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

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Basic information

Entry
Database: PDB / ID: 6hiz
TitleCryo-EM structure of the Trypanosoma brucei mitochondrial ribosome - This entry contains the head of the small mitoribosomal subunit
Components
  • (Unknown protein) x 2
  • RNA (143-MER)
  • mS29
  • mS33
  • mS35
  • mS48
  • mS49
  • mS50
  • mS52
  • mS53
  • mS54
  • mS55
  • mS57
  • mS58
  • mS59
  • mS67
  • mS69
  • mS70
  • mS71
  • mS72
  • uS10m
  • uS11m
  • uS14m
  • uS18m
  • uS19m
  • uS3m
  • uS9m
KeywordsRIBOSOME / mitoribosome / translation / Trypanosoma / small ribosomal subunit / 9S rRNA / ribosomal protein
Function / homologyMitochondrial ribosomal death-associated protein 3 / Ribosomal protein S23/S29, mitochondrial / Ribosomal protein S5 domain 2-type fold, subgroup / Tetratricopeptide-like helical domain superfamily / Rhodanese-like domain / Ribosomal protein S9 / Ribosomal protein S5 domain 2-type fold / LysM domain / LysM domain superfamily / Ribosomal protein S18 superfamily ...Mitochondrial ribosomal death-associated protein 3 / Ribosomal protein S23/S29, mitochondrial / Ribosomal protein S5 domain 2-type fold, subgroup / Tetratricopeptide-like helical domain superfamily / Rhodanese-like domain / Ribosomal protein S9 / Ribosomal protein S5 domain 2-type fold / LysM domain / LysM domain superfamily / Ribosomal protein S18 superfamily / Rhodanese-like domain superfamily / Ribosomal protein S11 superfamily / Ribosomal protein S9/S16 / LysM domain / Rhodanese domain profile. / positive regulation of mitochondrial translational initiation / mitochondrial mRNA editing complex / RNA polyadenylation / mitochondrial RNA processing / mitochondrial small ribosomal subunit / RNA modification / mRNA stabilization / structural constituent of ribosome / endonuclease activity / translation / mitochondrion / RNA binding / nucleus / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / gb:343546:
Function and homology information
Specimen sourceTrypanosoma brucei brucei (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.08 Å resolution
AuthorsRamrath, D.J.F. / Niemann, M. / Leibundgut, M. / Bieri, P. / Prange, C. / Horn, E.K. / Leitner, A. / Boehringer, A. / Schneider, A. / Ban, N.
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 31, 2018 / Release: Sep 26, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Sep 26, 2018Structure modelrepositoryInitial release
1.1Nov 7, 2018Structure modelData collection / Database referencescitation_citation.journal_volume

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Structure visualization

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  • Deposited structure unit
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Structure viewerMolecule:
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Assembly

Deposited unit
DA: mS48
DL: mS59
DB: mS49
DC: mS50
DE: mS52
DF: mS53
DG: mS54
DH: mS55
DJ: mS57
DK: mS58
DT: mS67
DV: mS69
DW: mS70
DX: mS71
DY: mS72
CC: uS3m
CI: uS9m
CJ: uS10m
CK: uS11m
CN: uS14m
CR: uS18m
CS: uS19m
Cg: mS29
Ci: mS33
Ck: mS35
CA: RNA (143-MER)
UO: Unknown protein
UP: Unknown protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,650,36735
Polyers1,648,99628
Non-polymers1,3717
Water543
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/peptide , 27 types, 27 molecules DADLDBDCDEDFDGDHDJDKDTDVDWDXDYCCCICJCKCNCRCSCgCiCkUOUP

#1: Protein/peptide mS48


Mass: 201811.188 Da / Num. of mol.: 1 / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q57UJ2
#2: Protein/peptide mS59


Mass: 35395.676 Da / Num. of mol.: 1 / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q38BS2
#3: Protein/peptide mS49


Mass: 137234.125 Da / Num. of mol.: 1 / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q586P5
#4: Protein/peptide mS50


