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- PDB-6sg9: Head domain of the mt-SSU assemblosome from Trypanosoma brucei -

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Basic information

Entry
Database: PDB / ID: 6sg9
TitleHead domain of the mt-SSU assemblosome from Trypanosoma brucei
Components
  • 9S rRNA
  • UNK-a
  • UNK-b
  • UNK-c
  • UNK-d
  • UNK-e
  • UNK-f
  • UNK-g
  • UNK-h
  • UNK-i
  • UNK-j
  • UNK-k
  • UNK-l
  • UNK-m
  • UNK-x
  • mS29
  • mS33
  • mS35
  • mS38
  • mS49
  • mS50
  • mS52
  • mS53
  • mS54
  • mS55 (KRIPP8)
  • mS57
  • mS58
  • mS67
  • mS69
  • mS70
  • mS71
  • mS72
  • mt-SAF1 (RSM22)
  • mt-SAF12 (KRIPP18)
  • mt-SAF14
  • mt-SAF15
  • mt-SAF16
  • mt-SAF17
  • mt-SAF18
  • mt-SAF19
  • mt-SAF20
  • mt-SAF25
  • mt-SAF28
  • mt-SAF30
  • mt-SAF34
  • mt-SAF4
  • uS10m
  • uS11m
  • uS14m
  • uS19m
  • uS3m
  • uS5m
  • uS9m
KeywordsRIBOSOME / mitochondrial ribosome / assembly intermediate / translation
Function / homology
Function and homology information


rRNA (cytosine-N4-)-methyltransferase activity / mitochondrial mRNA editing complex / mitochondrial RNA processing / kinetoplast / thiosulfate sulfurtransferase activity / nuclear lumen / rRNA base methylation / ciliary plasm / mRNA stabilization / mitochondrial small ribosomal subunit ...rRNA (cytosine-N4-)-methyltransferase activity / mitochondrial mRNA editing complex / mitochondrial RNA processing / kinetoplast / thiosulfate sulfurtransferase activity / nuclear lumen / rRNA base methylation / ciliary plasm / mRNA stabilization / mitochondrial small ribosomal subunit / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / structural constituent of ribosome / mitochondrial matrix / translation / mitochondrion / RNA binding / metal ion binding / cytoplasm
Similarity search - Function
Mitochondrial glycoprotein / Mitochondrial glycoprotein superfamily / Mitochondrial glycoprotein / Ribosomal RNA small subunit methyltransferase H / S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily / MraW methylase family / Ribosomal protein Rsm22-like / : / Mitochondrial small ribosomal subunit Rsm22 / Ribosomal protein S23/S29, mitochondrial ...Mitochondrial glycoprotein / Mitochondrial glycoprotein superfamily / Mitochondrial glycoprotein / Ribosomal RNA small subunit methyltransferase H / S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily / MraW methylase family / Ribosomal protein Rsm22-like / : / Mitochondrial small ribosomal subunit Rsm22 / Ribosomal protein S23/S29, mitochondrial / Mitochondrial ribosomal death-associated protein 3 / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / Ribosomal protein S9 / Ribosomal protein S9/S16 / Ribosomal protein S11 superfamily / Thioredoxin-like superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / S-ADENOSYL-L-HOMOCYSTEINE / RNA / RNA (> 10) / RNA (> 100) / Uncharacterized protein / Ribosomal protein S24/S35 mitochondrial conserved domain-containing protein / Uncharacterized protein / Methyltransferase / Mitochondrial SSU ribosomal protein ...GUANOSINE-5'-TRIPHOSPHATE / S-ADENOSYL-L-HOMOCYSTEINE / RNA / RNA (> 10) / RNA (> 100) / Uncharacterized protein / Ribosomal protein S24/S35 mitochondrial conserved domain-containing protein / Uncharacterized protein / Methyltransferase / Mitochondrial SSU ribosomal protein / Mitochondrial SSU ribosomal protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Glutaredoxin domain-containing protein / S-adenosyl-methyltransferase mraW-like protein, putative / Ribosomal protein S9 / Uncharacterized protein / Mitochondrial glycoprotein-like protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Small ribosomal subunit protein mS29 / Rhodanese domain-containing 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 1.2May 22, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
CE: uS5m
CK: uS11m
Cn: mS38
FJ: mt-SAF18
FY: mt-SAF28
Fa: mt-SAF30
CA: 9S rRNA
CC: uS3m
CI: uS9m
CJ: uS10m
CN: uS14m
CS: uS19m
Cg: mS29
Ci: mS33
Ck: mS35
DB: mS49
DC: mS50
DE: mS52
DF: mS53
DG: mS54
DH: mS55 (KRIPP8)
DJ: mS57
DK: mS58
DT: mS67
DV: mS69
DW: mS70
DX: mS71
DY: mS72
F1: mt-SAF1 (RSM22)
F4: mt-SAF4
FD: mt-SAF12 (KRIPP18)
FF: mt-SAF14
FG: mt-SAF15
FH: mt-SAF16
FI: mt-SAF17
FK: mt-SAF19
FL: mt-SAF20
FV: mt-SAF25
Fe: mt-SAF34
Ua: UNK-a
Ub: UNK-b
Uc: UNK-c
Ud: UNK-d
Ue: UNK-e
Uf: UNK-f
Ug: UNK-g
Uh: UNK-h
Ui: UNK-i
Uj: UNK-j
Uk: UNK-k
Ul: UNK-l
Um: UNK-m
Ux: UNK-x
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,281,31062
Polymers2,279,66753
Non-polymers1,6439
Water543
1


