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: https://doi.org/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. 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.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
mS48A [auth DA]1,788Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
mS51B [auth DD]812Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q385L8 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
mS56C [auth DI]407Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q587C2 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
mS59D [auth DL]307Trypanosoma brucei bruceiMutation(s): 0 
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Find proteins for Q38BS2 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
mS60E [auth DM]294Trypanosoma brucei bruceiMutation(s): 0 
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Find proteins for Q57XL2 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
mS61F [auth DN]293Trypanosoma brucei bruceiMutation(s): 0 
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Find proteins for Q38D60 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
mS62G [auth DO]282Trypanosoma brucei bruceiMutation(s): 0 
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Find proteins for Q383D1 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
mS63H [auth DP]274Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q38F25 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
mS64I [auth DQ]268Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q382E8 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
mS65J [auth DR]270Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q57UA2 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
mS66K [auth DS]261Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q388L7 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
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
MoleculeChains Sequence LengthOrganismDetailsImage
mS73M [auth DZ]94Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q587C4 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
mS74N [auth Da]64Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
mS49O [auth DB]1,181Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q586P5 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
mS50P [auth DC]1,165Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q57YB5 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
mS52Q [auth DE]747Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q386Q7 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
mS53R [auth DF]666Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q38ET1 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
mS54S [auth DG]631Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q57ZP8 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
mS55T [auth DH]581Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q580V1 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
mS57U [auth DJ]396Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q584U8 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
mS58V [auth DK]324Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q38BP1 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
mS67W [auth DT]247Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q586G5 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
mS69X [auth DV]183Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q57UZ6 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
mS70Y [auth DW]179Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q383N9 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
mS71Z [auth DX]169Trypanosoma brucei bruceiMutation(s): 0 
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Find proteins for Q383G5 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
mS72AA [auth DY]163Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
uS3mBA [auth CC]74Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
uS5mCA [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: 30
MoleculeChains Sequence LengthOrganismDetailsImage
bS6mDA [auth CF]160Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q38BW5 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
uS8mEA [auth CH]282Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q388R7 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
uS9mFA [auth CI]443Trypanosoma brucei bruceiMutation(s): 0 
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Find proteins for Q57W62 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
uS10mGA [auth CJ]817Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
uS11mHA [auth CK]326Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q389T7 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
uS12mIA [auth CL]87Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
uS14mJA [auth CN]166Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q580I0 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
uS15mKA [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: 38
MoleculeChains Sequence LengthOrganismDetailsImage
bS16mLA [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: 39
MoleculeChains Sequence LengthOrganismDetailsImage
uS17mMA [auth CQ]307Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q38DP8 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
bS18mNA [auth CR]320Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q38AS2 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
uS19mOA [auth CS]244Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q584T8 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
bS21mPA [auth CU]193Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q580M9 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
mt-IF-3QA [auth CZ]360Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q57WU2 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
mS22RA [auth Ca]602Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q38DR3 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
mS23SA [auth Cb]325Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q57VB2 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
mS26TA [auth Cd]440Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q38DK6 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
mS29UA [auth Cg]498Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q585C2 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
mS33VA [auth Ci]181Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q57WW0 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
mS34WA [auth Cj]257Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q57UK0 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
mS35XA [auth Ck]874Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q387C7 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
mS37YA [auth Cm]215Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q38C96 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
mS38ZA [auth Cn]250Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q57VQ9 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
mS41AB [auth Cp]187Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q389L3 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
mS42BB [auth Cq]263Trypanosoma brucei bruceiMutation(s): 0 
EC: 1.15.1.1
UniProt
Find proteins for Q586A1 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
mS43CB [auth Cr]439Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q585I1 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
mS47DB [auth Cv]1,211Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q383R4 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown ProteinFB [auth UO]5Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown ProteinGB [auth UP]7Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown ProteinHB [auth UQ]32Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown ProteinIB [auth UR]8Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown ProteinJB [auth US]54Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown ProteinKB [auth UT]44Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 57
MoleculeChains LengthOrganismImage
9S rRNAEB [auth CA]621Trypanosoma brucei brucei
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Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

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RB [auth Cg]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
UTP
Query on UTP

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OB [auth DJ]URIDINE 5'-TRIPHOSPHATE
C9 H15 N2 O15 P3
PGAVKCOVUIYSFO-XVFCMESISA-N
SPM
Query on SPM

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ID [auth CA]SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
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
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
MG
Query on MG

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AC [auth CA]
AD [auth CA]
BC [auth CA]
BD [auth CA]
CC [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
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.37 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTCoot
MODEL REFINEMENTPHENIX

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: 2019-12-18
    Changes: Other