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- EMDB-10176: mt-SSU assemblosome of wild-type Trypanosoma brucei brucei -

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Basic information

Entry
Database: EMDB / ID: EMD-10176
Titlemt-SSU assemblosome of wild-type Trypanosoma brucei brucei
Map datamt-SSU assemblosome of wild-type Trypanosoma brucei brucei
Sample
  • Complex: wild-type mt-SSU assemblosome
Function / homology
Function and homology information


modulation of formation of structure involved in a symbiotic process / rRNA (cytosine-N4-)-methyltransferase activity / mitochondrial mRNA editing complex / mitochondrial RNA processing / ATP-activated inward rectifier potassium channel activity / thiosulfate sulfurtransferase activity / kinetoplast / quorum sensing / rRNA base methylation / mRNA stabilization ...modulation of formation of structure involved in a symbiotic process / rRNA (cytosine-N4-)-methyltransferase activity / mitochondrial mRNA editing complex / mitochondrial RNA processing / ATP-activated inward rectifier potassium channel activity / thiosulfate sulfurtransferase activity / kinetoplast / quorum sensing / rRNA base methylation / mRNA stabilization / nuclear lumen / response to arsenic-containing substance / ciliary plasm / mitochondrial small ribosomal subunit / acyl binding / acyl carrier activity / mitochondrial respiratory chain complex I / voltage-gated potassium channel activity / voltage-gated potassium channel complex / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / protein homooligomerization / potassium ion transport / fatty acid biosynthetic process / methylation / mitochondrial matrix / structural constituent of ribosome / translation / mRNA binding / mitochondrion / RNA binding / membrane / cytosol / cytoplasm
Similarity search - Function
T-cell activation inhibitor, mitochondrial / Domain of unknown function DUF4460 / Domain of unknown function (DUF4460) / Mitochondrial glycoprotein / Mitochondrial glycoprotein superfamily / Mitochondrial glycoprotein / Probable Zinc-ribbon domain / Probable Zinc-ribbon domain / Ribosomal RNA small subunit methyltransferase H / S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily ...T-cell activation inhibitor, mitochondrial / Domain of unknown function DUF4460 / Domain of unknown function (DUF4460) / Mitochondrial glycoprotein / Mitochondrial glycoprotein superfamily / Mitochondrial glycoprotein / Probable Zinc-ribbon domain / Probable Zinc-ribbon domain / 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 / Protein Fyv4 / IGR protein motif / IGR / Phosphotyrosine protein phosphatase I / Phosphotyrosine protein phosphatase I superfamily / Low molecular weight phosphotyrosine protein phosphatase / Low molecular weight phosphatase family / Pentatricopeptide repeat domain / Pentatricopeptide (PPR) repeat profile. / Ribosomal protein S23/S29, mitochondrial / Mitochondrial ribosomal death-associated protein 3 / Pentatricopeptide repeat / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / Acyl carrier protein (ACP) / Phosphopantetheine attachment site / SKP1/BTB/POZ domain superfamily / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S9 / Ribosomal protein S9/S16 / Ribosomal protein S11 superfamily / Tetratricopeptide-like helical domain superfamily / S15/NS1, RNA-binding / 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
Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Methyltransferase / Mitochondrial SSU ribosomal protein / Uncharacterized protein / Mitochondrial SSU ribosomal protein / CENP-V/GFA domain-containing protein / Potassium voltage-gated channel, putative / Uncharacterized protein ...Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Methyltransferase / Mitochondrial SSU ribosomal protein / Uncharacterized protein / Mitochondrial SSU ribosomal protein / CENP-V/GFA domain-containing protein / Potassium voltage-gated channel, putative / Uncharacterized protein / Small ribosomal subunit protein mS41 / Uncharacterized protein / Uncharacterized protein / Alpha/beta-Hydrolases superfamily protein / Uncharacterized protein / Uncharacterized protein / Target SNARE / Phosphotyrosine protein phosphatase I domain-containing protein / DUF4460 domain-containing protein / Uncharacterized protein / Uncharacterized protein / Pentacotripeptide-repeat region of PRORP domain-containing protein / Uncharacterized protein / Uncharacterized protein / Glutaredoxin domain-containing protein / S-adenosyl-methyltransferase mraW-like protein, putative / Ribosomal protein S9 / Uncharacterized protein / Acyl carrier protein / Mitochondrial glyco protein / Uncharacterized protein / Pentacotripeptide-repeat region of PRORP domain-containing protein / Uncharacterized protein / Probable Zinc-ribbon domain-containing protein / Succinate dehydrogenase assembly factor 3, mitochondrial / Uncharacterized protein / Uncharacterized protein / Small ribosomal subunit protein mS29 / Rhodanese domain-containing protein / Uncharacterized protein
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsSaurer M / Ramrath D / Niemann M / Calderaro S / Prange C / Mattei S / Scaiola A / Leitner A / Bieri P / Horn EK ...Saurer M / Ramrath D / Niemann M / Calderaro S / Prange C / Mattei S / Scaiola A / Leitner A / Bieri P / Horn EK / Leibundgut M / Schneider A / Boehringer D / 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 ...Authors: Martin Saurer / David J F Ramrath / Moritz Niemann / Salvatore Calderaro / Céline Prange / Simone Mattei / Alain Scaiola / Alexander Leitner / Philipp Bieri / Elke K Horn / Marc Leibundgut / Daniel Boehringer / André Schneider / Nenad Ban /
Abstract: Mitochondrial ribosomes (mitoribosomes) are large ribonucleoprotein complexes that synthesize proteins encoded by the mitochondrial genome. An extensive cellular machinery responsible for ribosome ...Mitochondrial ribosomes (mitoribosomes) are large ribonucleoprotein complexes that synthesize proteins encoded by the mitochondrial genome. An extensive cellular machinery responsible for ribosome assembly has been described only for eukaryotic cytosolic ribosomes. Here we report that the assembly of the small mitoribosomal subunit in involves a large number of factors and proceeds through the formation of assembly intermediates, which we analyzed by using cryo-electron microscopy. One of them is a 4-megadalton complex, referred to as the small subunit assemblosome, in which we identified 34 factors that interact with immature ribosomal RNA (rRNA) and recognize its functionally important regions. The assembly proceeds through large-scale conformational changes in rRNA coupled with successive incorporation of mitoribosomal proteins, providing an example for the complexity of the ribosomal assembly process in mitochondria.
History
DepositionAug 3, 2019-
Header (metadata) releaseSep 25, 2019-
Map releaseSep 25, 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: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10176.png

