[English] 日本語
Yorodumi
- EMDB-0232: Cryo-EM structure of the Trypanosoma brucei mitochondrial ribosom... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 0232
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
Map datamap of the T. brucei mitoribosome small subunit body in complex with mt-IF3
Samplebody of the T. brucei mitoribosome small subunit in complex with mt-IF-3:
mS48 / mS51 / mS56 / mS59 / mS60 / mS61 / mS62 / mS63 / mS64 / mS65 ...mS48 / mS51 / mS56 / mS59 / mS60 / mS61 / mS62 / mS63 / mS64 / mS65 / mS66 / mS68 / mS73 / mS74 / mS55m / bS6m / uS8m / uS9m / uS11m / uS12m / uS15m / bS16m / uS17m / bS18m / uS21m / mt-IF-3 / mS22 / mS23 / mS26 / mS34 / mS37 / mS38 / mS41 / mS42 / mS43 / mS47 / nucleic-acidNucleic acid / (Unknown protein) x 4 / (ligand) x 4
Function / homologyManganese/iron superoxide dismutase, N-terminal domain superfamily / Manganese/iron superoxide dismutase, C-terminal / Ribosomal protein S15, bacterial-type / Ribosomal protein S5, C-terminal / S15/NS1, RNA-binding / Cyclic phosphodiesterase / Tetratricopeptide-like helical domain superfamily / Nucleic acid-binding, OB-fold / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S5 domain 2-type fold, subgroup ...Manganese/iron superoxide dismutase, N-terminal domain superfamily / Manganese/iron superoxide dismutase, C-terminal / Ribosomal protein S15, bacterial-type / Ribosomal protein S5, C-terminal / S15/NS1, RNA-binding / Cyclic phosphodiesterase / Tetratricopeptide-like helical domain superfamily / Nucleic acid-binding, OB-fold / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S5 domain 2-type fold, subgroup / IGR protein motif / Protein kinase A anchor protein, nuclear localisation signal domain / Manganese/iron superoxide dismutase, N-terminal / Ribosomal protein S5 domain 2-type fold / Ubiquitin family / Ribosomal protein S16 domain superfamily / Probable Zinc-ribbon domain / ClpP/crotonase-like domain superfamily / Ubiquitin-like domain superfamily / Mitochondrial 28S ribosomal protein S34 / Enoyl-CoA hydratase/isomerase, HIBYL-CoA-H type / Ribosomal protein S8 superfamily / Manganese/iron superoxide dismutase, C-terminal domain superfamily / Ribosomal protein S18 superfamily / Nucleoid-associated protein YbaB-like domain superfamily / Ribosomal protein S11 superfamily / Ribosomal protein S9 / Ribosomal protein S8 / Ubiquitin domain / Ribosomal protein S9/S16 / Ubiquitin domain profile. / Enoyl-CoA hydratase/isomerase / Mitochondrial 28S ribosomal protein S34 / Probable Zinc-ribbon domain / AKAP7 2'5' RNA ligase-like domain / Ribosomal protein S5, C-terminal domain / Iron/manganese superoxide dismutases, C-terminal domain / Ribosomal protein S15 / Ribosomal protein S8 / Iron/manganese superoxide dismutases, alpha-hairpin domain / Ribosomal protein S17 / Ribosomal protein S17/S11 / Ribosomal protein S15 / modulation of development of symbiont involved in interaction with host / quorum sensing involved in interaction with host / organellar small ribosomal subunit / mitochondrial mRNA editing complex / 3-hydroxyisobutyryl-CoA hydrolase activity / RNA polyadenylation / mitochondrial RNA processing / mitochondrial small ribosomal subunit / enoyl-CoA hydratase activity / mRNA stabilization / regulation of protein kinase A signaling / fatty acid beta-oxidation / protein kinase A regulatory subunit binding / superoxide dismutase / superoxide dismutase activity / protein localization / cytosolic small ribosomal subunit / ribosome / structural constituent of ribosome / translation / intracellular / mitochondrion / RNA binding / metal ion binding / cytosol / 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 / Superoxide dismutase, putative / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / 30S Ribosomal protein S17, putative / 30S ribosomal protein S8, putative / 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 / 3.27 Å resolution
AuthorsRamrath DJF / Niemann M / Leibundgut M / Bieri P / Prange C / Horn EK / Leitner A / Boehringer D / 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: 6hiy

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

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

Downloads & links

-
Map

Fileemd_0232.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:0.0115 (by author), 0.15 (movie #1):
Minimum - Maximum-0.26455936 - 0.51369876
Average (Standard dev.)0.0014350519 (0.017512508)
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-0.2650.5140.001

-
Supplemental data

-
Sample components

+
Entire body of the T. brucei mitoribosome small subunit in complex with ...

EntireName: body of the T. brucei mitoribosome small subunit in complex with mt-IF-3
Number of components: 46

+
Component #1: protein, body of the T. brucei mitoribosome small subunit in comp...

