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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 / 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 / Superoxide dismutase, putative / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / 30S ribosomal protein S8, putative / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / 30S Ribosomal protein S17, putative / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein
Function and homology information
Specimen sourceTrypanosoma brucei brucei (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.27 Å resolution
AuthorsRamrath, D.J.F. / Niemann, M. / Leibundgut, M. / Bieri, P. / Prange, C. / Horn, E.K. / 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 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
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
Polyers1,750,27541
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/peptide , 40 types, 40 molecules DADDDIDLDMDNDODPDQDRDSDUDZDaCECFCHCICKCLCOCPCQCRCUCZCaCbCdCj...

#1: Protein/peptide mS48


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


Mass: 50201.016 Da / Num. of mol.: 1 / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q57W62
#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 uS12m


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


Mass: 137935.000 Da / Num. of mol.: 1 / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: UniProt: Q383R4
#38: Protein/peptide Unknown protein


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


Mass: 4613.678 Da / Num. of mol.: 1 / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427
#41: Protein/peptide Unknown protein


Mass: 3762.629 Da / Num. of mol.: 1 / Details: unassigned UNK residues / 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: (natural) Trypanosoma brucei brucei (eukaryote) / Variant: Lister 427 / References: GenBank: 343546

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Non-polymers , 4 types, 43 molecules

#42: Chemical
ChemComp-ZN / ZINC ION


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


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


Mass: 145.246 Da / Num. of mol.: 2 / Formula: C7H19N3 / Spermidine
#45: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 1 / Formula: C10H26N4 / Spermine

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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: body of the T. brucei mitoribosome small subunit in complex with mt-IF-3
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, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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 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 / 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 / Number of particles: 31911 / 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: 41.4 / Ref protocol: AB INITIO MODEL

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