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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


modulation of formation of structure involved in a symbiotic process / rRNA (cytosine-N4-)-methyltransferase activity / ATP-activated inward rectifier potassium channel activity / kinetoplast / quorum sensing / rRNA base methylation / response to arsenic-containing substance / ciliary plasm / mitochondrial small ribosomal subunit / acyl binding ...modulation of formation of structure involved in a symbiotic process / rRNA (cytosine-N4-)-methyltransferase activity / ATP-activated inward rectifier potassium channel activity / kinetoplast / quorum sensing / rRNA base methylation / response to arsenic-containing substance / ciliary plasm / mitochondrial small ribosomal subunit / acyl binding / acyl carrier activity / iron-sulfur cluster binding / voltage-gated potassium channel activity / voltage-gated potassium channel complex / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / potassium ion transport / protein homooligomerization / fatty acid biosynthetic process / structural constituent of ribosome / mitochondrial matrix / translation / mRNA binding / mitochondrion / metal ion binding / membrane / cytosol / cytoplasm
Similarity search - Function
T-cell activation inhibitor, mitochondrial / Domain of unknown function DUF4460 / Domain of unknown function (DUF4460) / Probable Zinc-ribbon domain / Probable Treble clef zinc finger domain / Ribosomal protein Rsm22-like / : / Mitochondrial small ribosomal subunit Rsm22 / Ribosomal RNA small subunit methyltransferase H / S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily ...T-cell activation inhibitor, mitochondrial / Domain of unknown function DUF4460 / Domain of unknown function (DUF4460) / Probable Zinc-ribbon domain / Probable Treble clef zinc finger domain / Ribosomal protein Rsm22-like / : / Mitochondrial small ribosomal subunit Rsm22 / Ribosomal RNA small subunit methyltransferase H / S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily / MraW methylase family / Protein Fyv4 / IGR protein motif / IGR / Phosphotyrosine protein phosphatase I / Phosphotyrosine protein phosphatase I superfamily / Low molecular weight phosphotyrosine protein phosphatase / Low molecular weight phosphatase family / Pentatricopeptide repeat domain / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Pentatricopeptide (PPR) repeat profile. / Pentatricopeptide repeat / Acyl carrier protein (ACP) / Phosphopantetheine attachment site / SKP1/BTB/POZ domain superfamily / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Translation elongation factor EF1B/ribosomal protein S6 / Tetratricopeptide-like helical domain superfamily / Ribosomal protein S11 superfamily / S15/NS1, RNA-binding / Thioredoxin-like superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Chem-PM8 / PHOSPHATE ION / RNA / RNA (> 10) / RNA (> 100) / Uncharacterized protein / Uncharacterized protein / Methyltransferase / Uncharacterized protein / Potassium voltage-gated channel, putative ...Chem-PM8 / PHOSPHATE ION / RNA / RNA (> 10) / RNA (> 100) / Uncharacterized protein / Uncharacterized protein / Methyltransferase / Uncharacterized protein / Potassium voltage-gated channel, putative / Uncharacterized protein / Small ribosomal subunit protein mS41 / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Target SNARE / Phosphotyrosine protein phosphatase I domain-containing protein / DUF4460 domain-containing protein / Uncharacterized protein / Uncharacterized protein / Pentacotripeptide-repeat region of PRORP domain-containing protein / Uncharacterized protein / Glutaredoxin domain-containing protein / S-adenosyl-methyltransferase mraW-like protein, putative / Acyl carrier protein / Pentacotripeptide-repeat region of PRORP domain-containing protein / Treble clef zinc finger domain-containing protein / Succinate dehydrogenase assembly factor 3, mitochondrial / Uncharacterized protein
Similarity search - Component
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.
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
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_entry_details.has_protein_modification / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

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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
Water00
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


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


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


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

-
Details

Has ligand of interestN
Has protein modificationY

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Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: 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
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Body domain of the mitochondrial ribosomal small subunit assemblosome of Trypanosoma brucei brucei Lister strain 427
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 FIELD / Nominal magnification: 59000 X / Calibrated magnification: 100719 X
Specimen holderCryogen: NITROGEN / Specimen holder 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)

-
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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