Mitochondrial glycoprotein / Mitochondrial glycoprotein superfamily / Mitochondrial glycoprotein / Ribosomal RNA small subunit methyltransferase H / S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily / MraW methylase family / Ribosomal protein Rsm22-like / Mitochondrial small ribosomal subunit Rsm22 / Ribosomal protein S23/S29, mitochondrial / Mitochondrial ribosomal death-associated protein 3 ...Mitochondrial glycoprotein / Mitochondrial glycoprotein superfamily / Mitochondrial glycoprotein / Ribosomal RNA small subunit methyltransferase H / S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily / MraW methylase family / Ribosomal protein Rsm22-like / Mitochondrial small ribosomal subunit Rsm22 / Ribosomal protein S23/S29, mitochondrial / Mitochondrial ribosomal death-associated protein 3 / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / Ribosomal protein S9 / Ribosomal protein S9/S16 / Ribosomal protein S11 superfamily / Thioredoxin-like superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / S-adenosyl-L-methionine-dependent methyltransferase superfamily Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / S-ADENOSYL-L-HOMOCYSTEINE / RNA / RNA (> 10) / RNA (> 100) / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Methyltransferase / Mitochondrial SSU ribosomal protein ...GUANOSINE-5'-TRIPHOSPHATE / S-ADENOSYL-L-HOMOCYSTEINE / RNA / RNA (> 10) / RNA (> 100) / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Methyltransferase / Mitochondrial SSU ribosomal protein / Mitochondrial SSU ribosomal protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Glutaredoxin domain-containing protein / S-adenosyl-methyltransferase mraW-like protein, putative / Ribosomal protein S9 / Uncharacterized protein / Mitochondrial glycoprotein-like protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Small ribosomal subunit protein mS29 / Rhodanese domain-containing protein Similarity search - Component
Biological species
Trypanosoma brucei brucei (eukaryote)
Method
ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
Journal: Science / Year: 2019 Title: Mitoribosomal small subunit biogenesis in trypanosomes involves an extensive assembly machinery. Authors: Martin Saurer / David J F Ramrath / Moritz Niemann / Salvatore Calderaro / Céline Prange / Simone Mattei / Alain Scaiola / Alexander Leitner / Philipp Bieri / Elke K Horn / Marc Leibundgut ...Authors: Martin Saurer / David J F Ramrath / Moritz Niemann / Salvatore Calderaro / Céline Prange / Simone Mattei / Alain Scaiola / Alexander Leitner / Philipp Bieri / Elke K Horn / Marc Leibundgut / Daniel Boehringer / André Schneider / Nenad Ban / Abstract: Mitochondrial ribosomes (mitoribosomes) are large ribonucleoprotein complexes that synthesize proteins encoded by the mitochondrial genome. An extensive cellular machinery responsible for ribosome ...Mitochondrial ribosomes (mitoribosomes) are large ribonucleoprotein complexes that synthesize proteins encoded by the mitochondrial genome. An extensive cellular machinery responsible for ribosome assembly has been described only for eukaryotic cytosolic ribosomes. Here we report that the assembly of the small mitoribosomal subunit in involves a large number of factors and proceeds through the formation of assembly intermediates, which we analyzed by using cryo-electron microscopy. One of them is a 4-megadalton complex, referred to as the small subunit assemblosome, in which we identified 34 factors that interact with immature ribosomal RNA (rRNA) and recognize its functionally important regions. The assembly proceeds through large-scale conformational changes in rRNA coupled with successive incorporation of mitoribosomal proteins, providing an example for the complexity of the ribosomal assembly process in mitochondria.
Protein , 43 types, 43 molecules CECKCnFJFYFaCCCICJCNCSCgCiCkDBDCDEDFDGDHDJDKDTDVDWDXDYF1F4FD...
