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: 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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uL29mB [auth A2]471Trypanosoma brucei bruceiMutation(s): 0 
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uL30mC [auth A3]218Trypanosoma brucei bruceiMutation(s): 0 
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bL32mD [auth A5]80Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 5
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bL35mE [auth A8]181Trypanosoma brucei bruceiMutation(s): 0 
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mL67G [auth BA]831Trypanosoma brucei bruceiMutation(s): 0 
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mt-EngAH [auth EA]576Trypanosoma brucei bruceiMutation(s): 0 
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mL68I [auth BB]541Trypanosoma brucei bruceiMutation(s): 0 
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mt-LAF2J [auth EB]754Trypanosoma brucei bruceiMutation(s): 0 
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mt-LAF3K [auth EC]406Trypanosoma brucei bruceiMutation(s): 0 
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mL70L [auth BD]547Trypanosoma brucei bruceiMutation(s): 0 
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mt-LAF4M [auth ED]616Trypanosoma brucei bruceiMutation(s): 0 
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uL3mN [auth AE]473Trypanosoma brucei bruceiMutation(s): 0 
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mL71O [auth BE]449Trypanosoma brucei bruceiMutation(s): 0 
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mt-LAF5P [auth EE]586Trypanosoma brucei bruceiMutation(s): 0 
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UNKQ [auth UE]33Trypanosoma brucei bruceiMutation(s): 0 
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uL4mR [auth AF]459Trypanosoma brucei bruceiMutation(s): 0 
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mL72S [auth BF]426Trypanosoma brucei bruceiMutation(s): 0 
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mt-LAF6T [auth EF]373Trypanosoma brucei bruceiMutation(s): 0 
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mt-LAF7U [auth EG]156Trypanosoma brucei bruceiMutation(s): 0 
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mL74V [auth BH]349Trypanosoma brucei bruceiMutation(s): 0 
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mt-LAF8W [auth EH]634Trypanosoma brucei bruceiMutation(s): 0 
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bL9mX [auth AI]263Trypanosoma brucei bruceiMutation(s): 0 
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mL75Y [auth BI]342Trypanosoma brucei bruceiMutation(s): 0 
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MALSU1Z [auth EI]349Trypanosoma brucei bruceiMutation(s): 0 
EC: 2.7.7.52
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UNKAA [auth UI]23Trypanosoma brucei bruceiMutation(s): 0 
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mL76BA [auth BJ]333Trypanosoma brucei bruceiMutation(s): 0 
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L0R8F8CA [auth EJ]116Trypanosoma brucei bruceiMutation(s): 0 
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uL11mDA [auth AK]342Trypanosoma brucei bruceiMutation(s): 0 
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mL77EA [auth BK]386Trypanosoma brucei bruceiMutation(s): 0 
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mt-ACPFA [auth EK], YA [auth ER]148Trypanosoma brucei bruceiMutation(s): 0 
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UNKGA [auth UK]25Trypanosoma brucei bruceiMutation(s): 0 
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mL78HA [auth BL]312Trypanosoma brucei bruceiMutation(s): 0 
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mt-LAF12IA [auth EL]691Trypanosoma brucei bruceiMutation(s): 0 
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UNKJA [auth UL]72Trypanosoma brucei bruceiMutation(s): 0 
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Mtg1KA [auth EM]451Trypanosoma brucei bruceiMutation(s): 0 
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UNKLA [auth UM]8Trypanosoma brucei bruceiMutation(s): 0 
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uL13mMA [auth AN]202Trypanosoma brucei bruceiMutation(s): 0 
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mL80NA [auth BN]302Trypanosoma brucei bruceiMutation(s): 0 
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mt-LAF14OA [auth EN]731Trypanosoma brucei bruceiMutation(s): 0 
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uL14mPA [auth AO]217Trypanosoma brucei bruceiMutation(s): 0 
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mL81QA [auth BO]262Trypanosoma brucei bruceiMutation(s): 0 
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mt-LAF15aRA [auth EO], TA [auth EP]319Trypanosoma brucei bruceiMutation(s): 0 
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uL15mSA [auth AP]374Trypanosoma brucei bruceiMutation(s): 0 
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mL83UA [auth BQ]231Trypanosoma brucei bruceiMutation(s): 0 
EC: 5.2.1.8
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mt-EngBVA [auth EQ]655Trypanosoma brucei bruceiMutation(s): 0 
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bL17mWA [auth AR]301Trypanosoma brucei bruceiMutation(s): 0 
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mL84XA [auth BR]205Trypanosoma brucei bruceiMutation(s): 0 
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mL85ZA [auth BS]198Trypanosoma brucei bruceiMutation(s): 0 
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mt-LAF18AB [auth ES]524Trypanosoma brucei bruceiMutation(s): 0 
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bL19mBB [auth AT]144Trypanosoma brucei bruceiMutation(s): 0 
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mL86CB [auth BT]191Trypanosoma brucei bruceiMutation(s): 0 
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mt-LAF19DB [auth ET]102Trypanosoma brucei bruceiMutation(s): 0 
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bL20mEB [auth AU]213Trypanosoma brucei bruceiMutation(s): 0 
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mL87FB [auth BU]185Trypanosoma brucei bruceiMutation(s): 0 
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mt-LAF20GB [auth EU]56Trypanosoma brucei bruceiMutation(s): 0 
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bL21mHB [auth AV]188Trypanosoma brucei bruceiMutation(s): 0 
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Find proteins for C9ZT11 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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Entity ID: 59
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mL88IB [auth BV]190Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 60
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uL22mJB [auth AW]278Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 61
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mL89KB [auth BW]188Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q57WW5 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 62
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uL23mLB [auth AX]246Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 63
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mL90MB [auth BX]190Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q585P1 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 64
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UNKNB [auth UX]180Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 65
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uL24mOB [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: 66
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mL92PB [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: 67
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mL93QB [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: 68
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mL94RB [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: 69
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mL95SB [auth Bc]146Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 70
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mL41TB [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: 71
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mL42UB [auth Af]189Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 72
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mL98VB [auth Bf]113Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 73
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mL43WB [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: 74
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mL99XB [auth Bg]105Trypanosoma brucei bruceiMutation(s): 0 
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Find proteins for Q587H8 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 75
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mL100YB [auth Bh]92Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for A0A3L6L2V1 (Trypanosoma brucei equiperdum)
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Entity ID: 76
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mL101ZB [auth Bi]245Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q4GZ80 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 77
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mL49AC [auth Al]218Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q57Z82 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 78
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mL52BC [auth Ao]1520Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 79
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mL53CC [auth Ap]309Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for A0A3L6L3K9 (Trypanosoma brucei equiperdum)
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Entity ID: 80
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mL63DC [auth At]154Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 81
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mL64EC [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: 6
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12S ribosomal RNAF [auth AA]1176Trypanosoma brucei brucei
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Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD (Subject of Investigation/LOI)
Query on NAD

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AE [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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KD [auth EA], ND [auth EA], UD [auth EQ]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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QD [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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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
 Ligand Interaction
SPD
Query on SPD

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JD [auth AA]SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
 Ligand Interaction
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
 Ligand Interaction
MG
Query on MG

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AD [auth AA] , BD [auth AA] , CD [auth AA] , DD [auth AA] , ED [auth AA] , FD [auth AA] , GC [auth AA] , GD [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
 Ligand Interaction
NA
Query on NA

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 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