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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 ribosome binding / RNA polyadenylation / mitochondrial RNA processing / positive regulation of mitochondrial translation / kinetoplast / mitochondrial small ribosomal subunit / translation activator activity / nuclear lumen ...rRNA (cytosine-N4-)-methyltransferase activity / mitochondrial mRNA editing complex / mitochondrial ribosome binding / RNA polyadenylation / mitochondrial RNA processing / positive regulation of mitochondrial translation / kinetoplast / mitochondrial small ribosomal subunit / translation activator activity / nuclear lumen / rRNA base methylation / mRNA stabilization / ciliary plasm / Transferases, Transferring one-carbon groups, Methyltransferases / methyltransferase activity / structural constituent of ribosome / mitochondrial matrix / translation / mRNA binding / mitochondrion / RNA binding / cytoplasm
Thioredoxin-like superfamily / S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily / Ribosomal protein S9 / Mitochondrial glycoprotein / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein Rsm22-like / Mitochondrial glycoprotein superfamily / Ribosomal protein S23/S29, mitochondrial / Ribosomal RNA small subunit methyltransferase H / Ribosomal protein S5 domain 2-type fold ...Thioredoxin-like superfamily / S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily / Ribosomal protein S9 / Mitochondrial glycoprotein / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein Rsm22-like / Mitochondrial glycoprotein superfamily / Ribosomal protein S23/S29, mitochondrial / Ribosomal RNA small subunit methyltransferase H / Ribosomal protein S5 domain 2-type fold / Rhodanese-like domain superfamily / Ribosomal protein S11 superfamily / S-adenosyl-L-methionine-dependent methyltransferase / Ribosomal protein S9/S16 / MraW methylase family / Mitochondrial glycoprotein / Mitochondrial small ribosomal subunit Rsm22 / Mitochondrial ribosomal death-associated protein 3 / Rhodanese domain profile. / Rhodanese-like domain
Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / S-adenosyl-methyltransferase mraW-like protein, putative ...Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / S-adenosyl-methyltransferase mraW-like protein, putative / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Rhodanese domain-containing protein
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. / 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 / 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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  • Deposited structure unit
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-10175
  • Imaged by UCSF Chimera
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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/peptide , 52 types, 52 molecules CECKCnFJFYFaCCCICJCNCSCgCiCkDBDCDEDFDGDHDJDKDTDVDWDXDYF1F4FD...

#1: Protein/peptide uS5m


Mass: 50147.355 Da / Num. of mol.: 1
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where ...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 method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#2: Protein/peptide uS11m


Mass: 37953.965 Da / Num. of mol.: 1
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where ...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 method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q389T7
#3: Protein/peptide mS38


Mass: 28240.600 Da / Num. of mol.: 1
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where ...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 method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q57VQ9
#4: Protein/peptide mt-SAF18


Mass: 42508.039 Da / Num. of mol.: 1
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where ...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 method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: D0A8R9
#5: Protein/peptide mt-SAF28


Mass: 21468.707 Da / Num. of mol.: 1
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where ...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 method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: A0A3L6L5M9
#6: Protein/peptide mt-SAF30


Mass: 19659.756 Da / Num. of mol.: 1
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where ...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 method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q57VU7
#8: Protein/peptide uS3m


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


Mass: 50201.016 Da / Num. of mol.: 1
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where ...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 method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q57W62
#10: Protein/peptide uS10m


Mass: 94321.055 Da / Num. of mol.: 1
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where ...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 method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#11: Protein/peptide uS14m


Mass: 19900.014 Da / Num. of mol.: 1
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where ...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 method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q580I0
#12: Protein/peptide uS19m


Mass: 28364.604 Da / Num. of mol.: 1
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where ...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 method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#13: Protein/peptide mS29


Mass: 57048.836 Da / Num. of mol.: 1
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where ...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 method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q585C2
#14: Protein/peptide mS33


Mass: 21244.104 Da / Num. of mol.: 1
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where ...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 method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q57WW0
#15: Protein/peptide mS35


