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


This is version 1.0 of the entry. See complete history


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 pathway, involving many assembly factors ...

    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
bL28mA [auth A1]241Trypanosoma brucei bruceiMutation(s): 0 
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Find proteins for Q586A2 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 2
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mt-LAF21B [auth E1]482Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q57WG6 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 3
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uL29mC [auth A2]471Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q38EM7 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DUF4379 domain-containing proteinD [auth E2]568Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for C9ZTN9 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
uL30mE [auth A3]218Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for C9ZY77 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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Entity ID: 6
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mt-LAF23F [auth E3]557Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for D0A795 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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Entity ID: 7
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mt-LAF24G [auth E4]439Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 8
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bL32mH [auth A5]80Trypanosoma brucei bruceiMutation(s): 0 
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Find proteins for Q584F4 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 9
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mt-LAF25I [auth E5]376Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 10
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KRIPP3J [auth E6]531Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 11
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bL35mK [auth A8]181Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 13
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mL67M [auth BA]831Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 14
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mt-EngAN [auth EA]576Trypanosoma brucei bruceiMutation(s): 0 
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Find proteins for Q57TZ4 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 15
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UNKO [auth UA], TB [auth Uf]10Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
mL68P [auth BB]541Trypanosoma brucei bruceiMutation(s): 0 
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Find proteins for D0A135 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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Entity ID: 17
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DEAD-box helicase, putativeQ [auth EB]754Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 18
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Pseudouridylate synthase, putativeR [auth EC]406Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q38FJ3 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 19
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mL70S [auth BD]547Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 20
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mt-LAF4T [auth ED]616Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 21
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Ribosomal protein L3 mitochondrial, putativeU [auth AE]473Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 22
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mL71V [auth BE]449Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 23
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SpoU_methylase domain-containing proteinW [auth EE]586Trypanosoma brucei bruceiMutation(s): 0 
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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, putativeX [auth AF]459Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for A0A1G4HYD1 (Trypanosoma equiperdum)
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Entity ID: 25
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Tetratricopeptide repeatY [auth BF]426Trypanosoma brucei bruceiMutation(s): 0 
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Find proteins for A0A3L6LA84 (Trypanosoma brucei equiperdum)
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Entity ID: 26
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SpoU_methylase domain-containing proteinZ [auth EF]373Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for C9ZWD9 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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Entity ID: 27
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mt-LAF7AA [auth EG]156Trypanosoma brucei bruceiMutation(s): 0 
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Find proteins for Q387S8 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 28
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mL74BA [auth BH]349Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 29
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mt-LAF8CA [auth EH]634Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for A0A1G4IEQ9 (Trypanosoma equiperdum)
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Entity ID: 30
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RIBOSOMAL_L9 domain-containing proteinDA [auth AI]263Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q57UC5 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
mL75EA [auth BI]342Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for D0A108 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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Entity ID: 32
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UNKFA [auth UI], FC [auth Ur]21Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 33
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mL76GA [auth BJ]333Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 34
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Ribosomal protein L11, putativeHA [auth AK]342Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 35
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Chaperone protein DNAj, putativeIA [auth BK]386Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 36
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UNKJA [auth UK]25Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 37
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mL78KA [auth BL]312Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 38
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mt-LAF12LA [auth EL]691Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 39
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GTP-binding protein, putativeMA [auth EM]451Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q38E75 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 40
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UNKNA [auth UM]8Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 41
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50S ribosomal protein L13, putativeOA [auth AN]202Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 42
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mL80PA [auth BN]302Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 43
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mt-LAF14QA [auth EN]731Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 44
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mL81RA [auth BO]262Trypanosoma brucei bruceiMutation(s): 0 
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mt-LAF15aSA [auth EO], UA [auth EP]319Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 46
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Ribosomal_L18e/L15P domain-containing proteinTA [auth AP]374Trypanosoma brucei bruceiMutation(s): 0 
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Peptidyl-prolyl cis-trans isomeraseVA [auth BQ]231Trypanosoma brucei bruceiMutation(s): 0 
