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- EMDB-0233: Cryo-EM structure of the Trypanosoma brucei mitochondrial ribosom... -

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Entry
Database: EMDB / ID: 0233
TitleCryo-EM structure of the Trypanosoma brucei mitochondrial ribosome - This entry contains the head of the small mitoribosomal subunit
Map datamap of the head of the T. brucei mitoribosome small subunit
Samplehead of the T. brucei mitoribosome small subunit:
mS48 / mS59 / mS49 / mS50 / mS52 / mS53 / mS54 / mS55 / mS57 / mS58 ...mS48 / mS59 / mS49 / mS50 / mS52 / mS53 / mS54 / mS55 / mS57 / mS58 / mS67 / mS69 / mS70 / mS71 / mS72 / uS3m / uS9m / uS10m / uS11m / uS14m / uS18m / uS19m / mS29 / mS33 / mS35 / nucleic-acidNucleic acid / (Unknown protein) x 2 / (ligand) x 5
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
Function and homology information
SourceTrypanosoma brucei brucei (eukaryote)
Methodsingle particle reconstruction / cryo EM / 3.08 Å resolution
AuthorsRamrath DJF / Niemann M / Leibundgut M / Bieri P / Prange C / Horn EK / 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 ReportPDB-ID: 6hiz

SummaryFull reportAbout validation report
DateDeposition: Aug 31, 2018 / Header (metadata) release: Sep 26, 2018 / Map release: Sep 26, 2018 / Last update: Nov 7, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.15
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.15
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6hiz
  • Surface level: 0.15
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_0233.map.gz (map file in CCP4 format, 131073 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
320 pix
1.39 Å/pix.
= 444.8 Å
320 pix
1.39 Å/pix.
= 444.8 Å
320 pix
1.39 Å/pix.
= 444.8 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 Level:0.01 (by author), 0.15 (movie #1):
Minimum - Maximum-0.2582923 - 0.5873829
Average (Standard dev.)0.0010537558 (0.015823135)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions320320320
Origin0.00.00.0
Limit319.0319.0319.0
Spacing320320320
CellA=B=C: 444.8 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.391.391.39
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z444.800444.800444.800
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.2580.5870.001

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Supplemental data

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Sample components

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Entire head of the T. brucei mitoribosome small subunit

EntireName: head of the T. brucei mitoribosome small subunit / Number of components: 34

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Component #1: protein, head of the T. brucei mitoribosome small subunit

ProteinName: head of the T. brucei mitoribosome small subunit / Recombinant expression: No
MassExperimental: 1.25 MDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427

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Component #2: protein, mS48

ProteinName: mS48 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 201.811188 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

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Component #3: protein, mS59

ProteinName: mS59 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 35.395676 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

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Component #4: protein, mS49

ProteinName: mS49 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 137.234125 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

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Component #5: protein, mS50

ProteinName: mS50 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 131.71925 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

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Component #6: protein, mS52

ProteinName: mS52 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 85.012258 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

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Component #7: protein, mS53

ProteinName: mS53 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 75.338914 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

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Component #8: protein, mS54

ProteinName: mS54 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 72.046031 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

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Component #9: protein, mS55

ProteinName: mS55 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 66.67668 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

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Component #10: protein, mS57

ProteinName: mS57 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 45.956293 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

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Component #11: protein, mS58

ProteinName: mS58 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 35.62391 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

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Component #12: protein, mS67

ProteinName: mS67 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.096051 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

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Component #13: protein, mS69

ProteinName: mS69 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.589732 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

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Component #14: protein, mS70

ProteinName: mS70 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.247398 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

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Component #15: protein, mS71

ProteinName: mS71 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.093227 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

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Component #16: protein, mS72

ProteinName: mS72 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.317293 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

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Component #17: protein, uS3m

ProteinName: uS3m / Details: Mitochondrial gene uS3m (MURF-5) / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.07094 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

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Component #18: protein, uS9m

ProteinName: uS9m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 50.128926 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

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Component #19: protein, uS10m

ProteinName: uS10m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 94.351039 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

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Component #20: protein, uS11m

ProteinName: uS11m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 37.92591 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

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Component #21: protein, uS14m

ProteinName: uS14m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.900014 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

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Component #22: protein, uS18m

ProteinName: uS18m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 36.988691 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

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Component #23: protein, uS19m

ProteinName: uS19m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.364604 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

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Component #24: protein, mS29

ProteinName: mS29 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 57.048836 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

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Component #25: protein, mS33

ProteinName: mS33 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.244104 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

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Component #26: protein, mS35

ProteinName: mS35 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 98.377773 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

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Component #27: nucleic-acid, RNA (143-MER)

Nucleic-acidName: RNA (143-MER) / Class: RNA / 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 UAUAAAUUAU AUUAUAUUAU AUUUAUUCAU AUAAUUAAUA GGAUAAUAUU UGUAGUUUUU GAUACCAUGA UAAGGAUUAU AAAUUGAAAG UGUUAAUAUC AUAAUCAAAA UUUAUUAUUU AUAUUAAAUA UGUAUGUGUA GAUAAAAUAA GAAAUUAAAA AGGUAUUGUU GCCCACCAAU UUUUAUAAUA AAAAUAACGU GCAGUAAUUA AUAUAUUUAU AAAAAUAUAU U
MassTheoretical: 195.379688 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

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Component #28: protein, Unknown protein

ProteinName: Unknown protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.443539 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

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Component #29: protein, Unknown protein

ProteinName: Unknown protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.613749 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

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Component #30: ligand, SPERMIDINE

LigandName: SPERMIDINE / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.145246 kDa

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Component #31: ligand, URIDINE 5'-TRIPHOSPHATE

LigandName: URIDINE 5'-TRIPHOSPHATE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.484141 kDa

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Component #32: ligand, GUANOSINE-5'-TRIPHOSPHATE

LigandName: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.52318 kDa

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Component #33: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #34: ligand, water

LigandName: water / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 1.801505 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: OTHER / Temperature: 278 K / Humidity: 98 %

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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: 4 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON III (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 101308
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Details: We used Coot and O for initial model building and refined the structure using Phenix
Overall bvalue: 45
Output model

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