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- PDB-6hiy: Cryo-EM structure of the Trypanosoma brucei mitochondrial ribosom... -

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Entry
Database: PDB / ID: 6hiy
TitleCryo-EM structure of the Trypanosoma brucei mitochondrial ribosome - This entry contains the body of the small mitoribosomal subunit in complex with mt-IF-3
Components
  • (Unknown protein) x 4
  • 9S rRNA
  • bS16m
  • bS18m
  • bS6m
  • mS22
  • mS23
  • mS26
  • mS34
  • mS37
  • mS38
  • mS41
  • mS42
  • mS43
  • mS47
  • mS48
  • mS51
  • mS55m
  • mS56
  • mS59
  • mS60
  • mS61
  • mS62
  • mS63
  • mS64
  • mS65
  • mS66
  • mS68
  • mS73
  • mS74
  • mt-IF-3
  • uS11m
  • uS12m
  • uS15m
  • uS17m
  • uS21m
  • uS8m
  • uS9m
KeywordsRIBOSOME / mitoribosome / translation / Trypanosoma / small ribosomal subunit / 9S rRNA / ribosomal protein / mitochondrial initiation factor IF-3
Function / homology
Function and homology information


modulation of formation of structure involved in a symbiotic process / organellar small ribosomal subunit / 3-hydroxyisobutyryl-CoA hydrolase / 3-hydroxyisobutyryl-CoA hydrolase activity / mitochondrial mRNA editing complex / mitochondrial RNA processing / kinetoplast / quorum sensing / enoyl-CoA hydratase activity / regulation of protein kinase A signaling ...modulation of formation of structure involved in a symbiotic process / organellar small ribosomal subunit / 3-hydroxyisobutyryl-CoA hydrolase / 3-hydroxyisobutyryl-CoA hydrolase activity / mitochondrial mRNA editing complex / mitochondrial RNA processing / kinetoplast / quorum sensing / enoyl-CoA hydratase activity / regulation of protein kinase A signaling / mRNA stabilization / ciliary plasm / mitochondrial small ribosomal subunit / fatty acid beta-oxidation / superoxide dismutase / protein kinase A regulatory subunit binding / superoxide dismutase activity / ribosome / structural constituent of ribosome / translation / mitochondrion / RNA binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Nucleoid-associated protein YbaB-like domain superfamily / Protein kinase A anchor protein, nuclear localisation signal domain / AKAP7 2'5' RNA ligase-like domain / Probable Zinc-ribbon domain / : / Probable Zinc-ribbon domain / Enoyl-CoA hydratase/isomerase domain / Enoyl-CoA hydratase/isomerase, HIBYL-CoA-H type / Enoyl-CoA hydratase/isomerase / Protein Fyv4 ...Nucleoid-associated protein YbaB-like domain superfamily / Protein kinase A anchor protein, nuclear localisation signal domain / AKAP7 2'5' RNA ligase-like domain / Probable Zinc-ribbon domain / : / Probable Zinc-ribbon domain / Enoyl-CoA hydratase/isomerase domain / Enoyl-CoA hydratase/isomerase, HIBYL-CoA-H type / Enoyl-CoA hydratase/isomerase / Protein Fyv4 / IGR protein motif / IGR / Cyclic phosphodiesterase / Manganese/iron superoxide dismutase, C-terminal / Manganese/iron superoxide dismutase, C-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain / Manganese/iron superoxide dismutase, N-terminal domain superfamily / ClpP/crotonase-like domain superfamily / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 superfamily / Ubiquitin family / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S5, C-terminal / Ribosomal protein S8 / Ribosomal protein S5, C-terminal domain / Ubiquitin-like domain / Ribosomal protein S9 / Ribosomal protein S17/S11 / Ribosomal protein S9/S16 / Ribosomal protein S17 / Ubiquitin domain profile. / Tetratricopeptide-like helical domain superfamily / Ribosomal protein S11 superfamily / S15/NS1, RNA-binding / Ribosomal protein S5 domain 2-type fold, subgroup / Ubiquitin-like domain superfamily / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