Downloads & links

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Map

FileDownload / File: emd_10176.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmt-SSU assemblosome of wild-type Trypanosoma brucei brucei
Voxel sizeX=Y=Z: 1.5318 Å
Density
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.14604793 - 0.32192507
Average (Standard dev.)0.0009849102 (±0.008526604)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 520.812 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.53181.53181.5318
M x/y/z340340340
origin x/y/z0.0000.0000.000
length x/y/z520.812520.812520.812
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS340340340
D min/max/mean-0.1460.3220.001

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Supplemental data

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Sample components

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Entire : wild-type mt-SSU assemblosome

EntireName: wild-type mt-SSU assemblosome
Components
  • Complex: wild-type mt-SSU assemblosome

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Supramolecule #1: wild-type mt-SSU assemblosome

SupramoleculeName: wild-type mt-SSU assemblosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#103
Source (natural)Organism: Trypanosoma brucei brucei (eukaryote) / Strain: Lister strain 427

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Details: 15 mA
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsMitochondrial ribosomal small subunit assemblosome of wild-type Trypanosoma brucei brucei Lister strain 427

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 4.5 µm / Calibrated defocus min: 1.0 µm / Calibrated magnification: 129032 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Sampling interval: 14.0 µm / Number grids imaged: 1 / Number real images: 13503 / Average exposure time: 1.5 sec. / Average electron dose: 75.0 e/Å2
Details: Images were collected in movie-mode at 40 frames per second
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1243432
CTF correctionSoftware - Name: Gctf (ver. 1.06) / Details: On the fly in RELION
Startup modelType of model: NONE
Details: The starting model was determined ab-initio using RELION 3D initial model routine based on SGD.
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.5)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.5)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.5) / Number images used: 28663

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Atomic model buiding 1

DetailsStarting 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.
RefinementProtocol: OTHER

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