6YXY

State B of the Trypanosoma brucei mitoribosomal large subunit assembly intermediate


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 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: https://doi.org/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. 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.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
bL28mA [auth A1]241Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q586A2 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
uL29mB [auth A2]471Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
uL30mC [auth A3]218Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
bL32mD [auth A5]80Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
bL35mE [auth A8]181Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
mL67G [auth BA]831Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
mt-EngAH [auth EA]576Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
mL68I [auth BB]541Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
mt-LAF2J [auth EB]754Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
mt-LAF3K [auth EC]406Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
mL70L [auth BD]547Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
mt-LAF4M [auth ED]616Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
uL3mN [auth AE]473Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
mL71O [auth BE]449Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
mt-LAF5P [auth EE]586Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
UNKQ [auth UE]33Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
uL4mR [auth AF]459Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for D0A7A6 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
mL72S [auth BF]426Trypanosoma brucei bruceiMutation(s): 0 
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Find proteins for A0A3L6LA84 (Trypanosoma brucei equiperdum)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
mt-LAF6T [auth EF]373Trypanosoma brucei bruceiMutation(s): 0 
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Find proteins for C9ZWD9 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
mt-LAF7U [auth EG]156Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
mL74V [auth BH]349Trypanosoma brucei bruceiMutation(s): 0 
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Find proteins for Q38AM5 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
mt-LAF8W [auth EH]634Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
bL9mX [auth AI]263Trypanosoma brucei bruceiMutation(s): 0 
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Find proteins for Q57UC5 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
mL75Y [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: 26
MoleculeChains Sequence LengthOrganismDetailsImage
MALSU1Z [auth EI]349Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q584Y2 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
UNKAA [auth UI]23Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
mL76BA [auth BJ]333Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
L0R8F8CA [auth EJ]116Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
uL11mDA [auth AK]342Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
mL77EA [auth BK]386Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
mt-ACPFA [auth EK],
YA [auth ER]
148Trypanosoma brucei bruceiMutation(s): 0 
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Find proteins for Q57WW9 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
UNKGA [auth UK]25Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
mL78HA [auth BL]312Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
mt-LAF12IA [auth EL]691Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
UNKJA [auth UL]72Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Mtg1KA [auth EM]451Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
UNKLA [auth UM]8Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
uL13mMA [auth AN]202Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
mL80NA [auth BN]302Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
mt-LAF14OA [auth EN]731Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
uL14mPA [auth AO]217Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
mL81QA [auth BO]262Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
mt-LAF15aRA [auth EO],
TA [auth EP]
319Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
uL15mSA [auth AP]374Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
mL83UA [auth BQ]231Trypanosoma brucei bruceiMutation(s): 0 
EC: 5.2.1.8
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Find proteins for Q57WF8 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
mt-EngBVA [auth EQ]655Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
bL17mWA [auth AR]301Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
mL84XA [auth BR]205Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
mL85ZA [auth BS]198Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
mt-LAF18AB [auth ES]524Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
bL19mBB [auth AT]144Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
mL86CB [auth BT]191Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
mt-LAF19DB [auth ET]102Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
bL20mEB [auth AU]213Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
mL87FB [auth BU]185Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
mt-LAF20GB [auth EU]56Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
bL21mHB [auth AV]188Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
mL88IB [auth BV]190Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
uL22mJB [auth AW]278Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
mL89KB [auth BW]188Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
uL23mLB [auth AX]246Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
mL90MB [auth BX]190Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
UNKNB [auth UX]180Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
uL24mOB [auth AY]378Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
mL92PB [auth BZ]190Trypanosoma brucei bruceiMutation(s): 0 
EC: 5.2.1.8
UniProt
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
mL93QB [auth Ba]153Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
mL94RB [auth Bb]162Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
mL95SB [auth Bc]146Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
mL41TB [auth Ae]197Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
mL42UB [auth Af]189Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
mL98VB [auth Bf]113Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
mL43WB [auth Ag]260Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
mL99XB [auth Bg]105Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
mL100YB [auth Bh]92Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
mL101ZB [auth Bi]245Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
mL49AC [auth Al]218Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
mL52BC [auth Ao]1,520Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
mL53CC [auth Ap]309Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 80
MoleculeChains Sequence LengthOrganismDetailsImage
mL63DC [auth At]154Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 81
MoleculeChains Sequence LengthOrganismDetailsImage
mL64EC [auth Av]242Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains LengthOrganismImage
12S ribosomal RNAF [auth AA]1,176Trypanosoma brucei brucei
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Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

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AE [auth Av]NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
GTP
Query on GTP

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KD [auth EA],
ND [auth EA],
UD [auth EQ]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
ATP
Query on ATP

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QD [auth EB]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
PM8
Query on PM8

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TD [auth EK],
WD [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
SPD
Query on SPD

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JD [auth AA]SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
ZN
Query on ZN

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FC [auth A5],
SD [auth EG],
XD [auth BX],
YD [auth BX],
ZD [auth Bh]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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AD [auth AA]
BD [auth AA]
CD [auth AA]
DD [auth AA]
ED [auth AA]
AD [auth AA],
BD [auth AA],
CD [auth AA],
DD [auth AA],
ED [auth AA],
FD [auth AA],
GC [auth AA],
GD [auth AA],
HC [auth AA],
HD [auth AA],
IC [auth AA],
ID [auth AA],
JC [auth AA],
KC [auth AA],
LC [auth AA],
LD [auth EA],
MC [auth AA],
NC [auth AA],
OC [auth AA],
OD [auth EA],
PC [auth AA],
QC [auth AA],
RC [auth AA],
RD [auth EB],
SC [auth AA],
TC [auth AA],
UC [auth AA],
VC [auth AA],
VD [auth EQ],
WC [auth AA],
XC [auth AA],
YC [auth AA],
ZC [auth AA]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

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MD [auth EA],
PD [auth EA]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0

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