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



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 
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Entity ID: 2
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uL29mA2471Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 3
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uL30mA3218Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 4
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bL32mA580Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 5
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bL35mA8181Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 7
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mL67BA831Trypanosoma brucei bruceiMutation(s): 0 
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mt-EngAEA576Trypanosoma brucei bruceiMutation(s): 0 
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mL68BB541Trypanosoma brucei bruceiMutation(s): 0 
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mt-LAF2EB754Trypanosoma brucei bruceiMutation(s): 0 
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mt-LAF3EC406Trypanosoma brucei bruceiMutation(s): 0 
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mL70BD547Trypanosoma brucei bruceiMutation(s): 0 
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mt-LAF4ED616Trypanosoma brucei bruceiMutation(s): 0 
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uL3mAE473Trypanosoma brucei bruceiMutation(s): 0 
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mL71BE449Trypanosoma brucei bruceiMutation(s): 0 
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mt-LAF5EE586Trypanosoma brucei bruceiMutation(s): 0 
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UNKUE33Trypanosoma brucei bruceiMutation(s): 0 
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uL4mAF459Trypanosoma brucei bruceiMutation(s): 0 
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mL72BF426Trypanosoma brucei bruceiMutation(s): 0 
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mt-LAF6EF373Trypanosoma brucei bruceiMutation(s): 0 
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mt-LAF7EG156Trypanosoma brucei bruceiMutation(s): 0 
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mL74BH349Trypanosoma brucei bruceiMutation(s): 0 
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mt-LAF8EH634Trypanosoma brucei bruceiMutation(s): 0 
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bL9mAI263Trypanosoma brucei bruceiMutation(s): 0 
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mL75BI342Trypanosoma brucei bruceiMutation(s): 0 
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MALSU1EI349Trypanosoma brucei bruceiMutation(s): 0 
EC: 2.7.7.52
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UNKUI23Trypanosoma brucei bruceiMutation(s): 0 
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mL76BJ333Trypanosoma brucei bruceiMutation(s): 0 
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L0R8F8EJ116Trypanosoma brucei bruceiMutation(s): 0 
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uL11mAK342Trypanosoma brucei bruceiMutation(s): 0 
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mL77BK386Trypanosoma brucei bruceiMutation(s): 0 
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mt-ACPEKER148Trypanosoma brucei bruceiMutation(s): 0 
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UNKUK25Trypanosoma brucei bruceiMutation(s): 0 
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mL78BL312Trypanosoma brucei bruceiMutation(s): 0 
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mt-LAF12EL691Trypanosoma brucei bruceiMutation(s): 0 
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UNKUL72Trypanosoma brucei bruceiMutation(s): 0 
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Mtg1EM451Trypanosoma brucei bruceiMutation(s): 0 
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UNKUM8Trypanosoma brucei bruceiMutation(s): 0 
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uL13mAN202Trypanosoma brucei bruceiMutation(s): 0 
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mL80BN302Trypanosoma brucei bruceiMutation(s): 0 
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mt-LAF14EN731Trypanosoma brucei bruceiMutation(s): 0 
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uL14mAO217Trypanosoma brucei bruceiMutation(s): 0 
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mL81BO262Trypanosoma brucei bruceiMutation(s): 0 
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mt-LAF15aEOEP319Trypanosoma brucei bruceiMutation(s): 0 
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uL15mAP374Trypanosoma brucei bruceiMutation(s): 0 
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mL83BQ231Trypanosoma brucei bruceiMutation(s): 0 
EC: 5.2.1.8
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mt-EngBEQ655Trypanosoma brucei bruceiMutation(s): 0 
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bL17mAR301Trypanosoma brucei bruceiMutation(s): 0 
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mL84BR205Trypanosoma brucei bruceiMutation(s): 0 
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mL85BS198Trypanosoma brucei bruceiMutation(s): 0 
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mt-LAF18ES524Trypanosoma brucei bruceiMutation(s): 0 
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bL19mAT144Trypanosoma brucei bruceiMutation(s): 0 
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mL86BT191Trypanosoma brucei bruceiMutation(s): 0 
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mt-LAF19ET102Trypanosoma brucei bruceiMutation(s): 0 
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bL20mAU213Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetailsImage
mL87BU185Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for D0A7Z9 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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Entity ID: 57
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mt-LAF20EU56Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 58
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bL21mAV188Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for C9ZT11 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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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 
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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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mL90BX190Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 64
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UNKUX180Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 65
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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: 66
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mL92BZ190Trypanosoma 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: 67
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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: 68
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mL94Bb162Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 69
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mL95Bc146Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 70
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mL41Ae197Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 71
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mL42Af189Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetailsImage
mL98Bf113Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 73
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mL43Ag260Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for Q583E5 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 74
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mL99Bg105Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for Q587H8 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 75
MoleculeChainsSequence LengthOrganismDetailsImage
mL100Bh92Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for A0A3L6L2V1 (Trypanosoma brucei equiperdum)
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Entity ID: 76
MoleculeChainsSequence LengthOrganismDetailsImage
mL101Bi245Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for Q4GZ80 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 77
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mL49Al218Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for Q57Z82 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 78
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mL52Ao1520Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 79
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mL53Ap309Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for A0A3L6L3K9 (Trypanosoma brucei equiperdum)
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Entity ID: 80
MoleculeChainsSequence LengthOrganismDetailsImage
mL63At154Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for C9ZU82 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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Entity ID: 81
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: 6
MoleculeChainsLengthOrganismImage
12S ribosomal RNAAA1176Trypanosoma brucei brucei
Small Molecules
Ligands 8 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, EQ
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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EK, 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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AA
SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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A5, BX, Bh, EG
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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AA, EA, EB, EQ
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: 3.10 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