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- EMDB-10177: Body domain of the mt-SSU assemblosome from Trypanosoma brucei -

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Basic information

Entry
Database: EMDB / ID: EMD-10177
TitleBody domain of the mt-SSU assemblosome from Trypanosoma brucei
Map data
SampleBody domain of the mt-SSU assemblosome:
uS5m / bS6m / uS8m / uS11m / uS15m / bS16m / uS17m / bS18m / mS22 / mS23 ...uS5m / bS6m / uS8m / uS11m / uS15m / bS16m / uS17m / bS18m / mS22 / mS23 / mS26 / mS34 / mS38 / mS41 / mS51 (KRIPP1) / mS56 / mS59 / mS62 (KRIPP14) / mS63 (KRIPP16) / mS65 / mS68 / mS73 / mt-SAF2 (KRIPP2) / mt-SAF3 / mt-SAF5 / mt-SAF6 / mt-SAF7 (KRIPP10) / mt-SAF8 / mt-SAF9 / mt-SAF10 / mt-SAF11 / mt-SAF13 / mt-SAF18 / mt-SAF21 / mt-SAF22 (KRIPP17) / mt-SAF23 / mt-SAF24 / mt-SAF26 / mt-SAF27 / mt-SAF28 / mt-SAF29 / mt-SAF30 / mt-SAF31 / mt-SAF32 / mt-SAF33 / UNK-A / UNK-B / UNK-C / UNK-D, UNK-M, UNK-Q / UNK-E, UNK-P / UNK-F / UNK-G / UNK-H / UNK-I, UNK-M / UNK-J / UNK-L / UNK-O / UNK-U / UNK-I / nucleic-acidNucleic acid / mt-SAF1 (RSM22) / mt-SAF14 / (ligand) x 4
Function / homology
Function and homology information


rRNA (cytosine-N4-)-methyltransferase activity / modulation of development of symbiont involved in interaction with host / quorum sensing involved in interaction with host / ATP-activated inward rectifier potassium channel activity / kinetoplast / mitochondrial small ribosomal subunit / mitochondrial respiratory chain complex I / acyl carrier activity / rRNA base methylation / acyl binding ...rRNA (cytosine-N4-)-methyltransferase activity / modulation of development of symbiont involved in interaction with host / quorum sensing involved in interaction with host / ATP-activated inward rectifier potassium channel activity / kinetoplast / mitochondrial small ribosomal subunit / mitochondrial respiratory chain complex I / acyl carrier activity / rRNA base methylation / acyl binding / ciliary plasm / potassium ion transmembrane transport / voltage-gated potassium channel activity / voltage-gated potassium channel complex / Transferases, Transferring one-carbon groups, Methyltransferases / methyltransferase activity / potassium ion transport / fatty acid biosynthetic process / protein homooligomerization / structural constituent of ribosome / mitochondrial matrix / translation / mitochondrion / membrane / integral component of membrane / cytosol / cytoplasm
T-cell activation inhibitor, mitochondrial / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal RNA small subunit methyltransferase H / Potassium channel tetramerisation-type BTB domain / Acyl carrier protein (ACP) / Phosphopantetheine attachment site / S15/NS1, RNA-binding / Phosphopantetheine binding ACP domain / SKP1/BTB/POZ domain superfamily / Tetratricopeptide-like helical domain superfamily ...T-cell activation inhibitor, mitochondrial / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal RNA small subunit methyltransferase H / Potassium channel tetramerisation-type BTB domain / Acyl carrier protein (ACP) / Phosphopantetheine attachment site / S15/NS1, RNA-binding / Phosphopantetheine binding ACP domain / SKP1/BTB/POZ domain superfamily / Tetratricopeptide-like helical domain superfamily / Ribosomal protein Rsm22-like / Ribosomal protein S11 superfamily / IGR protein motif / S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily / Phosphotyrosine protein phosphatase I / Ribosomal protein S16 domain superfamily / Probable Zinc-ribbon domain / Domain of unknown function DUF4460 / S-adenosyl-L-methionine-dependent methyltransferase / Phosphotyrosine protein phosphatase I superfamily / Thioredoxin-like superfamily / Pentatricopeptide repeat / ACP-like superfamily / Mitochondrial small ribosomal subunit Rsm22 / BTB/POZ domain / Pentatricopeptide (PPR) repeat profile. / Carrier protein (CP) domain profile. / Protein Fyv4 / Phosphopantetheine attachment site. / Domain of unknown function (DUF4460) / Phosphopantetheine attachment site / Low molecular weight phosphotyrosine protein phosphatase / Probable Zinc-ribbon domain / MraW methylase family / Pentatricopeptide repeat domain
Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / S-adenosyl-methyltransferase mraW-like protein, putative / Acyl carrier protein / DUF4379 domain-containing protein / Uncharacterized protein / DUF4460 domain-containing protein ...Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / S-adenosyl-methyltransferase mraW-like protein, putative / Acyl carrier protein / DUF4379 domain-containing protein / Uncharacterized protein / DUF4460 domain-containing protein / Uncharacterized protein / IGR domain-containing protein / LMWPc domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Potassium voltage-gated channel, putative / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein
Biological speciesTrypanosoma brucei brucei (eukaryote)
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: 6sga

