ0
#74: Protein/peptide UNK


Mass: 3932.839 Da / Num. of mol.: 1 / Details: unassigned residues built as UNK / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427
#75: Protein/peptide UNK


Mass: 3422.209 Da / Num. of mol.: 1 / Details: unassigned residues built as UNK / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427
#76: Protein/peptide UNK


Mass: 1039.273 Da / Num. of mol.: 2 / Details: unassigned residues built as UNK / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427
#77: Protein/peptide UNK


Mass: 15081.565 Da / Num. of mol.: 1 / Details: unassigned residues built as UNK / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427
#78: Protein/peptide UNK


Mass: 1890.321 Da / Num. of mol.: 1 / Details: unassigned residues built as UNK / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427
#79: Protein/peptide UNK


Mass: 2060.531 Da / Num. of mol.: 3 / Details: unassigned residues built as UNK / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427
#80: Protein/peptide UNK


Mass: 1464.797 Da / Num. of mol.: 1 / Details: unassigned residues built as UNK / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427
#81: Protein/peptide UNK


Mass: 869.063 Da / Num. of mol.: 1 / Details: unassigned residues built as UNK / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427
#82: Protein/peptide UNK


Mass: 1294.587 Da / Num. of mol.: 1 / Details: unassigned residues built as UNK / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427
#83: Protein/peptide UNK


Mass: 528.644 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427
#84: Protein/peptide UNK


Mass: 954.168 Da / Num. of mol.: 1 / Details: unassigned residues built as UNK / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427
#85: Protein/peptide UNK


Mass: 698.854 Da / Num. of mol.: 2 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427
#86: Protein/peptide UNK


Mass: 613.749 Da / Num. of mol.: 1 / Details: unassigned residues built as UNK / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427

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

#10: Protein/peptide Ribosomal protein L3 mitochondrial, putative / Ribosome


Mass: 55073.699 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: Tb927.3.5610 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: Q580R4
#11: Protein/peptide Ribosomal protein L4/L1 family, putative / Ribosome


Mass: 53156.664 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: TEOVI_000582800 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: A0A1G4HYD1
#14: Protein/peptide Ribosomal protein L11, putative / Ribosome


Mass: 40252.750 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: Tb927.2.4740, Tb927.2.4890 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: Q586R9

+
50S ribosomal protein ... , 3 types, 3 molecules ANAQAR

#15: Protein/peptide 50S ribosomal protein L13, putative / Ribosome


Mass: 24341.309 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: Tb927.4.1070 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: Q580D5
#17: Protein/peptide 50S ribosomal protein L16, putative / Ribosome


Mass: 19158.145 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: Tb927.7.3960 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: Q57UM6
#18: Protein/peptide 50S ribosomal protein L17, putative / Ribosome


Mass: 35117.824 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: Tb927.8.5860 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: Q57YI7

+
RNA chain , 1 types, 1 molecules AA

#39: RNA chain 12S rRNA / MT-RNR1


Mass: 376748.500 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: GenBank: 343546

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

#56: Protein/peptide Peptidyl-prolyl cis-trans isomerase / Prolyl isomerase / PPIase


Mass: 25579.004 Da / Num. of mol.: 1 / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: Tb927.7.3430 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: Q57WF8, peptidylprolyl isomerase
#65: Protein/peptide Peptidyl-prolyl cis-trans isomerase / Prolyl isomerase / PPIase


Mass: 20542.291 Da / Num. of mol.: 1 / Details: residues 46-64 built as polyalanines / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427 / Gene: Tb11.01.1215 / Production host: Trypanosoma brucei brucei (eukaryote) / Strain (production host): Lister 427 / References: UniProt: Q383Y4, peptidylprolyl isomerase

+
Non-polymers , 3 types, 14 molecules

#87: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Formula: Zn / Zinc
#88: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Formula: C21H27N7O14P2 / Nicotinamide adenine dinucleotide / Comment: NAD *YM
#89: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Formula: Mg / Magnesium

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: large subunit of the T. brucei mitoribosome / Type: RIBOSOME
Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86
Source: NATURAL
Molecular weightValue: 1.9 MDa / Experimental value: YES
Source (natural)Organism: Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 98 % / Chamber temperature: 278 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 40 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameCategory
1EMANparticle selection
4CTFFINDCTF correction
10RELIONfinal Euler assignment
11RELIONclassification
12RELION3D reconstruction
13Cootmodel refinement
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 31619 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingDetails: We used Coot and O ofr initial model building and refined the structure using PHENIX
Overall b value: 52.2 / Ref protocol: AB INITIO MODEL

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