6YXX

State A of the Trypanosoma brucei mitoribosomal large subunit assembly intermediate


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report



Literature

Structural Insights into the Mechanism of Mitoribosomal Large Subunit Biogenesis.

Jaskolowski, M.Ramrath, D.J.F.Bieri, P.Niemann, M.Mattei, S.Calderaro, S.Leibundgut, M.Horn, E.K.Boehringer, D.Schneider, A.Ban, N.

(2020) Mol Cell 79: 629-644.e4

  • DOI: 10.1016/j.molcel.2020.06.030
  • Primary Citation of Related Structures:  
    6YXX, 6YXY

  • PubMed Abstract: 
  • In contrast to the bacterial translation machinery, mitoribosomes and mitochondrial translation factors are highly divergent in terms of composition and architecture. There is increasing evidence that the biogenesis of mitoribosomes is an intricate p ...

    In contrast to the bacterial translation machinery, mitoribosomes and mitochondrial translation factors are highly divergent in terms of composition and architecture. There is increasing evidence that the biogenesis of mitoribosomes is an intricate pathway, involving many assembly factors. To better understand this process, we investigated native assembly intermediates of the mitoribosomal large subunit from the human parasite Trypanosoma brucei using cryo-electron microscopy. We identify 28 assembly factors, 6 of which are homologous to bacterial and eukaryotic ribosome assembly factors. They interact with the partially folded rRNA by specifically recognizing functionally important regions such as the peptidyltransferase center. The architectural and compositional comparison of the assembly intermediates indicates a stepwise modular assembly process, during which the rRNA folds toward its mature state. During the process, several conserved GTPases and a helicase form highly intertwined interaction networks that stabilize distinct assembly intermediates. The presented structures provide general insights into mitoribosomal maturation.


