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- EMDB-10175: Head domain of the mt-SSU assemblosome from Trypanosoma brucei -

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Basic information

Entry
Database: EMDB / ID: EMD-10175
TitleHead domain of the mt-SSU assemblosome from Trypanosoma brucei
Map data
SampleCryo-EM structure of the head domain of the mt-SSU assemblosome from Trypanosoma brucei:
uS5m / uS11m / mS38 / mt-SAF18 / mt-SAF28 / mt-SAF30 / nucleic-acidNucleic acid / uS3m / uS9m / uS10m ...uS5m / uS11m / mS38 / mt-SAF18 / mt-SAF28 / mt-SAF30 / nucleic-acidNucleic acid / uS3m / uS9m / uS10m / uS14m / uS19m / mS29 / mS33 / mS35 / mS49 / mS50 / mS52 / mS53 / mS54 / mS55 (KRIPP8) / mS57 / mS58 / mS67 / mS69 / mS70 / mS71 / mS72 / mt-SAF1 (RSM22) / mt-SAF4 / mt-SAF12 (KRIPP18) / mt-SAF14 / mt-SAF15 / mt-SAF16 / mt-SAF17 / mt-SAF19 / mt-SAF20 / mt-SAF25 / mt-SAF34 / 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 / (ligand) x 5
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) / Trypanosoma brucei brucei
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsSaurer M / Ramrath DJF / Niemann M / Calderaro S / Prange C / Mattei S / Scaiola A / Leitner A / Bieri P / Horn EK / Leibundgut M / Boehringer D / Schneider A / Ban N
Funding support Switzerland, 1 items
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 ReportPDB-ID: 6sg9

SummaryFull reportAbout validation report
History
DepositionAug 3, 2019-
Header (metadata) releaseSep 18, 2019-
Map releaseSep 18, 2019-
UpdateSep 25, 2019-
Current statusSep 25, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0793
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0793
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6sg9
  • Surface level: 0.0793
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_10175.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.39 Å/pix.
x 320 pix.
= 444.8 Å
1.39 Å/pix.
x 320 pix.
= 444.8 Å
1.39 Å/pix.
x 320 pix.
= 444.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.39 Å
Density
Contour LevelBy AUTHOR: 0.0793 / Movie #1: 0.0793
Minimum - Maximum-0.18639 - 0.4196252
Average (Standard dev.)0.0011354706 (±0.011508951)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin565656
Dimensions320320320
Spacing320320320
CellA=B=C: 444.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.391.391.39
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z444.800444.800444.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS565656
NC/NR/NS320320320
D min/max/mean-0.1860.4200.001

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Supplemental data

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Sample components

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Entire Cryo-EM structure of the head domain of the mt-SSU assemblosome f...

EntireName: Cryo-EM structure of the head domain of the mt-SSU assemblosome from Trypanosoma brucei
Number of components: 59

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Component #1: protein, Cryo-EM structure of the head domain of the mt-SSU assem...

ProteinName: Cryo-EM structure of the head domain of the mt-SSU assemblosome from Trypanosoma brucei
Recombinant expression: No
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #2: protein, uS5m

ProteinName: uS5m
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
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 50.147355 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #3: protein, uS11m

ProteinName: uS11m
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
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 37.953965 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #4: protein, mS38

ProteinName: mS38
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
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.2406 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #5: protein, mt-SAF18

ProteinName: mt-SAF18
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
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 42.508039 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #6: protein, mt-SAF28

ProteinName: mt-SAF28
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
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.468707 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #7: protein, mt-SAF30

ProteinName: mt-SAF30
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
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.659756 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #8: nucleic-acid, 9S rRNA

nucleic acidName: 9S rRNA / Class: RNA
Details: 9S ribosomal RNA from Trypanosoma brucei. GenBank: X02547.1 and S66467.1
Structure: OTHER / Synthetic: No
Sequence:
UAAAUUAUGG UCAAUUGUUA GUAUUCAUAU UAAUUUUUUU AAAUGUUUUA UCAUUUUAUA AAGGUUUAUU UUUGAAAGAU UUUUUGUAUA AAAUUUUAGG AAUAGUUAAU AAUAAUUUAU AAUUUUGAUU AGAUUGUUUU GUUAAUGCUA UUAGAUGGGU GUGGAAAAAU AAAAAAAAUA AUUAAUAUAU AUCAAUAAUA AAUUAAAUUA AUCUAUUAGU CAGAAAUGGA UGCCAGCCGU UGCGGUAAUU UCUAUGCUUU UAAAUAUUAU ACAAUUAUCA UAUUAAAUUG UUAAGUGUUG AUUUAACCAA UAAAAAUAUA AAUAAUUUUU AUUUGUUUUU AAACACCAUU AGGUAUAUGC AAAUAUAAAA UUAUAGUAAU UAUAAAUUAU AUUAUAUUAU AUUUAUUCAU AUAAUUAAUA GGAUAAUAUU UGUAGUUUUU GAUACCAUGA UAAGGAUUAU AAAUUGAAAG UGUUAAUAUC AUAAUCAAAA UUUAUUAUUU AUAUUAAAUA UGUAUGUGUA GAUAAAAUAA GAAAUUAAAA AGGUAUUGUU GCCCACCAAU UUUUAAAUUA UAUUAUAUUA UAUUUAUUCA UAUAAUUAAU AGGAUAAUAU UUGUAGUUUU UGAUACCAUG AUAAGGAUUA UAAAUUGAAA GUGUUAAUAU CAUAAUCAAA AUUUAUUAUU UAUAUUAAAU AUGUAUGUGU AGAUAAAAUA AGAAAUUAAA AAGGUAUUGU UGCCCACCAA UUUUUAUAAU AAAAAUAACG UGCAGUAAUU AAUAUAUUUA UAAAAAUAUA UUUUUUUUUU UA
MassTheoretical: 256.380734 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #9: protein, uS3m

