6HIX

Cryo-EM structure of the Trypanosoma brucei mitochondrial ribosome - This entry contains the large mitoribosomal subunit

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.39 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 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
bl27mA [auth A0]185Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: TEOVI_000532300
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UniProt GroupA0A1G4I8T3
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
bl28mB [auth A1]241Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: Tb927.6.4040
UniProt
Find proteins for Q586A2 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ul29mC [auth A2]471Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: Tb09.160.5240
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ul30mD [auth A3]218Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: TbgDal_IX4520
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
bl31mE [auth A4]183Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: Tb10.6k15.1920
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
bl32mF [auth A5]80Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: Tb927.4.2330
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
bl33mG [auth A6]114Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: Tb927.4.1810
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
bl35mH [auth A8]181Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: TbgDal_X2260
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
bl36mI [auth A9]184Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: TbgDal_IV4820
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L3 mitochondrial, putativeJ [auth AE]473Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: Tb927.3.5610
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L4/L1 family, putativeK [auth AF]459Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: TEOVI_000582800
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
bl9mL [auth AI]263Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: Tb927.5.3410
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
ul10mM [auth AJ]177Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: TbgDal_V3970
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L11, putativeN [auth AK]342Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: Tb927.2.4740, Tb927.2.4890
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Find proteins for Q586R9 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13, putativeO [auth AN]202Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: Tb927.4.1070
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
ul15mP [auth AP]374Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: Tb927.5.3980
UniProt
Find proteins for Q57U68 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16, putativeQ [auth AQ]167Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: Tb927.7.3960
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17, putativeR [auth AR]301Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: Tb927.8.5860
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
bl19mS [auth AT]144Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: TB927.1.1210
UniProt
Find proteins for Q4GZ98 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
bl20mT [auth AU]213Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: Tb11.01.1930
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
bl21mU [auth AV]188Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: TbgDal_VII4650
UniProt
Find proteins for C9ZT11 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
ul22mV [auth AW]278Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: TbgDal_VII3160
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
ul23mW [auth AX]246Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: Tb11.03.0260
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
ul24mX [auth AY]378Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: TbgDal_III1550
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
ml38Y [auth Ab]507Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: Tb11.01.6620
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
ml40Z [auth Ad]289Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: TbgDal_X14530
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
ml41AA [auth Ae]197Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: TbgDal_XI11060
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
ml42BA [auth Af]189Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: Tb11.01.1840
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
ml43CA [auth Ag]260Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: Tb927.4.4600
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
ml46DA [auth Aj]296Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: TbgDal_VII5370
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
ml49EA [auth Al]218Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: Tb927.5.3110
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
ml52FA [auth Ao]259Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: Tb11.02.2250
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
ml53GA [auth Ap]309Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: Tb927.7.2990, Tb927.7.3030
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
ml63HA [auth At]154Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: TbgDal_VII8230
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
ml64IA [auth Av]242Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: Tb11.01.3500
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
bL12mJA [auth AB]56Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
bL12mKA [auth AC],
LA [auth AD]		28Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
bL12mMA [auth AG]27Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
ml67OA [auth BA]831Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: TbgDal_XI1730
UniProt
Find proteins for D0A5V6 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
ml68PA [auth BB]541Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: TbgDal_X580
UniProt
Find proteins for D0A135 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
ml69QA [auth BC]523Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: Tb927.6.2010
UniProt
Find proteins for Q584V5 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
mL70RA [auth BD]547Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
ml71SA [auth BE]449Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: Tb927.7.3460
UniProt
Find proteins for Q57WG1 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
ml72TA [auth BF]426Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: TbgDal_VI3710
UniProt
Find proteins for C9ZR63 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
ml73UA [auth BG]378Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: Tb927.7.6800
