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 pathw ...

    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
bL28m A1241Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 2
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uL29m A2471Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 3
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uL30m A3218Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 4
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bL32m A580Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 5
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bL35m A8181Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 7
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mL67 BA831Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 8
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mt-EngA EA576Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 9
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mL68 BB541Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 10
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mt-LAF2 EB754Trypanosoma brucei bruceiMutation(s): 0 
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mt-LAF3 EC406Trypanosoma brucei bruceiMutation(s): 0 
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mL70 BD547Trypanosoma brucei bruceiMutation(s): 0 
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mt-LAF4 ED616Trypanosoma brucei bruceiMutation(s): 0 
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uL3m AE473Trypanosoma brucei bruceiMutation(s): 0 
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mL71 BE449Trypanosoma brucei bruceiMutation(s): 0 
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mt-LAF5 EE586Trypanosoma brucei bruceiMutation(s): 0 
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UNK UE33Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 18
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uL4m AF459Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 19
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mL72 BF426Trypanosoma brucei bruceiMutation(s): 0 
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mt-LAF6 EF373Trypanosoma brucei bruceiMutation(s): 0 
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mt-LAF7 EG156Trypanosoma brucei bruceiMutation(s): 0 
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mL74 BH349Trypanosoma brucei bruceiMutation(s): 0 
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mt-LAF8 EH634Trypanosoma brucei bruceiMutation(s): 0 
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bL9m AI263Trypanosoma brucei bruceiMutation(s): 0 
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mL75 BI342Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 26
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MALSU1 EI349Trypanosoma brucei bruceiMutation(s): 0 
EC: 2.7.7.52
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UNK UI23Trypanosoma brucei bruceiMutation(s): 0 
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mL76 BJ333Trypanosoma brucei bruceiMutation(s): 0 
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L0R8F8 EJ116Trypanosoma brucei bruceiMutation(s): 0 
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uL11m AK342Trypanosoma brucei bruceiMutation(s): 0 
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mL77 BK386Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 32
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mt-ACP EKER148Trypanosoma brucei bruceiMutation(s): 0 
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UNK UK25Trypanosoma brucei bruceiMutation(s): 0 
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mL78 BL312Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 35
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mt-LAF12 EL691Trypanosoma brucei bruceiMutation(s): 0 
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UNK UL72Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 37
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Mtg1 EM451Trypanosoma brucei bruceiMutation(s): 0 
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UNK UM8Trypanosoma brucei bruceiMutation(s): 0 
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uL13m AN202Trypanosoma brucei bruceiMutation(s): 0 
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mL80 BN302Trypanosoma brucei bruceiMutation(s): 0 
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mt-LAF14 EN731Trypanosoma brucei bruceiMutation(s): 0 
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uL14m AO217Trypanosoma brucei bruceiMutation(s): 0 
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mL81 BO262Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 44
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mt-LAF15a EOEP319Trypanosoma brucei bruceiMutation(s): 0 
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uL15m AP374Trypanosoma brucei bruceiMutation(s): 0 
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mL83 BQ231Trypanosoma brucei bruceiMutation(s): 0 
EC: 5.2.1.8
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mt-EngB EQ655Trypanosoma brucei bruceiMutation(s): 0 
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bL17m AR301Trypanosoma brucei bruceiMutation(s): 0 
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mL84 BR205Trypanosoma brucei bruceiMutation(s): 0 
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mL85 BS198Trypanosoma brucei bruceiMutation(s): 0 
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mt-LAF18 ES524Trypanosoma brucei bruceiMutation(s): 0 
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bL19m AT144Trypanosoma brucei bruceiMutation(s): 0 
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mL86 BT191Trypanosoma brucei bruceiMutation(s): 0 
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mt-LAF19 ET102Trypanosoma brucei bruceiMutation(s): 0 
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bL20m AU213Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 56
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mL87 BU185Trypanosoma brucei bruceiMutation(s): 0 
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mt-LAF20 EU56Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 58
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bL21m AV188Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 59
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mL88 BV190Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 60
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uL22m AW278Trypanosoma brucei bruceiMutation(s): 0 
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mL89 BW188Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 62
MoleculeChainsSequence LengthOrganismDetailsImage
uL23m AX246Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for Q387G3 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 63
MoleculeChainsSequence LengthOrganismDetailsImage
mL90 BX190Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for Q585P1 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetailsImage
UNK UX180Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 65
MoleculeChainsSequence LengthOrganismDetailsImage
uL24m AY378Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for C9ZK52 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetailsImage
mL92 BZ190Trypanosoma 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
MoleculeChainsSequence LengthOrganismDetailsImage
mL93 Ba153Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for D0A4T0 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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Entity ID: 68
MoleculeChainsSequence LengthOrganismDetailsImage
mL94 Bb162Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for Q38EP7 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 69
MoleculeChainsSequence LengthOrganismDetailsImage
mL95 Bc146Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for Q389K3 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 70
MoleculeChainsSequence LengthOrganismDetailsImage
mL41 Ae197Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for Q383U6 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 71
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mL42 Af189Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for Q383S1 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 72
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mL98 Bf113Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for Q388M2 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 73
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mL43 Ag260Trypanosoma 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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mL99 Bg105Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for Q587H8 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 75
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mL100 Bh92Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for A0A3L6L2V1 (Trypanosoma brucei equiperdum)
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Entity ID: 76
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mL101 Bi245Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for Q4GZ80 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetailsImage
mL49 Al218Trypanosoma 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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mL52 Ao1520Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for Q385V2 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 79
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mL53 Ap309Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for A0A3L6L3K9 (Trypanosoma brucei equiperdum)
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Entity ID: 80
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mL63 At154Trypanosoma 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
mL64 Av242Trypanosoma 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

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland--

Revision History 

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