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- PDB-6sga: Body domain of the mt-SSU assemblosome from Trypanosoma brucei -

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Basic information

Entry
Database: PDB / ID: 6sga
TitleBody domain of the mt-SSU assemblosome from Trypanosoma brucei
Components
  • 9S rRNA
  • UNK-A
  • UNK-B
  • UNK-C
  • UNK-D, UNK-M, UNK-Q
  • UNK-E, UNK-P
  • UNK-F
  • UNK-G
  • UNK-H
  • UNK-I
  • UNK-I, UNK-M
  • UNK-J
  • UNK-L
  • UNK-O
  • UNK-U
  • bS16m
  • bS18m
  • bS6m
  • mS22
  • mS23
  • mS26
  • mS34
  • mS38
  • mS41
  • mS51 (KRIPP1)
  • mS56
  • mS59
  • mS62 (KRIPP14)
  • mS63 (KRIPP16)
  • mS65
  • mS68
  • mS73
  • mt-SAF1 (RSM22)
  • mt-SAF10
  • mt-SAF11
  • mt-SAF13
  • mt-SAF14
  • mt-SAF18
  • mt-SAF2 (KRIPP2)
  • mt-SAF21
  • mt-SAF22 (KRIPP17)
  • mt-SAF23
  • mt-SAF24
  • mt-SAF26
  • mt-SAF27
  • mt-SAF28
  • mt-SAF29
  • mt-SAF3
  • mt-SAF30
  • mt-SAF31
  • mt-SAF32
  • mt-SAF33
  • mt-SAF5
  • mt-SAF6
  • mt-SAF7 (KRIPP10)
  • mt-SAF8
  • mt-SAF9
  • uS11m
  • uS15m
  • uS17m
  • uS5m
  • uS8m
KeywordsRIBOSOME / mitochondrial ribosome / assembly intermediate / translation
Function / homology
Function and homology information