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

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Components

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Protein , 43 types, 43 molecules CECKCnFJFYFaCCCICJCNCSCgCiCkDBDCDEDFDGDHDJDKDTDVDWDXDYF1F4FD...

#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 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
#3: 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
#4: 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 / References: UniProt: D0A8R9
#5: 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 / References: UniProt: A0A3L6L5M9
#6: 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
#8: Protein uS3m


Mass: 9070.940 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: uS3m of Trypanosoma brucei; encoded on mitochondrial DNA; GenBank: M94286.1
Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#9: Protein uS9m


Mass: 50201.016 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: Q57W62
#10: Protein uS10m


Mass: 94321.055 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 uS14m


Mass: 19900.014 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: Q580I0
#12: Protein uS19m


Mass: 28364.604 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
#13: Protein mS29


Mass: 57048.836 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 / References: UniProt: Q585C2
#14: Protein mS33


Mass: 21244.104 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: Q57WW0
#15: Protein mS35


Mass: 98377.773 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: Q387C7
#16: Protein mS49


Mass: 137234.125 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 mS50


Mass: 131719.250 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 mS52


Mass: 84998.234 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: Q386Q7
#19: Protein mS53


Mass: 75310.867 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 mS54


Mass: 72046.031 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 mS55 (KRIPP8)


Mass: 66676.680 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 mS57


Mass: 45956.293 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: Q584U8
#23: Protein mS58


Mass: 35623.910 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 mS67


Mass: 30096.051 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: Q586G5
#25: Protein mS69


Mass: 21589.732 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: Q57UZ6
#26: Protein mS70


Mass: 21247.398 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
#27: Protein mS71


Mass: 20093.227 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: Q383G5
#28: Protein mS72


Mass: 19340.352 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: Q57YD4
#29: 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
#30: Protein mt-SAF4


Mass: 91549.312 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
#31: Protein mt-SAF12 (KRIPP18)


Mass: 65049.215 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: Q583U2
#32: 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
#33: Protein mt-SAF15


Mass: 53273.867 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-SAF16


Mass: 50911.414 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
#35: Protein mt-SAF17


Mass: 50147.590 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
#36: Protein mt-SAF19


Mass: 41236.418 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 / Strain: Lister strain 427 / References: UniProt: Q57XS8
#37: Protein mt-SAF20


Mass: 40293.855 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
#38: Protein mt-SAF25


Mass: 29470.537 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: Q38C60
#39: Protein mt-SAF34


Mass: 14862.911 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 / Strain: Lister strain 427 / References: UniProt: Q387L0
#40: Protein UNK-a


Mass: 5975.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#43: Protein UNK-d


Mass: 5039.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#46: Protein UNK-g


Mass: 14230.525 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#47: Protein UNK-h


Mass: 21719.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#53: Protein UNK-x


Mass: 9209.344 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

#7: RNA chain 9S rRNA


Mass: 256380.734 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
Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Protein/peptide , 9 types, 9 molecules UbUcUeUfUiUjUkUlUm

#41: Protein/peptide UNK-b


Mass: 3592.419 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#42: Protein/peptide UNK-c


Mass: 1039.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#44: Protein/peptide UNK-e


Mass: 2486.056 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#45: Protein/peptide UNK-f


Mass: 783.958 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-i


Mass: 2741.370 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-j


Mass: 1635.006 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#50: Protein/peptide UNK-k


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
#51: Protein/peptide UNK-l


Mass: 1209.482 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-m


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

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Non-polymers , 5 types, 12 molecules

#54: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#55: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#56: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#57: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#58: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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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: Cryo-EM structure of the head domain of the mt-SSU assemblosome from Trypanosoma brucei
Type: RIBOSOME / Entity ID: #1-#53 / 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: Head 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)

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Processing

EM software
IDNameCategory
2EPUimage acquisition
4GctfCTF correction
9RELIONinitial Euler assignment
10RELIONfinal Euler assignment
11RELIONclassification
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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