ProteinName: body of the T. brucei mitoribosome small subunit in complex with mt-IF-3
Recombinant expression: No
MassExperimental: 1.35 MDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote) / Strain: Lister 427

+
Component #2: protein, mS48

ProteinName: mS48 / Details: residues 1470-1487 built as polyalanines / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 201.811188 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

+
Component #3: protein, mS51

ProteinName: mS51 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 95.080992 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

+
Component #4: protein, mS56

ProteinName: mS56 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 47.306836 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

+
Component #5: protein, mS59

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

+
Component #6: protein, mS60

ProteinName: mS60 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 34.546641 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

+
Component #7: protein, mS61

ProteinName: mS61 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 33.48234 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

+
Component #8: protein, mS62

ProteinName: mS62 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 32.0681 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

+
Component #9: protein, mS63

ProteinName: mS63 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 31.922178 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

+
Component #10: protein, mS64

ProteinName: mS64 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.742207 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

+
Component #11: protein, mS65

ProteinName: mS65 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.617381 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

+
Component #12: protein, mS66

ProteinName: mS66 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.960182 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

+
Component #13: protein, mS68

ProteinName: mS68 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.472807 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

+
Component #14: protein, mS73

ProteinName: mS73 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.360885 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

+
Component #15: protein, mS74

ProteinName: mS74 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.203408 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

+
Component #16: protein, mS55m

ProteinName: mS55m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 50.147355 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

+
Component #17: protein, bS6m

ProteinName: bS6m / Details: residues 105-114 built as polyalanines / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.861543 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

+
Component #18: protein, uS8m

ProteinName: uS8m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 32.766459 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

+
Component #19: protein, uS9m

ProteinName: uS9m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 50.201016 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

+
Component #20: protein, uS11m

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

+
Component #21: protein, uS12m

ProteinName: uS12m
Details: mitochondrial gene subject to RNA editing alternative start codon
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.421635 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

+
Component #22: protein, uS15m

ProteinName: uS15m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 50.401191 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

+
Component #23: protein, bS16m

ProteinName: bS16m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.077805 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

+
Component #24: protein, uS17m

ProteinName: uS17m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 35.632727 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

+
Component #25: protein, bS18m

ProteinName: bS18m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 36.988691 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

+
Component #26: protein, uS21m

ProteinName: uS21m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.087889 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

+
Component #27: protein, mt-IF-3

ProteinName: mt-IF-3 / Details: residues 294-304 built as polyalanines / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 41.086285 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

+
Component #28: protein, mS22

ProteinName: mS22 / Details: residues 20-37 built as polyalanines / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 73.064141 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

+
Component #29: protein, mS23

ProteinName: mS23 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 36.7845 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

+
Component #30: protein, mS26

ProteinName: mS26 / Details: residues 221-248 built as polyalanines / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 51.136684 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

+
Component #31: protein, mS34

ProteinName: mS34 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.72818 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

+
Component #32: protein, mS37

ProteinName: mS37 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.757896 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

+
Component #33: protein, mS38

ProteinName: mS38 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.2406 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

+
Component #34: protein, mS41

ProteinName: mS41 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.421469 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

+
Component #35: protein, mS42

ProteinName: mS42 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.748666 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

+
Component #36: protein, mS43

ProteinName: mS43 / Details: residues 27-35 built as polyalanines / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 48.59041 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

+
Component #37: protein, mS47

ProteinName: mS47 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 137.935 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

+
Component #38: nucleic-acid, 9S rRNA

Nucleic-acidName: 9S rRNA / 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 UUAAGUGUUG AUUUAACCAA UAAAAAUAUA AAUAAUUUUU AUUUGUUUUU AAACACCAUU AGGUAUAUGC AAAUAUAAAA UUAUAGUAAU UAUAAAUUAU AUUAUAUUAU AUUUAUUCAU AUAAUUAAUA GGAUAAUAUU UGUAGUUUUU GAUACCAUGA UAAGGAUUAU AAAUUGAAAG UGGUAAUAUC AUAAUCAAAA UUUAUUAUUU AUAUUAAAUA UGUAUGUGUA GAUAAAAUAA GAAAUUAAAA AGGUAUUGUU GCCCACCAAU UUUUAUAAUA AAAAUAACGU GCAGUAAUUA AUAUAUUUAU AAAAAUAUAU UUUUUUUUUU U
MassTheoretical: 198.481422 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

+
Component #39: protein, Unknown protein

ProteinName: Unknown protein / Details: unassigned UNK residues / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.74137 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

+
Component #40: protein, Unknown protein

ProteinName: Unknown protein / Details: unassigned UNK residues / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.698854 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

+
Component #41: protein, Unknown protein

ProteinName: Unknown protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 4.613678 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

+
Component #42: protein, Unknown protein

ProteinName: Unknown protein / Details: unassigned UNK residues / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 3.762629 kDa
SourceSpecies: Trypanosoma brucei brucei (eukaryote)

+
Component #43: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

+
Component #44: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 36 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

+
Component #45: ligand, SPERMIDINE

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

+
Component #46: ligand, SPERMINE

LigandName: SPERMINE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.20234 kDa

-
Experimental details

-
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 %

-
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)

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 31911
3D reconstructionAlgorithm: FOURIER SPACE / Resolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Modeling #1Details: We used Coot and O for initial model building and refined the structure using Phenix
Overall bvalue: 41.399999999999999
Output model

+
About Yorodumi

-
News

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more