rRNA (cytosine-N4-)-methyltransferase activity / modulation of development of symbiont involved in interaction with host / ATP-activated inward rectifier potassium channel activity / kinetoplast / mitochondrial small ribosomal subunit / rRNA base methylation / acyl binding / mitochondrial respiratory chain complex I / acyl carrier activity / ciliary plasm ...rRNA (cytosine-N4-)-methyltransferase activity / modulation of development of symbiont involved in interaction with host / ATP-activated inward rectifier potassium channel activity / kinetoplast / mitochondrial small ribosomal subunit / rRNA base methylation / acyl binding / mitochondrial respiratory chain complex I / acyl carrier activity / ciliary plasm / potassium ion transmembrane transport / voltage-gated potassium channel complex / voltage-gated potassium channel activity / potassium ion transport / protein homooligomerization / Transferases; Transferring one-carbon groups; Methyltransferases / fatty acid biosynthetic process / methyltransferase activity / structural constituent of ribosome / mitochondrial matrix / translation / mitochondrion / membrane / integral component of membrane / cytosol / cytoplasm
Probable Zinc-ribbon domain / Domain of unknown function DUF4460 / S15/NS1, RNA-binding / Phosphopantetheine binding ACP domain / SKP1/BTB/POZ domain superfamily / Tetratricopeptide-like helical domain superfamily / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein Rsm22-like / IGR protein motif / S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily ...Probable Zinc-ribbon domain / Domain of unknown function DUF4460 / S15/NS1, RNA-binding / Phosphopantetheine binding ACP domain / SKP1/BTB/POZ domain superfamily / Tetratricopeptide-like helical domain superfamily / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein Rsm22-like / IGR protein motif / S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily / Phosphotyrosine protein phosphatase I / Ribosomal protein S16 domain superfamily / T-cell activation inhibitor, mitochondrial / S-adenosyl-L-methionine-dependent methyltransferase / Acyl carrier protein (ACP) / Phosphotyrosine protein phosphatase I superfamily / Thioredoxin-like superfamily / ACP-like superfamily / Ribosomal protein S11 superfamily / Protein Fyv4 / Mitochondrial small ribosomal subunit Rsm22 / Domain of unknown function (DUF4460) / MraW methylase family / BTB/POZ domain / Low molecular weight phosphotyrosine protein phosphatase / Pentatricopeptide repeat domain / Phosphopantetheine attachment site / Phosphopantetheine attachment site / Probable Zinc-ribbon domain / Potassium channel tetramerisation-type BTB domain / Ribosomal RNA small subunit methyltransferase H / Pentatricopeptide repeat
Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / DUF4379 domain-containing protein / Uncharacterized protein / Acyl carrier protein / S-adenosyl-methyltransferase mraW-like protein, putative / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein ...Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / DUF4379 domain-containing protein / Uncharacterized protein / Acyl carrier protein / S-adenosyl-methyltransferase mraW-like protein, putative / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / DUF4460 domain-containing protein / LMWPc domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Potassium voltage-gated channel, putative / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Protein FYV4, mitochondrial
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsSaurer, M. / Ramrath, D.J.F. / Niemann, M. / Calderaro, S. / Prange, C. / Mattei, S. / Scaiola, A. / Leitner, A. / Bieri, P. / Horn, E.K. ...Saurer, M. / Ramrath, D.J.F. / Niemann, M. / Calderaro, S. / Prange, C. / Mattei, S. / Scaiola, A. / Leitner, A. / Bieri, P. / Horn, E.K. / Leibundgut, M. / Boehringer, D. / Schneider, A. / Ban, N.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Science / Year: 2019
Title: Mitoribosomal small subunit biogenesis in trypanosomes involves an extensive assembly machinery.
Authors: Martin Saurer / David J F Ramrath / Moritz Niemann / Salvatore Calderaro / Céline Prange / Simone Mattei / Alain Scaiola / Alexander Leitner / Philipp Bieri / Elke K Horn / Marc Leibundgut ...Authors: Martin Saurer / David J F Ramrath / Moritz Niemann / Salvatore Calderaro / Céline Prange / Simone Mattei / Alain Scaiola / Alexander Leitner / Philipp Bieri / Elke K Horn / Marc Leibundgut / Daniel Boehringer / André Schneider / Nenad Ban /
Abstract: Mitochondrial ribosomes (mitoribosomes) are large ribonucleoprotein complexes that synthesize proteins encoded by the mitochondrial genome. An extensive cellular machinery responsible for ribosome ...Mitochondrial ribosomes (mitoribosomes) are large ribonucleoprotein complexes that synthesize proteins encoded by the mitochondrial genome. An extensive cellular machinery responsible for ribosome assembly has been described only for eukaryotic cytosolic ribosomes. Here we report that the assembly of the small mitoribosomal subunit in involves a large number of factors and proceeds through the formation of assembly intermediates, which we analyzed by using cryo-electron microscopy. One of them is a 4-megadalton complex, referred to as the small subunit assemblosome, in which we identified 34 factors that interact with immature ribosomal RNA (rRNA) and recognize its functionally important regions. The assembly proceeds through large-scale conformational changes in rRNA coupled with successive incorporation of mitoribosomal proteins, providing an example for the complexity of the ribosomal assembly process in mitochondria.
Validation Report
SummaryFull reportAbout validation report
History
DepositionAug 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
CE: uS5m
CF: bS6m
CH: uS8m
CK: uS11m
CO: uS15m
CP: bS16m
CQ: uS17m
CR: bS18m
Ca: mS22
Cb: mS23
Cd: mS26
Cj: mS34
Cn: mS38
Cp: mS41
DD: mS51 (KRIPP1)
DI: mS56
DL: mS59
DO: mS62 (KRIPP14)
DP: mS63 (KRIPP16)
DR: mS65
DU: mS68
DZ: mS73
F2: mt-SAF2 (KRIPP2)
F3: mt-SAF3
F5: mt-SAF5
F6: mt-SAF6
F7: mt-SAF7 (KRIPP10)
F8: mt-SAF8
F9: mt-SAF9
FA: mt-SAF10
FB: mt-SAF11
FC: mt-SAF11
FE: mt-SAF13
FJ: mt-SAF18
FM: mt-SAF21
FN: mt-SAF21
FO: mt-SAF22 (KRIPP17)
FP: mt-SAF23
FQ: mt-SAF24
FR: mt-SAF24
FS: mt-SAF24
FT: mt-SAF24
FU: mt-SAF24
FW: mt-SAF26
FX: mt-SAF27
FY: mt-SAF28
FZ: mt-SAF29
Fa: mt-SAF30
Fb: mt-SAF31
Fc: mt-SAF32
Fd: mt-SAF33
UA: UNK-A
UB: UNK-B
UC: UNK-C
UD: UNK-D, UNK-M, UNK-Q
UE: UNK-E, UNK-P
UF: UNK-F
UG: UNK-G
UH: UNK-H
UI: UNK-I, UNK-M
UJ: UNK-J
UL: UNK-L
UM: UNK-D, UNK-M, UNK-Q
UN: UNK-I, UNK-M
UO: UNK-O
UP: UNK-E, UNK-P
UQ: UNK-D, UNK-M, UNK-Q
UU: UNK-U
UY: UNK-I
CA: 9S rRNA
F1: mt-SAF1 (RSM22)
FF: mt-SAF14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,643,87779
Polymers2,643,12272
Non-polymers7547
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 48 types, 54 molecules CECFCHCKCOCPCQCRCaCbCdCjCnCpDDDIDLDODPDRDUDZF2F3F5F6F7F8F9FA...