SPERMIDINE / SPERMINE / : / RNA / RNA (> 10) / RNA (> 100) / A-kinase anchor protein 7-like phosphoesterase domain-containing protein / Uncharacterized protein / 3-hydroxyisobutyryl-CoA hydrolase / Uncharacterized protein ...SPERMIDINE / SPERMINE / : / RNA / RNA (> 10) / RNA (> 100) / A-kinase anchor protein 7-like phosphoesterase domain-containing protein / Uncharacterized protein / 3-hydroxyisobutyryl-CoA hydrolase / Uncharacterized protein / Uncharacterized protein / Probable Zinc-ribbon domain-containing protein / 30S ribosomal protein S8, putative / Small ribosomal subunit protein mS41 / Uncharacterized protein / Mitochondrial ribosomal protein S18 / Small ribosomal subunit protein uS5 C-terminal domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Trans-sialidase / Uncharacterized protein / 30S Ribosomal protein S17, putative / Uncharacterized protein / Opioid growth factor receptor (OGFr) conserved domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Ribosomal protein S23 mitochondrial conserved domain-containing protein / Uncharacterized protein / Ribosomal protein S9 / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Ubiquitin-like domain-containing protein / Manganese/iron superoxide dismutase C-terminal domain-containing protein / Superoxide dismutase, putative / Uncharacterized protein / Uncharacterized protein
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsRamrath, D.J.F. / Niemann, M. / Leibundgut, M. / Bieri, P. / Prange, C. / Horn, E.K. / Leitner, A. / Boehringer, D. / Schneider, A. / Ban, N.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Science / Year: 2018
Title: Evolutionary shift toward protein-based architecture in trypanosomal mitochondrial ribosomes.
Authors: David J F Ramrath / Moritz Niemann / Marc Leibundgut / Philipp Bieri / Céline Prange / Elke K Horn / Alexander Leitner / Daniel Boehringer / André Schneider / Nenad Ban /
Abstract: Ribosomal RNA (rRNA) plays key functional and architectural roles in ribosomes. Using electron microscopy, we determined the atomic structure of a highly divergent ribosome found in mitochondria of , ...Ribosomal RNA (rRNA) plays key functional and architectural roles in ribosomes. Using electron microscopy, we determined the atomic structure of a highly divergent ribosome found in mitochondria of , a unicellular parasite that causes sleeping sickness in humans. The trypanosomal mitoribosome features the smallest rRNAs and contains more proteins than all known ribosomes. The structure shows how the proteins have taken over the role of architectural scaffold from the rRNA: They form an autonomous outer shell that surrounds the entire particle and stabilizes and positions the functionally important regions of the rRNA. Our results also reveal the "minimal" set of conserved rRNA and protein components shared by all ribosomes that help us define the most essential functional elements.
History
DepositionAug 31, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Dec 11, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
DA: mS48
DD: mS51
DI: mS56
DL: mS59
DM: mS60
DN: mS61
DO: mS62
DP: mS63
DQ: mS64
DR: mS65
DS: mS66
DU: mS68
DZ: mS73
Da: mS74
CE: mS55m
CF: bS6m
CH: uS8m
CI: uS9m
CK: uS11m
CL: uS12m
CO: uS15m
CP: bS16m
CQ: uS17m
CR: bS18m
CU: uS21m
CZ: mt-IF-3
Ca: mS22
Cb: mS23
Cd: mS26
Cj: mS34
Cm: mS37
Cn: mS38
Cp: mS41
Cq: mS42
Cr: mS43
Cv: mS47
CA: 9S rRNA
UQ: Unknown protein
UR: Unknown protein
US: Unknown protein
UT: Unknown protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,751,90484
Polymers1,750,27541
Non-polymers1,62943
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 37 types, 37 molecules DADDDIDLDMDNDODPDQDRDSDUDZDaCECFCHCICKCLCOCPCQCRCUCZCaCbCdCj...