Mass: 131719.250 Da / Num. of mol.: 1 / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q57YB5
#5: Protein/peptide mS52


Mass: 85012.258 Da / Num. of mol.: 1 / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q386Q7
#6: Protein/peptide mS53


Mass: 75338.914 Da / Num. of mol.: 1 / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q38ET1
#7: Protein/peptide mS54


Mass: 72046.031 Da / Num. of mol.: 1 / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q57ZP8
#8: Protein/peptide mS55


Mass: 66676.680 Da / Num. of mol.: 1 / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q580V1
#9: Protein/peptide mS57


Mass: 45956.293 Da / Num. of mol.: 1 / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q584U8
#10: Protein/peptide mS58


Mass: 35623.910 Da / Num. of mol.: 1 / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q38BP1
#11: Protein/peptide mS67


Mass: 30096.051 Da / Num. of mol.: 1 / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q586G5
#12: Protein/peptide mS69


Mass: 21589.732 Da / Num. of mol.: 1 / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q57UZ6
#13: Protein/peptide mS70


Mass: 21247.398 Da / Num. of mol.: 1 / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q383N9
#14: Protein/peptide mS71


Mass: 20093.227 Da / Num. of mol.: 1 / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q383G5
#15: Protein/peptide mS72


Mass: 19317.293 Da / Num. of mol.: 1 / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q57YD4
#16: Protein/peptide uS3m


Mass: 9070.940 Da / Num. of mol.: 1 / Details: Mitochondrial gene uS3m (MURF-5) / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427
#17: Protein/peptide uS9m


Mass: 50128.926 Da / Num. of mol.: 1 / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q57W62
#18: Protein/peptide uS10m


Mass: 94351.039 Da / Num. of mol.: 1 / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q57Z45
#19: Protein/peptide uS11m


Mass: 37925.910 Da / Num. of mol.: 1 / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q389T7
#20: Protein/peptide uS14m


Mass: 19900.014 Da / Num. of mol.: 1 / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q580I0
#21: Protein/peptide uS18m


Mass: 36988.691 Da / Num. of mol.: 1 / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q38AS2
#22: Protein/peptide uS19m


Mass: 28364.604 Da / Num. of mol.: 1 / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q584T8
#23: Protein/peptide mS29


Mass: 57048.836 Da / Num. of mol.: 1 / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q585C2
#24: Protein/peptide mS33


Mass: 21244.104 Da / Num. of mol.: 1 / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q57WW0
#25: Protein/peptide mS35


Mass: 98377.773 Da / Num. of mol.: 1 / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q387C7
#27: Protein/peptide Unknown protein


Mass: 443.539 Da / Num. of mol.: 1 / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427
#28: Protein/peptide Unknown protein


Mass: 613.749 Da / Num. of mol.: 1 / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427

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RNA chain , 1 types, 1 molecules CA

#26: RNA chain RNA (143-MER)


Mass: 195379.688 Da / Num. of mol.: 1 / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: GenBank: 343546

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Non-polymers , 5 types, 10 molecules

#29: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 2 / Formula: C7H19N3 / Spermidine
#30: Chemical ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE


Mass: 484.141 Da / Num. of mol.: 1 / Formula: C9H15N2O15P3 / Uridine triphosphate / Comment: UTP *YM
#31: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Formula: C10H16N5O14P3 / Guanosine triphosphate / Comment: GTP (energy-carrying molecule) *YM
#32: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Formula: Mg / Magnesium
#33: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Formula: H2O / Water

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: head of the T. brucei mitoribosome small subunit / Type: RIBOSOME
Entity ID: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28
Source: NATURAL
Molecular weightValue: 1.25 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 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: 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 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameCategory
1EMANparticle selection
4CTFFINDCTF correction
12RELION3D reconstruction
13Cootmodel refinement
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 101308 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingDetails: We used Coot and O for initial model building and refined the structure using Phenix
Overall b value: 45 / Ref protocol: AB INITIO MODEL

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