ProteinName: uS3m
Details: uS3m of Trypanosoma brucei; encoded on mitochondrial DNA; GenBank: M94286.1
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.07094 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #10: protein, uS9m

ProteinName: uS9m
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
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 50.201016 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #11: protein, uS10m

ProteinName: uS10m
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
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 94.321055 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #12: protein, uS14m

ProteinName: uS14m
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
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.900014 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #13: protein, uS19m

ProteinName: uS19m
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
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.364604 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #14: protein, mS29

ProteinName: mS29
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
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 57.048836 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #15: protein, mS33

ProteinName: mS33
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
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.244104 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #16: protein, mS35

ProteinName: mS35
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
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 98.377773 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #17: protein, mS49

ProteinName: mS49
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
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 137.234125 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #18: protein, mS50

ProteinName: mS50
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
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 131.71925 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #19: protein, mS52

ProteinName: mS52
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
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 84.998234 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #20: protein, mS53

ProteinName: mS53
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
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 75.310867 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #21: protein, mS54

ProteinName: mS54
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
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 72.046031 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #22: protein, mS55 (KRIPP8)

ProteinName: mS55 (KRIPP8)
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
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 66.67668 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #23: protein, mS57

ProteinName: mS57
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
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 45.956293 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #24: protein, mS58

ProteinName: mS58
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
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 35.62391 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #25: protein, mS67

ProteinName: mS67
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
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.096051 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #26: protein, mS69

ProteinName: mS69
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
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.589732 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #27: protein, mS70

ProteinName: mS70
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
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.247398 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #28: protein, mS71

ProteinName: mS71
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
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.093227 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #29: protein, mS72

ProteinName: mS72
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
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.340352 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #30: protein, mt-SAF1 (RSM22)

ProteinName: mt-SAF1 (RSM22)
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
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 119.799398 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #31: protein, mt-SAF4

ProteinName: mt-SAF4
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
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 91.549312 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #32: protein, mt-SAF12 (KRIPP18)

ProteinName: mt-SAF12 (KRIPP18)
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
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 65.049215 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #33: protein, mt-SAF14

ProteinName: mt-SAF14
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
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 53.32082 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #34: protein, mt-SAF15

ProteinName: mt-SAF15
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
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 53.273867 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #35: protein, mt-SAF16

ProteinName: mt-SAF16
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
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 50.911414 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #36: protein, mt-SAF17

ProteinName: mt-SAF17
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
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 50.14759 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #37: protein, mt-SAF19

ProteinName: mt-SAF19
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
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 41.236418 kDa
SourceSpecies: Trypanosoma brucei brucei / Strain: Lister strain 427

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Component #38: protein, mt-SAF20

ProteinName: mt-SAF20
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
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 40.293855 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #39: protein, mt-SAF25

ProteinName: mt-SAF25
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
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.470537 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #40: protein, mt-SAF34

ProteinName: mt-SAF34
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
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.862911 kDa
SourceSpecies: Trypanosoma brucei brucei / Strain: Lister strain 427

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Component #41: protein, UNK-a

ProteinName: UNK-a / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 5.975357 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #42: protein, UNK-b

ProteinName: UNK-b / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 3.592419 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #43: protein, UNK-c

ProteinName: UNK-c / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 1.039273 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #44: protein, UNK-d

ProteinName: UNK-d / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 5.039203 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #45: protein, UNK-e

ProteinName: UNK-e / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.486056 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #46: protein, UNK-f

ProteinName: UNK-f / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.783958 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #47: protein, UNK-g

ProteinName: UNK-g / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.230525 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #48: protein, UNK-h

ProteinName: UNK-h / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.719672 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #49: protein, UNK-i

ProteinName: UNK-i / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.74137 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #50: protein, UNK-j

ProteinName: UNK-j / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 1.635006 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #51: protein, UNK-k

ProteinName: UNK-k / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.315846 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #52: protein, UNK-l

ProteinName: UNK-l / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 1.209482 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #53: protein, UNK-m

ProteinName: UNK-m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.954168 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #54: protein, UNK-x

ProteinName: UNK-x / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.209344 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #55: ligand, GUANOSINE-5'-TRIPHOSPHATE

LigandName: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.52318 kDa

+
Component #56: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

+
Component #57: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

+
Component #58: ligand, S-ADENOSYL-L-HOMOCYSTEINE

LigandName: S-ADENOSYL-L-HOMOCYSTEINE / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.384411 kDa

+
Component #59: ligand, water

LigandName: water / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 1.801505 MDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: OTHER / Temperature: 278 K / Humidity: 90 %

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 59000.0 X (nominal), 100719.0 X (calibrated) / Imaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON III (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 161661
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / CTF correction: On the fly in RELION / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Modeling #1Details: 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.
Output model

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