#1: Protein mS48


Mass: 201811.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: residues 1470-1487 built as polyalanines / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q57UJ2
#2: Protein mS51


Mass: 95080.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q385L8
#3: Protein mS56


Mass: 47306.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q587C2
#4: Protein mS59


Mass: 35395.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q38BS2
#5: Protein mS60


Mass: 34546.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q57XL2
#6: Protein mS61


Mass: 33482.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q38D60
#7: Protein mS62


Mass: 32068.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q383D1
#8: Protein mS63


Mass: 31922.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q38F25
#9: Protein mS64


Mass: 30742.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q382E8
#10: Protein mS65


Mass: 30617.381 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q57UA2
#11: Protein mS66


Mass: 29960.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q388L7
#12: Protein mS68


Mass: 26472.807 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q582T9
#13: Protein mS73


Mass: 11360.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q587C4
#14: Protein mS74


Mass: 8203.408 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427
#15: Protein mS55m


Mass: 50147.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q38AX6
#16: Protein bS6m


Mass: 18861.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: residues 105-114 built as polyalanines / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q38BW5
#17: Protein uS8m


Mass: 32766.459 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q388R7
#18: Protein uS9m


Mass: 50201.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q57W62
#19: Protein uS11m


Mass: 37925.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q389T7
#20: Protein uS12m


Mass: 10421.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: mitochondrial gene subject to RNA editing alternative start codon
Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427
#21: Protein uS15m


Mass: 50401.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q4GZ99
#22: Protein bS16m


Mass: 22077.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q384N9
#23: Protein uS17m


Mass: 35632.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q38DP8
#24: Protein bS18m


Mass: 36988.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q38AS2
#25: Protein uS21m


Mass: 23087.889 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q580M9
#26: Protein mt-IF-3


Mass: 41086.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: residues 294-304 built as polyalanines / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q57WU2
#27: Protein mS22


Mass: 73064.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: residues 20-37 built as polyalanines / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q38DR3
#28: Protein mS23


Mass: 36784.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q57VB2
#29: Protein mS26


Mass: 51136.684 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: residues 221-248 built as polyalanines / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q38DK6
#30: Protein mS34


Mass: 28728.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q57UK0
#31: Protein mS37


Mass: 24757.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q38C96
#32: Protein mS38


Mass: 28240.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q57VQ9
#33: Protein mS41


Mass: 22421.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q389L3
#34: Protein mS42


Mass: 29748.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q586A1, superoxide dismutase
#35: Protein mS43


Mass: 48590.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: residues 27-35 built as polyalanines / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q585I1
#36: Protein mS47


Mass: 137935.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q383R4
#40: Protein Unknown protein


Mass: 4613.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427

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RNA chain , 1 types, 1 molecules CA

#37: RNA chain 9S rRNA


Mass: 198481.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: GenBank: 343546

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Protein/peptide , 3 types, 3 molecules UQURUT

#38: Protein/peptide Unknown protein


Mass: 2741.370 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: unassigned UNK residues / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427
#39: Protein/peptide Unknown protein


Mass: 698.854 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: unassigned UNK residues / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427
#41: Protein/peptide Unknown protein


Mass: 3762.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: unassigned UNK residues / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427

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Non-polymers , 4 types, 43 molecules

#42: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#43: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: Mg
#44: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34) / Spermidine


Mass: 145.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H19N3
#45: Chemical ChemComp-SPM / SPERMINE / Spermine


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: body of the T. brucei mitoribosome small subunit in complex with mt-IF-3
Type: RIBOSOME / Entity ID: #1-#41 / Source: NATURAL
Molecular weightValue: 1.35 MDa / Experimental value: YES
Source (natural)Organism: Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 98 % / Chamber temperature: 278 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameCategory
1EMANparticle selection
4CTFFINDCTF correction
10RELIONfinal Euler assignment
11RELIONclassification
13Cootmodel refinement
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 31911 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingB value: 41.4 / Protocol: AB INITIO MODEL
Details: We used Coot and O for initial model building and refined the structure using Phenix

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