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: 0.0902
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0902
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6sga
  • Surface level: 0.0902
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6sga
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_10177.map.gz / Format: CCP4 / Size: 52.7 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 240 pix.
= 333.6 Å
1.39 Å/pix.
x 240 pix.
= 333.6 Å
1.39 Å/pix.
x 240 pix.
= 333.6 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: 0.0902 / Movie #1: 0.0902
Minimum - Maximum-0.1928046 - 0.45507842
Average (Standard dev.)0.0041514924 (±0.023178147)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin969696
Dimensions240240240
Spacing240240240
CellA=B=C: 333.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.391.391.39
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z333.600333.600333.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS969696
NC/NR/NS240240240
D min/max/mean-0.1930.4550.004

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Supplemental data

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Sample components

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Entire Body domain of the mt-SSU assemblosome

EntireName: Body domain of the mt-SSU assemblosome / Number of components: 67

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Component #1: protein, Body domain of the mt-SSU assemblosome

ProteinName: Body domain of the mt-SSU assemblosome / 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, bS6m

ProteinName: bS6m
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: 18.861543 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #4: protein, uS8m

ProteinName: uS8m
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: 32.766459 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #5: 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 #6: protein, uS15m

ProteinName: uS15m
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: 50.401191 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #7: protein, bS16m

ProteinName: bS16m
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: 22.077805 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #8: protein, uS17m

ProteinName: uS17m
Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence; C-terminal PTP-tag
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 39.012414 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #9: protein, bS18m

ProteinName: bS18m
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: 36.988691 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #10: protein, mS22

ProteinName: mS22
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: 73.064141 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #11: protein, mS23

ProteinName: mS23
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: 35.358805 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #12: protein, mS26

ProteinName: mS26
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: 51.136684 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #13: protein, mS34

ProteinName: mS34
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: 28.72818 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #14: 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 #15: protein, mS41

ProteinName: mS41
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: 22.421469 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #16: protein, mS51 (KRIPP1)

ProteinName: mS51 (KRIPP1)
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: 95.080992 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #17: protein, mS56

ProteinName: mS56
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: 47.306836 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #18: protein, mS59

ProteinName: mS59
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: 35.395676 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #19: protein, mS62 (KRIPP14)

ProteinName: mS62 (KRIPP14)
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: 32.0681 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #20: protein, mS63 (KRIPP16)

ProteinName: mS63 (KRIPP16)
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: 31.922178 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #21: protein, mS65

ProteinName: mS65
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: 30.617381 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #22: protein, mS68

ProteinName: mS68
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: 26.472807 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #23: protein, mS73

ProteinName: mS73
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: 11.360885 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #24: protein, mt-SAF2 (KRIPP2)

ProteinName: mt-SAF2 (KRIPP2)
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: 116.189547 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #25: protein, mt-SAF3

ProteinName: mt-SAF3
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: 106.621727 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #26: protein, mt-SAF5

ProteinName: mt-SAF5
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: 86.949414 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #27: protein, mt-SAF6

ProteinName: mt-SAF6
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: 76.781398 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #28: protein, mt-SAF7 (KRIPP10)

ProteinName: mt-SAF7 (KRIPP10)
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: 76.675156 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #29: protein, mt-SAF8