#1: Protein uS5m


Mass: 50147.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#2: Protein bS6m


Mass: 18861.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q38BW5
#3: Protein uS8m


Mass: 32766.459 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#4: Protein uS11m


Mass: 37953.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q389T7
#5: Protein uS15m


Mass: 50401.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q4GZ99
#6: Protein bS16m


Mass: 22077.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q384N9
#7: Protein uS17m


Mass: 39012.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence; C-terminal PTP-tag
Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#8: Protein bS18m


Mass: 36988.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#9: Protein mS22


Mass: 73064.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q38DR3
#10: Protein mS23


Mass: 35358.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#11: Protein mS26


Mass: 51136.684 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q38DK6
#12: Protein mS34


Mass: 28728.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q57UK0
#13: Protein mS38


Mass: 28240.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q57VQ9
#14: Protein mS41


Mass: 22421.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q389L3
#15: Protein mS51 (KRIPP1)


Mass: 95080.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#16: Protein mS56


Mass: 47306.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#17: Protein mS59


Mass: 35395.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#18: Protein mS62 (KRIPP14)


Mass: 32068.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q383D1
#19: Protein mS63 (KRIPP16)


Mass: 31922.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#20: Protein mS65


Mass: 30617.381 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#21: Protein mS68


Mass: 26472.807 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#22: Protein mS73


Mass: 11360.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q587C4
#23: Protein mt-SAF2 (KRIPP2)


Mass: 116189.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#24: Protein mt-SAF3


Mass: 106621.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q38E61
#25: Protein mt-SAF5


Mass: 86949.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#26: Protein mt-SAF6


Mass: 76781.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q38FQ8
#27: Protein mt-SAF7 (KRIPP10)


Mass: 76675.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q57UW6
#28: Protein mt-SAF8


Mass: 76725.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#29: Protein mt-SAF9


Mass: 69781.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#30: Protein mt-SAF10


Mass: 69306.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q386U1
#31: Protein mt-SAF11


Mass: 64916.957 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#32: Protein mt-SAF13


Mass: 63690.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#33: Protein mt-SAF18


Mass: 42508.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#34: Protein mt-SAF21


