6HIW

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.37 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 
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Entity ID: 2
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mS51B [auth DD]812Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 3
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mS56C [auth DI]407Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
mS59D [auth DL]307Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 5
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mS60E [auth DM]294Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 6
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mS61F [auth DN]293Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 7
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mS62G [auth DO]282Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 8
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mS63H [auth DP]274Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 9
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mS64I [auth DQ]268Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 10
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mS65J [auth DR]270Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 11
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mS66K [auth DS]261Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 12
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mS68L [auth DU]228Trypanosoma brucei bruceiMutation(s): 0 
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Find proteins for Q582T9 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 13
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mS73M [auth DZ]94Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 14
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mS74N [auth Da]64Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 15
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mS49O [auth DB]1181Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 16
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mS50P [auth DC]1165Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 17
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mS52Q [auth DE]747Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 18
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mS53R [auth DF]666Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 19
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mS54S [auth DG]631Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 20
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mS55T [auth DH]581Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 21
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mS57U [auth DJ]396Trypanosoma brucei bruceiMutation(s): 0 
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Find proteins for Q584U8 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 22
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mS58V [auth DK]324Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 23
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mS67W [auth DT]247Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 24
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mS69X [auth DV]183Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 25
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mS70Y [auth DW]179Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 26
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mS71Z [auth DX]169Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 27
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mS72AA [auth DY]163Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 28
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uS3mBA [auth CC]74Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
uS5mCA [auth CE]435Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 30
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bS6mDA [auth CF]160Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 31
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uS8mEA [auth CH]282Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 32
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uS9mFA [auth CI]443Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 33
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uS10mGA [auth CJ]817Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 34
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uS11mHA [auth CK]326Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 35
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uS12mIA [auth CL]87Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 36
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uS14mJA [auth CN]166Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 37
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uS15mKA [auth CO]429Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 38
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bS16mLA [auth CP]188Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 39
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uS17mMA [auth CQ]307Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 40
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bS18mNA [auth CR]320Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 41
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uS19mOA [auth CS]244Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 42
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bS21mPA [auth CU]193Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 43
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mt-IF-3QA [auth CZ]360Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 44
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mS22RA [auth Ca]602Trypanosoma brucei bruceiMutation(s): 0 
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mS23SA [auth Cb]325Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 46
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mS26TA [auth Cd]440Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 47
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mS29UA [auth Cg]498Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 48
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mS33VA [auth Ci]181Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 49
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mS34WA [auth Cj]257Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 50
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mS35XA [auth Ck]874Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 51
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mS37YA [auth Cm]215Trypanosoma brucei bruceiMutation(s): 0 
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Find proteins for Q38C96 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 52
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mS38ZA [auth Cn]250Trypanosoma brucei bruceiMutation(s): 0 
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Find proteins for Q57VQ9 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 53
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mS41AB [auth Cp]187Trypanosoma brucei bruceiMutation(s): 0 
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Find proteins for Q389L3 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 54
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mS42BB [auth Cq]263Trypanosoma brucei bruceiMutation(s): 0 
EC: 1.15.1.1
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Find proteins for Q586A1 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 55
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mS43CB [auth Cr]439Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetailsImage
mS47DB [auth Cv]1211Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q383R4 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Explore Q383R4 
Go to UniProtKB:  Q383R4
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown ProteinFB [auth UO]5Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown ProteinGB [auth UP]7Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown ProteinHB [auth UQ]32Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown ProteinIB [auth UR]8Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 62
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown ProteinJB [auth US]54Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 63
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown ProteinKB [auth UT]44Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 57
MoleculeChainsLengthOrganismImage
9S rRNAEB [auth CA]621Trypanosoma brucei brucei
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Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP (Subject of Investigation/LOI)
Query on GTP

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RB [auth Cg]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
UTP (Subject of Investigation/LOI)
Query on UTP

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OB [auth DJ]URIDINE 5'-TRIPHOSPHATE
C9 H15 N2 O15 P3
PGAVKCOVUIYSFO-XVFCMESISA-N
 Ligand Interaction
SPM (Subject of Investigation/LOI)
Query on SPM

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

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ED [auth CA], FD [auth CA], GD [auth CA], HD [auth CA]SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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LB [auth DA], MB [auth DS], NB [auth DS], TB [auth Cr]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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AC [auth CA] , AD [auth CA] , BC [auth CA] , BD [auth CA] , CC [auth CA] , CD [auth CA] , DC [auth CA] , DD [auth CA] , 
AC [auth CA], AD [auth CA], BC [auth CA], BD [auth CA], CC [auth CA], CD [auth CA], DC [auth CA], DD [auth CA], EC [auth CA], FC [auth CA], GC [auth CA], HC [auth CA], IC [auth CA], JC [auth CA], KC [auth CA], LC [auth CA], MC [auth CA], NC [auth CA], OC [auth CA], PB [auth CQ], PC [auth CA], QB [auth Ca], QC [auth CA], RC [auth CA], SB [auth Cg], SC [auth CA], TC [auth CA], UB [auth Cv], UC [auth CA], VB [auth CA], VC [auth CA], WB [auth CA], WC [auth CA], XB [auth CA], XC [auth CA], YB [auth CA], YC [auth CA], ZB [auth CA], ZC [auth CA]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.37 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




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: 2019-12-18
    Changes: Other