Mass: 98377.773 Da / Num. of mol.: 1
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where ...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 method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q387C7
#16: Protein/peptide mS49


Mass: 137234.125 Da / Num. of mol.: 1
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where ...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 method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#17: Protein/peptide mS50


Mass: 131719.250 Da / Num. of mol.: 1
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where ...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 method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#18: Protein/peptide mS52


Mass: 84998.234 Da / Num. of mol.: 1
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where ...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 method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q386Q7
#19: Protein/peptide mS53


Mass: 75310.867 Da / Num. of mol.: 1
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where ...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 method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#20: Protein/peptide mS54


Mass: 72046.031 Da / Num. of mol.: 1
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where ...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 method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#21: Protein/peptide mS55 (KRIPP8)


Mass: 66676.680 Da / Num. of mol.: 1
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where ...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 method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#22: Protein/peptide mS57


Mass: 45956.293 Da / Num. of mol.: 1
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where ...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 method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q584U8
#23: Protein/peptide mS58


Mass: 35623.910 Da / Num. of mol.: 1
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where ...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 method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#24: Protein/peptide mS67


Mass: 30096.051 Da / Num. of mol.: 1
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where ...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 method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q586G5
#25: Protein/peptide mS69


Mass: 21589.732 Da / Num. of mol.: 1
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where ...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 method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q57UZ6
#26: Protein/peptide mS70


Mass: 21247.398 Da / Num. of mol.: 1
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where ...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 method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#27: Protein/peptide mS71


Mass: 20093.227 Da / Num. of mol.: 1
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where ...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 method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q383G5
#28: Protein/peptide mS72


Mass: 19340.352 Da / Num. of mol.: 1
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where ...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 method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q57YD4
#29: Protein/peptide mt-SAF1 (RSM22)


Mass: 119799.398 Da / Num. of mol.: 1
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where ...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 method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q385R2
#30: Protein/peptide mt-SAF4


Mass: 91549.312 Da / Num. of mol.: 1
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where ...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 method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#31: Protein/peptide mt-SAF12 (KRIPP18)


Mass: 65049.215 Da / Num. of mol.: 1
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where ...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 method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q583U2
#32: Protein/peptide mt-SAF14


Mass: 53320.820 Da / Num. of mol.: 1
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where ...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 method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q57W60
#33: Protein/peptide mt-SAF15


Mass: 53273.867 Da / Num. of mol.: 1
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where ...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 method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#34: Protein/peptide mt-SAF16


Mass: 50911.414 Da / Num. of mol.: 1
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where ...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 method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#35: Protein/peptide mt-SAF17


Mass: 50147.590 Da / Num. of mol.: 1
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where ...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 method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#36: Protein/peptide mt-SAF19


Mass: 41236.418 Da / Num. of mol.: 1
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where ...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 method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei / Strain: Lister strain 427 / References: UniProt: Q57XS8
#37: Protein/peptide mt-SAF20


Mass: 40293.855 Da / Num. of mol.: 1
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where ...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 method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#38: Protein/peptide mt-SAF25


Mass: 29470.537 Da / Num. of mol.: 1
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where ...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 method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q38C60
#39: Protein/peptide mt-SAF34


Mass: 14862.911 Da / Num. of mol.: 1
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where ...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 method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei / Strain: Lister strain 427 / References: UniProt: Q387L0
#40: Protein/peptide 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
#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
#43: Protein/peptide 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
#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
#46: Protein/peptide 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/peptide 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
#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
#53: Protein/peptide 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
Details: 9S ribosomal RNA from Trypanosoma brucei. GenBank: X02547.1 and S66467.1
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 / Guanosine triphosphate / 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 / Magnesium
#56: Chemical
ChemComp-ZN / ZINC ION


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


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


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

-
Details

Has ligand of interestN

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Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Cryo-EM structure of the head domain of the mt-SSU assemblosome from Trypanosoma brucei
Type: RIBOSOME
Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53
Source: NATURAL
Source (natural)Organism: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
Buffer solutionpH: 7.4
SpecimenDetails: Head 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
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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