6HIY

Cryo-EM structure of the Trypanosoma brucei mitochondrial ribosome - This entry contains the body of the small mitoribosomal subunit in complex with mt-IF-3


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.27 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Evolutionary shift toward protein-based architecture in trypanosomal mitochondrial ribosomes.

Ramrath, D.J.F.Niemann, M.Leibundgut, M.Bieri, P.Prange, C.Horn, E.K.Leitner, A.Boehringer, D.Schneider, A.Ban, N.

(2018) Science 362

  • DOI: 10.1126/science.aau7735
  • Primary Citation of Related Structures:  
    6HIV, 6HIW, 6HIX, 6HIY, 6HIZ

  • PubMed 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 Trypanosoma brucei , a unicellular parasite that causes sleeping sickness in humans ...

    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 Trypanosoma brucei , 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.


    Organizational Affiliation

    Department of Biology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, ETH Zurich, CH-8093 Zurich, Switzerland. ban@mol.biol.ethz.ch.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
mS48A [auth DA]1788Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
mS51B [auth DD]812Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
mS56C [auth DI]407Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
mS59D [auth DL]307Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
mS60E [auth DM]294Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
mS61F [auth DN]293Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q38D60 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
mS62G [auth DO]282Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
mS63H [auth DP]274Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
mS64I [auth DQ]268Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
mS65J [auth DR]270Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
mS66K [auth DS]261Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 12
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mS68L [auth DU]228Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q582T9 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
mS73M [auth DZ]94Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
mS74N [auth Da]64Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
mS55mO [auth CE]435Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q38AX6 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
bS6mP [auth CF]160Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
uS8mQ [auth CH]282Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
uS9mR [auth CI]443Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
uS11mS [auth CK]326Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 20
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uS12mT [auth CL]87Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
uS15mU [auth CO]429Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q4GZ99 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
bS16mV [auth CP]188Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q384N9 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
uS17mW [auth CQ]307Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
bS18mX [auth CR]320Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
uS21mY [auth CU]193Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
mt-IF-3Z [auth CZ]360Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
mS22AA [auth Ca]602Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
mS23BA [auth Cb]324Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
mS26CA [auth Cd]440Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
mS34DA [auth Cj]257Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
mS37EA [auth Cm]215Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
mS38FA [auth Cn]250Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
mS41GA [auth Cp]187Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
mS42HA [auth Cq]263Trypanosoma brucei bruceiMutation(s): 0 
EC: 1.15.1.1
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
mS43IA [auth Cr]439Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
mS47JA [auth Cv]1211Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown proteinLA [auth UQ]32Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown proteinMA [auth UR]8Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown proteinNA [auth US]54Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown proteinOA [auth UT]44Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 37
MoleculeChainsLengthOrganismImage
9S rRNAKA [auth CA]621Trypanosoma brucei brucei
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Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SPM (Subject of Investigation/LOI)
Query on SPM

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FC [auth CA]SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
 Ligand Interaction
SPD
Query on SPD

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DC [auth CA], EC [auth CA]SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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PA [auth DA], QA [auth DS], RA [auth DS], VA [auth Cr]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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AB [auth CA] , AC [auth CA] , BB [auth CA] , BC [auth CA] , CB [auth CA] , CC [auth CA] , DB [auth CA] , EB [auth CA] , 
AB [auth CA], AC [auth CA], BB [auth CA], BC [auth CA], CB [auth CA], CC [auth CA], DB [auth CA], EB [auth CA], FB [auth CA], GB [auth CA], HB [auth CA], IB [auth CA], JB [auth CA], KB [auth CA], LB [auth CA], MB [auth CA], NB [auth CA], OB [auth CA], PB [auth CA], QB [auth CA], RB [auth CA], SA [auth CO], SB [auth CA], TA [auth CQ], TB [auth CA], UA [auth Ca], UB [auth CA], VB [auth CA], WA [auth Cv], WB [auth CA], XA [auth CA], XB [auth CA], YA [auth CA], YB [auth CA], ZA [auth CA], ZB [auth CA]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.27 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland--

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-26
    Type: Initial release
  • Version 1.1: 2018-11-07
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-11
    Changes: Other