UniProt
Find proteins for Q57Y49 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
ml74VA [auth BH]349Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: Tb10.6k15.3290
UniProt
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
ml75WA [auth BI]343Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: Tb10.70.7960
UniProt
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
ml76XA [auth BJ]333Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: Tb11.01.2340
UniProt
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Chaperone protein DNAj, putativeYA [auth BK]386Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: TbgDal_VI2240
UniProt
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
ml78ZA [auth BL]312Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: TbgDal_X13360
UniProt
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
ml79AB [auth BM]283Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: Tb11.01.7140
UniProt
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
ml80BB [auth BN]302Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: Tb927.6.1440
UniProt
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
ml81CB [auth BO]262Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: TbgDal_XI6240
UniProt
Find proteins for D0A755 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
ml82DB [auth BP]266Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: TbgDal_X19420
UniProt
Find proteins for D0A0S6 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomeraseEB [auth BQ]231Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: Tb927.7.3430
EC: 5.2.1.8
UniProt
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
ml84FB [auth BR]205Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: Tb927.6.4080
UniProt
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
ml85GB [auth BS]198Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: Tb09.160.2250
UniProt
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
ml86HB [auth BT]191Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: TbgDal_V5660
UniProt
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
ml87IB [auth BU]185Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: TbgDal_XI9190
UniProt
Find proteins for D0A7Z9 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
ml88JB [auth BV]190Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: TbgDal_VIII1510
UniProt
Find proteins for C9ZUW3 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
ml89KB [auth BW]188Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: Tb927.3.820
UniProt
Find proteins for Q57WW5 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
ml90LB [auth BX]190Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: Tb927.6.1700
UniProt
Find proteins for Q585P1 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
ml91MB [auth BY]172Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: Tb927.3.5300
UniProt
Find proteins for Q580U5 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomeraseNB [auth BZ]190Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: Tb11.01.1215
EC: 5.2.1.8
UniProt
Find proteins for Q383Y4 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
ml93OB [auth Ba]153Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: TbgDal_X13710
UniProt
Find proteins for D0A4T0 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
ml94PB [auth Bb]162Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: Tb09.160.5050
UniProt
Find proteins for Q38EP7 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
ml95QB [auth Bc]146Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: Tb10.26.0585
UniProt
Find proteins for Q389K3 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
ml96RB [auth Bd]144Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: Tb11.01.6285
UniProt
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
ml97SB [auth Be]113Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: Tb10.61.3115
UniProt
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
ml98TB [auth Bf]113Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: Tb10.61.3155
UniProt
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
ml99UB [auth Bg]105Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: Tb927.2.2590
UniProt
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
ml100VB [auth Bh]92Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: TEOVI_000790200
UniProt
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
UNKWB [auth UA]46Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
UNKXB [auth UB]40Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
UNKDC [auth UH],
YB [auth UC]		12Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
UNKZB [auth UD]177Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
UNKAC [auth UE]22Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
UNKBC [auth UF],
CC [auth UG],
IC [auth UN]		24Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 80
MoleculeChains Sequence LengthOrganismDetailsImage
UNKEC [auth UI]17Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 81
MoleculeChains Sequence LengthOrganismDetailsImage
UNKFC [auth UK]10Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 82
MoleculeChains Sequence LengthOrganismDetailsImage
UNKGC [auth UL]15Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 83
MoleculeChains Sequence LengthOrganismDetailsImage
UNKHC [auth UM]6Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 84
MoleculeChains Sequence LengthOrganismDetailsImage
UNKJC [auth UU]11Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 85
MoleculeChains Sequence LengthOrganismDetailsImage
UNKKC [auth UV],
MC [auth UX]		8Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 86
MoleculeChains Sequence LengthOrganismDetailsImage
UNKLC [auth UW]7Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 39
MoleculeChains LengthOrganismImage
12S rRNANA [auth AA]1,178Trypanosoma brucei brucei
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD
Download Ideal Coordinates CCD File 
PC [auth Av]NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
AD [auth Bh]
NC [auth A5]
OC [auth A9]
XC [auth BX]
YC [auth BX]
AD [auth Bh],
NC [auth A5],
OC [auth A9],
XC [auth BX],
YC [auth BX],
ZC [auth Be]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
QC [auth AA]
RC [auth AA]
SC [auth AA]
TC [auth AA]
UC [auth AA]
QC [auth AA],
RC [auth AA],
SC [auth AA],
TC [auth AA],
UC [auth AA],
VC [auth AA],
WC [auth AA]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.39 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION
MODEL REFINEMENTCoot
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



View more in-depth experimental data
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, Source and taxonomy
  • Version 2.0: 2019-02-06
    Changes: Atomic model, Data collection, Derived calculations