EC: 5.2.1.8
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Entity ID: 48
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50S ribosomal protein L17, putativeWA [auth AR]301Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 49
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mL84XA [auth BR]205Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 50
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Acyl carrier proteinYA [auth ER]148Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 51
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mL85ZA [auth BS]198Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 52
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Lipase (Class 3)AB [auth ES]524Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for A0A3L6L1Y4 (Trypanosoma brucei equiperdum)
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Entity ID: 53
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bL19mBB [auth AT]144Trypanosoma brucei bruceiMutation(s): 0 
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Find proteins for Q4GZ98 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 54
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mL86CB [auth BT]191Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for A0A3L6L8W0 (Trypanosoma brucei equiperdum)
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Entity ID: 55
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mt-LAF19DB [auth ET]102Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 56
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bL20mEB [auth AU]213Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetailsImage
mL87FB [auth BU]185Trypanosoma brucei bruceiMutation(s): 0 
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Find proteins for D0A7Z9 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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Entity ID: 58
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bL21mGB [auth AV]188Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 59
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mL88HB [auth BV]190Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 60
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uL22mIB [auth AW]278Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for C9ZSI8 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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Entity ID: 61
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mL89JB [auth BW]188Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 62
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uL23mKB [auth AX]246Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 63
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uL24mLB [auth AY]378Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for C9ZK52 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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Entity ID: 64
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Peptidyl-prolyl cis-trans isomeraseMB [auth BZ]190Trypanosoma brucei bruceiMutation(s): 0 
EC: 5.2.1.8
UniProt
Find proteins for Q383Y4 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 65
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mL93NB [auth Ba]153Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for D0A4T0 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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Entity ID: 66
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mL94OB [auth Bb]162Trypanosoma brucei bruceiMutation(s): 0 
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Find proteins for Q38EP7 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 67
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mL95PB [auth Bc]146Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 68
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mL41QB [auth Ae]197Trypanosoma brucei bruceiMutation(s): 0 
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Find proteins for Q383U6 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 69
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mL42RB [auth Af]189Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 70
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mL98SB [auth Bf]113Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 71
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L51_S25_CI-B8 domain-containing proteinUB [auth Ag]260Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q583E5 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 72
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mt-LAF27VB [auth E7]97Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 73
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KRIPP9WB [auth E8]786Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 74
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mt-LAF29XB [auth E9]343Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for A0A3L6L206 (Trypanosoma brucei equiperdum)
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Entity ID: 75
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mL49YB [auth Al]218Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 76
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UNKZB [auth Ul]238Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 77
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UNKAC [auth Um]27Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 78
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UNKBC [auth Un]28Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 79
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mL52CC [auth Ao]1520Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 80
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mL53DC [auth Ap]309Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 81
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UNKEC [auth Up]87Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 82
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UNKGC [auth Us]79Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 83
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mL63HC [auth At]154Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 84
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mL64IC [auth Av]242Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for D0A934 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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Entity ID: 12
MoleculeChainsLengthOrganismImage
12S ribosomal RNAL [auth AA]1176Trypanosoma brucei brucei
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Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD (Subject of Investigation/LOI)
Query on NAD

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ND [auth Av]NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
GTP (Subject of Investigation/LOI)
Query on GTP

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CD [auth EA], FD [auth EA]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
ATP (Subject of Investigation/LOI)
Query on ATP

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ID [auth EB]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
PM8 (Subject of Investigation/LOI)
Query on PM8

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LD [auth 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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JC [auth E2], KC [auth E2], KD [auth EG], LC [auth E2], MC [auth E2], MD [auth E9], NC [auth A5]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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AD [auth AA] , BD [auth AA] , DD [auth EA] , GD [auth EA] , JD [auth EB] , OC [auth A8] , PC [auth A8] , QC [auth AA] , 
AD [auth AA], BD [auth AA], DD [auth EA], GD [auth EA], JD [auth EB], OC [auth A8], PC [auth A8], QC [auth AA], RC [auth AA], SC [auth AA], TC [auth AA], UC [auth AA], VC [auth AA], WC [auth AA], XC [auth AA], YC [auth AA], ZC [auth AA]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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ED [auth EA], HD [auth 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

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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: 2020-10-14
    Type: Initial release