ProteinName: mt-SAF8
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: 76.72518 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #30: protein, mt-SAF9

ProteinName: mt-SAF9
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: 69.781789 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #31: protein, mt-SAF10

ProteinName: mt-SAF10
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: 69.306758 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #32: protein, mt-SAF11

ProteinName: mt-SAF11
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: 2 / Recombinant expression: No
MassTheoretical: 64.916957 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #33: protein, mt-SAF13

ProteinName: mt-SAF13
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: 63.690703 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #34: 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 #35: protein, mt-SAF21

ProteinName: mt-SAF21
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: 2 / Recombinant expression: No
MassTheoretical: 39.610793 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #36: protein, mt-SAF22 (KRIPP17)

ProteinName: mt-SAF22 (KRIPP17)
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: 39.132621 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #37: protein, mt-SAF23

ProteinName: mt-SAF23
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: 38.240164 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #38: protein, mt-SAF24

ProteinName: mt-SAF24
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: 5 / Recombinant expression: No
MassTheoretical: 34.648047 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #39: protein, mt-SAF26

ProteinName: mt-SAF26
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: 30.538557 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #40: protein, mt-SAF27

ProteinName: mt-SAF27
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: 26.936748 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #41: 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 #42: protein, mt-SAF29

ProteinName: mt-SAF29
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: 20.048514 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Component #43: 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 #44: protein, mt-SAF31

ProteinName: mt-SAF31
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: 17.673535 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #45: protein, mt-SAF32

ProteinName: mt-SAF32
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: 16.550807 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #46: protein, mt-SAF33

ProteinName: mt-SAF33
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: 16.291121 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #47: protein, UNK-A

ProteinName: UNK-A / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 1.805216 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #48: protein, UNK-B

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

+
Component #49: protein, UNK-C

ProteinName: UNK-C / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.869063 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #50: protein, UNK-D, UNK-M, UNK-Q

ProteinName: UNK-D, UNK-M, UNK-Q / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.783958 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #51: protein, UNK-E, UNK-P

ProteinName: UNK-E, UNK-P / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 3.847734 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #52: protein, UNK-F

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

+
Component #53: protein, UNK-G

ProteinName: UNK-G / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 1.464797 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #54: protein, UNK-H

ProteinName: UNK-H / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.443539 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #55: protein, UNK-I, UNK-M

ProteinName: UNK-I, UNK-M / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.698854 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #56: protein, UNK-J

ProteinName: UNK-J / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 1.379692 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #57: protein, UNK-L

ProteinName: UNK-L / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 1.890321 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #58: protein, UNK-O

ProteinName: UNK-O / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.571161 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #59: protein, UNK-U

ProteinName: UNK-U / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.060531 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #60: protein, UNK-I

ProteinName: UNK-I / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 39.847105 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #61: nucleic-acid, 9S rRNA

nucleic acidName: 9S rRNA / Class: RNA
Details: 9S ribosomal RNA from Trypanosoma brucei. GenBank: X02547.1 and S66467.1 Sequence of 3'-major domain omitted.
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 UUAAGUGCUG AUUUAACCAA UAAAAAUAUA AAUAAUUUUU AUUUGUUUUU AAACACCAUU AGGUAUAUGC AAAUAUAAAA UUAUAGUAAU UAUAGAAAUU AAAAAGGUAU UGUUGCCCAC CAAUUUUUAU AAUAAAAAUA ACGUGCAGUA AUUAAUAUAU UUAUAAAAAU AUAUUUUUUU UUU(UBD)
MassTheoretical: 151.505578 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

+
Component #62: 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

+
Component #63: 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

+
Component #64: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

+
Component #65: ligand, PHOSPHATE ION

LigandName: PHOSPHATE IONPhosphate / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.497105 MDa

+
Component #66: ligand, S-(2-{[N-(2-HYDROXY-4-{[HYDROXY(OXIDO)PHOSPHINO]OXY}-3,3-...

LigandName: S-(2-{[N-(2-HYDROXY-4-{[HYDROXY(OXIDO)PHOSPHINO]OXY}-3,3-DIMETHYLBUTANOYL)-BETA-ALANYL]AMINO}ETHYL) DECANETHIOATE
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.496598 kDa

+
Component #67: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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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 %

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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

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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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