    Organizational Affiliation

    Department of Biology, ETH Zurich, Zurich 8093, Switzerland. Electronic address: ban@mol.biol.ethz.ch.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
bL28mA1241Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for Q586A2 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 2
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mt-LAF21E1482Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for Q57WG6 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
uL29mA2471Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for Q38EM7 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DUF4379 domain-containing proteinE2568Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for C9ZTN9 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
uL30mA3218Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for C9ZY77 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
mt-LAF23E3557Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for D0A795 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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Entity ID: 7
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mt-LAF24E4439Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 8
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bL32mA580Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 9
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mt-LAF25E5376Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 10
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KRIPP3E6531Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 11
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bL35mA8181Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 13
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mL67BA831Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
mt-EngAEA576Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
UNKUAUf10Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 16
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mL68BB541Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 17
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DEAD-box helicase, putativeEB754Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 18
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Pseudouridylate synthase, putativeEC406Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 19
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mL70BD547Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 20
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mt-LAF4ED616Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 21
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Ribosomal protein L3 mitochondrial, putativeAE473Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for Q580R4 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 22
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mL71BE449Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 23
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SpoU_methylase domain-containing proteinEE586Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for C9ZZ65 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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Entity ID: 24
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Ribosomal protein L4/L1 family, putativeAF459Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for A0A1G4HYD1 (Trypanosoma equiperdum)
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Tetratricopeptide repeatBF426Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for A0A3L6LA84 (Trypanosoma brucei equiperdum)
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Entity ID: 26
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SpoU_methylase domain-containing proteinEF373Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for C9ZWD9 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
mt-LAF7EG156Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for Q387S8 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
mL74BH349Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 29
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mt-LAF8EH634Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL_L9 domain-containing proteinAI263Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 31
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mL75BI342Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for D0A108 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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Entity ID: 32
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UNKUIUr21Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 33
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mL76BJ333Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 34
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Ribosomal protein L11, putativeAK342Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 35
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Chaperone protein DNAj, putativeBK386Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for C9ZQR6 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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Entity ID: 36
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UNKUK25Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 37
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mL78BL312Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for D0A4P5 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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Entity ID: 38
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mt-LAF12EL691Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for C9ZVC0 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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Entity ID: 39
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GTP-binding protein, putativeEM451Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
UNKUM8Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 41
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50S ribosomal protein L13, putativeAN202Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 42
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mL80BN302Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for C9ZQF0 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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Entity ID: 43
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mt-LAF14EN731Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 44
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mL81BO262Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for D0A755 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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Entity ID: 45
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mt-LAF15aEOEP319Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 46
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Ribosomal_L18e/L15P domain-containing proteinAP374Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for Q57U68 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 47
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Peptidyl-prolyl cis-trans isomeraseBQ231Trypanosoma brucei bruceiMutation(s): 0 
EC: 5.2.1.8
Find proteins for Q57WF8 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 48
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50S ribosomal protein L17, putativeAR301Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 49
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mL84BR205Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 50
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Acyl carrier proteinER148Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for Q57WW9 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 51
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mL85BS198Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 52
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Lipase (Class 3)ES524Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for A0A3L6L1Y4 (Trypanosoma brucei equiperdum)
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Entity ID: 53
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bL19mAT144Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for Q4GZ98 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 54
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mL86BT191Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for A0A3L6L8W0 (Trypanosoma brucei equiperdum)
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
mt-LAF19ET102Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for Q383S4 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 56
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bL20mAU213Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 57
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mL87BU185Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for D0A7Z9 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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Entity ID: 58
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bL21mAV188Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 59
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mL88BV190Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 60
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uL22mAW278Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for C9ZSI8 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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Entity ID: 61
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mL89BW188Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 62
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uL23mAX246Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 63
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uL24mAY378Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for C9ZK52 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomeraseBZ190Trypanosoma brucei bruceiMutation(s): 0 
EC: 5.2.1.8
Find proteins for Q383Y4 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 65
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mL93Ba153Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for D0A4T0 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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Entity ID: 66
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mL94Bb162Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for Q38EP7 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 67
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mL95Bc146Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for Q389K3 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 68
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mL41Ae197Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for Q383U6 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 69
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mL42Af189Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for Q383S1 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 70
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mL98Bf113Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 71
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L51_S25_CI-B8 domain-containing proteinAg260Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for Q583E5 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 72
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mt-LAF27E797Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 73
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KRIPP9E8786Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for Q57YZ6 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 74
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mt-LAF29E9343Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for A0A3L6L206 (Trypanosoma brucei equiperdum)
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Entity ID: 75
MoleculeChainsSequence LengthOrganismDetailsImage
mL49Al218Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for Q57Z82 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 76
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UNKUl238Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 77
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UNKUm27Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 78
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UNKUn28Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 79
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mL52Ao1520Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 80
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mL53Ap309Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for A0A3L6L3K9 (Trypanosoma brucei equiperdum)
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Entity ID: 81
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UNKUp87Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 82
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UNKUs79Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 83
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mL63At154Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for C9ZU82 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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Entity ID: 84
MoleculeChainsSequence LengthOrganismDetailsImage
mL64Av242Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for D0A934 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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Entity ID: 12
MoleculeChainsLengthOrganismImage
12S ribosomal RNAAA1176Trypanosoma brucei brucei
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

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Av
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
GTP
Query on GTP

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EA
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
ATP
Query on ATP

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EB
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
PM8
Query on PM8

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ER
S-(2-{[N-(2-HYDROXY-4-{[HYDROXY(OXIDO)PHOSPHINO]OXY}-3,3-DIMETHYLBUTANOYL)-BETA-ALANYL]AMINO}ETHYL) DECANETHIOATE
C21 H41 N2 O7 P S
BPRKYNVKIAROET-IBGZPJMESA-N
 Ligand Interaction
ZN
Query on ZN

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A5, E2, E9, EG
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A8, AA, EA, EB
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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EA
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 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 

  • Version 1.0: 2020-10-14
    Type: Initial release