#1: Protein
uS5m
Mass: 50147.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#2: Protein
uS11m
Mass: 37953.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q389T7
#3: Protein
mS38
Mass: 28240.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q57VQ9
#4: Protein
mt-SAF18
Mass: 42508.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: D0A8R9
#5: Protein
mt-SAF28
Mass: 21468.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: A0A3L6L5M9
#6: Protein
mt-SAF30
Mass: 19659.756 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q57VU7
#8: Protein
uS3m
Mass: 9070.940 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: uS3m of Trypanosoma brucei; encoded on mitochondrial DNA; GenBank: M94286.1 Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#9: Protein
uS9m
Mass: 50201.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q57W62
#10: Protein
uS10m
Mass: 94321.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#11: Protein
uS14m
Mass: 19900.014 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q580I0
#12: Protein
uS19m
Mass: 28364.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#13: Protein
mS29
Mass: 57048.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q585C2
#14: Protein
mS33
Mass: 21244.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q57WW0
#15: Protein
mS35
Mass: 98377.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q387C7
#16: Protein
mS49
Mass: 137234.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#17: Protein
mS50
Mass: 131719.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#18: Protein
mS52
Mass: 84998.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q386Q7
#19: Protein
mS53
Mass: 75310.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#20: Protein
mS54
Mass: 72046.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#21: Protein
mS55 (KRIPP8)
Mass: 66676.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#22: Protein
mS57
Mass: 45956.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q584U8
#23: Protein
mS58
Mass: 35623.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#24: Protein
mS67
Mass: 30096.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q586G5
#25: Protein
mS69
Mass: 21589.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q57UZ6
#26: Protein
mS70
Mass: 21247.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#27: Protein
mS71
Mass: 20093.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q383G5
#28: Protein
mS72
Mass: 19340.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q57YD4
#29: Protein
mt-SAF1 (RSM22)
Mass: 119799.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q385R2
#30: Protein
mt-SAF4
Mass: 91549.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#31: Protein
mt-SAF12 (KRIPP18)
Mass: 65049.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q583U2
#32: Protein
mt-SAF14
Mass: 53320.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q57W60
#33: Protein
mt-SAF15
Mass: 53273.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#34: Protein
mt-SAF16
Mass: 50911.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#35: Protein
mt-SAF17
Mass: 50147.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#36: Protein
mt-SAF19
Mass: 41236.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence Source: (natural) Trypanosoma brucei brucei / Strain: Lister strain 427 / References: UniProt: Q57XS8
#37: Protein
mt-SAF20
Mass: 40293.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#38: Protein
mt-SAF25
Mass: 29470.537 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427 / References: UniProt: Q38C60
#39: Protein
mt-SAF34
Mass: 14862.911 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Protein of Trypanosoma brucei brucei Lister strain 427; sequence accessible on TriTrypDB; where necessary, the reference strain TREU927 was used to complete the sequence Source: (natural) Trypanosoma brucei brucei / Strain: Lister strain 427 / References: UniProt: Q387L0
#40: Protein
UNK-a
Mass: 5975.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#43: Protein
UNK-d
Mass: 5039.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#46: Protein
UNK-g
Mass: 14230.525 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#47: Protein
UNK-h
Mass: 21719.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
#53: Protein
UNK-x
Mass: 9209.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
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RNA chain , 1 types, 1 molecules CA
#7: RNA chain
9SrRNA
Mass: 256380.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: 9S ribosomal RNA from Trypanosoma brucei. GenBank: X02547.1 and S66467.1 Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Head domain of the mitochondrial ribosomal small subunit assemblosome of Trypanosoma brucei brucei Lister strain 427
Electron dose: 40 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k)
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Processing
EM software
ID
Name
Category
2
EPU
imageacquisition
4
Gctf
CTFcorrection
9
RELION
initialEulerassignment
10
RELION
finalEulerassignment
11
RELION
classification
12
RELION
3Dreconstruction
CTF correction
Details: On the fly in RELION / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Symmetry
Point symmetry: C1 (asymmetric)
3D reconstruction
Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 161661 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model building
Protocol: 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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