Mass: 39610.793 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#35: Protein mt-SAF22 (KRIPP17)


Mass: 39132.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q389F9
#36: Protein mt-SAF23


Mass: 38240.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#37: Protein
mt-SAF24


Mass: 34648.047 Da / Num. of mol.: 5 / Source method: isolated from a natural source
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q387P8
#38: Protein mt-SAF26


Mass: 30538.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q38FI3
#39: Protein mt-SAF27


Mass: 26936.748 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q57YK5
#40: Protein mt-SAF28


Mass: 21468.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#41: Protein mt-SAF29


Mass: 20048.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#42: Protein mt-SAF30


Mass: 19659.756 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q57VU7
#43: Protein mt-SAF31


Mass: 17673.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q581U4
#44: Protein mt-SAF32


Mass: 16550.807 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q57WW9
#45: Protein mt-SAF33


Mass: 16291.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q581T4
#59: Protein UNK-I


Mass: 39847.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#61: Protein mt-SAF1 (RSM22)


Mass: 119799.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q385R2
#62: Protein mt-SAF14


Mass: 53320.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence
Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q57W60

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Protein/peptide , 13 types, 17 molecules UAUBUCUDUMUQUEUPUFUGUHUIUNUJULUOUU

#46: Protein/peptide UNK-A


Mass: 1805.216 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#47: Protein/peptide UNK-B


Mass: 2315.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#48: Protein/peptide UNK-C


Mass: 869.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#49: Protein/peptide UNK-D, UNK-M, UNK-Q


Mass: 783.958 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#50: Protein/peptide UNK-E, UNK-P


Mass: 3847.734 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#51: Protein/peptide UNK-F


Mass: 954.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#52: Protein/peptide UNK-G


Mass: 1464.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#53: Protein/peptide UNK-H


Mass: 443.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#54: Protein/peptide UNK-I, UNK-M


Mass: 698.854 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#55: Protein/peptide UNK-J


Mass: 1379.692 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#56: Protein/peptide UNK-L


Mass: 1890.321 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#57: Protein/peptide UNK-O


Mass: 2571.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#58: Protein/peptide UNK-U


Mass: 2060.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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RNA chain , 1 types, 1 molecules CA

#60: RNA chain 9S rRNA


Mass: 151505.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 9S ribosomal RNA from Trypanosoma brucei. GenBank: X02547.1 and S66467.1 Sequence of 3'-major domain omitted.
Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Non-polymers , 4 types, 7 molecules

#63: Chemical
ChemComp-MG / MAGNESIUM ION / Magnesium


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#64: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#65: Chemical ChemComp-PM8 / S-(2-{[N-(2-HYDROXY-4-{[HYDROXY(OXIDO)PHOSPHINO]OXY}-3,3-DIMETHYLBUTANOYL)-BETA-ALANYL]AMINO}ETHYL) DECANETHIOATE


Mass: 496.598 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H41N2O7PS
#66: Chemical ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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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: Body domain of the mt-SSU assemblosome / Type: RIBOSOME / Entity ID: #1-#62 / Source: NATURAL
Source (natural)Organism: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
Buffer solutionpH: 7.4
SpecimenDetails: Body domain of the mitochondrial ribosomal small subunit assemblosome of Trypanosoma brucei brucei Lister strain 427
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 90 % / Chamber temperature: 278 K

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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 / Nominal magnification: 59000 X / Calibrated magnification: 100719 X
Specimen holderCryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER
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
2EPUimage acquisition
4GctfCTF correction
9RELIONinitial Euler assignment
10RELIONfinal Euler assignment
12RELION3D reconstruction
CTF correctionDetails: On the fly in RELION / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 161661 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: OTHER
Details: Starting models of ribosomal proteins of the T. brucei mitochondrial ribosomal small subunit were taken from PDB 6HIW. Mitchondrial ribosomal small subunit assembly factors were built de novo.

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