7AM2

Intermediate assembly of the Large subunit from Leishmania major mitochondrial ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 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

Structure of the mature kinetoplastids mitoribosome and insights into its large subunit biogenesis.

Soufari, H.Waltz, F.Parrot, C.Durrieu-Gaillard, S.Bochler, A.Kuhn, L.Sissler, M.Hashem, Y.

(2020) Proc Natl Acad Sci U S A 117: 29851-29861

  • DOI: 10.1073/pnas.2011301117
  • Primary Citation of Related Structures:  
    7AIH, 7AM2, 7ANE, 7AOR

  • PubMed Abstract: 
  • Kinetoplastids are unicellular eukaryotic parasites responsible for such human pathologies as Chagas disease, sleeping sickness, and leishmaniasis. They have a single large mitochondrion, essential for the parasite survival. In kinetoplastid mitochondria, most of the molecular machineries and gene expression processes have significantly diverged and specialized, with an extreme example being their mitochondrial ribosomes ...

    Kinetoplastids are unicellular eukaryotic parasites responsible for such human pathologies as Chagas disease, sleeping sickness, and leishmaniasis. They have a single large mitochondrion, essential for the parasite survival. In kinetoplastid mitochondria, most of the molecular machineries and gene expression processes have significantly diverged and specialized, with an extreme example being their mitochondrial ribosomes. These large complexes are in charge of translating the few essential mRNAs encoded by mitochondrial genomes. Structural studies performed in Trypanosoma brucei already highlighted the numerous peculiarities of these mitoribosomes and the maturation of their small subunit. However, several important aspects mainly related to the large subunit (LSU) remain elusive, such as the structure and maturation of its ribosomal RNA. Here we present a cryo-electron microscopy study of the protozoans Leishmania tarentolae and Trypanosoma cruzi mitoribosomes. For both species, we obtained the structure of their mature mitoribosomes, complete rRNA of the LSU, as well as previously unidentified ribosomal proteins. In addition, we introduce the structure of an LSU assembly intermediate in the presence of 16 identified maturation factors. These maturation factors act on both the intersubunit and the solvent sides of the LSU, where they refold and chemically modify the rRNA and prevent early translation before full maturation of the LSU.


    Organizational Affiliation

    Institut Européen de Chimie et Biologie, U1212 INSERM, UMR5320 CNRS, Université de Bordeaux, F-33600 Pessac, France; m.sissler@iecb.u-bordeaux.fr yaser.hashem@inserm.fr.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L3-like proteinA467Leishmania tarentolaeMutation(s): 0 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
uL4mB436Leishmania tarentolaeMutation(s): 0 
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Find proteins for Q4QGU6 (Leishmania major)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL_L9 domain-containing proteinC262Leishmania tarentolaeMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Putative ribosomal protein L11D [auth E]346Leishmania tarentolaeMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13-like proteinE [auth F]171Leishmania tarentolaeMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal_L18e/L15P domain-containing proteinF [auth G]374Leishmania tarentolaeMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Putative 50S ribosomal protein L17G [auth I]305Leishmania tarentolaeMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
bL19mH [auth J]144Leishmania tarentolaeMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
bL20mI [auth K]194Leishmania tarentolaeMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
bL21mJ [auth L]186Leishmania tarentolaeMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
uL22mK [auth M]279Leishmania tarentolaeMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
uL23mL [auth N]252Leishmania tarentolaeMutation(s): 0 
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Entity ID: 13
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uL24mM [auth O]476Leishmania tarentolaeMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
bL28mN [auth Q]234Leishmania tarentolaeMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
uL29mO [auth R]480Leishmania tarentolaeMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
uL30mP [auth S]409Leishmania tarentolaeMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
bL32mQ [auth T]83Leishmania tarentolaeMutation(s): 0 
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Entity ID: 18
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bL35mR [auth V]151Leishmania tarentolaeMutation(s): 0 
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Entity ID: 19
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mL41S [auth Z]197Leishmania tarentolaeMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
mL94T [auth BA]167Leishmania tarentolaeMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
TRUD domain-containing proteinU [auth CA]618Leishmania tarentolaeMutation(s): 0 
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Entity ID: 22
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UAV [auth UA]203Leishmania tarentolaeMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
mL95W [auth BB]156Leishmania tarentolaeMutation(s): 0 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
RNA uridylyltransferaseX [auth CB]202Leishmania tarentolaeMutation(s): 0 
EC: 2.7.7.52
UniProt
Find proteins for Q9NE59 (Leishmania major)
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
mL67Y [auth BK]893Leishmania tarentolaeMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
mL71Z [auth BQ]445Leishmania tarentolaeMutation(s): 0 
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Entity ID: 27
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mL81AA [auth BN]344Leishmania tarentolaeMutation(s): 0 
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Entity ID: 28
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mL98BA [auth BE]118Leishmania tarentolaeMutation(s): 0 
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Entity ID: 29
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Putative ribosomal protein L14CA [auth BO]190Leishmania tarentolaeMutation(s): 0 
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Entity ID: 30
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mL86DA [auth At]183Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 31
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mL87EA [auth Au]186Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 32
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mL53FA [auth Ae]311Leishmania tarentolaeMutation(s): 0 
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Entity ID: 33
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mL63GA [auth Af]155Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
mL68HA [auth Ah]570Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 35
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mL80IA [auth Ap]240Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 36
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mL74JA [auth Al]346Leishmania tarentolaeMutation(s): 0 
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Entity ID: 37
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L51_S25_CI-B8 domain-containing proteinKA [auth Ab]262Leishmania tarentolaeMutation(s): 0 
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Entity ID: 38
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mL42LA [auth Aa]195Leishmania tarentolaeMutation(s): 0 
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Entity ID: 39
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mL52,mL52MA [auth BP]254Leishmania tarentolaeMutation(s): 0 
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Entity ID: 40
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mL93NA [auth Az]152Leishmania tarentolaeMutation(s): 0 
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Entity ID: 41
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mL75OA [auth Am]340Leishmania tarentolaeMutation(s): 0 
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Entity ID: 42
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mL85PA [auth As]249Leishmania tarentolaeMutation(s): 0 
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Entity ID: 43
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mL100QA [auth BG]1347Leishmania tarentolaeMutation(s): 0 
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Entity ID: 44
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mL49RA [auth Ad]237Leishmania tarentolaeMutation(s): 0 
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Entity ID: 45
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mL89SA [auth Aw]187Leishmania tarentolaeMutation(s): 0 
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Entity ID: 46
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Peptidyl-prolyl cis-trans isomeraseTA [auth BH]229Leishmania tarentolaeMutation(s): 0 
EC: 5.2.1.8
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Entity ID: 47
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mL72UA [auth Aj]503Leishmania tarentolaeMutation(s): 0 
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Entity ID: 48
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mL84VA [auth Ar]205Leishmania tarentolaeMutation(s): 0 
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Entity ID: 49
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mL76WA [auth An]331Leishmania tarentolaeMutation(s): 0 
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Entity ID: 50
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mL99XA [auth BF]109Leishmania tarentolaeMutation(s): 0 
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Entity ID: 51
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mL88YA [auth Av]192Leishmania tarentolaeMutation(s): 0 
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Entity ID: 52
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mL70ZA [auth BM]457Leishmania tarentolaeMutation(s): 0 
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Entity ID: 53
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mL59/64AB [auth Ag]244Leishmania tarentolaeMutation(s): 0 
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Entity ID: 54
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Peptidyl-prolyl cis-trans isomeraseBB [auth Bl]266Leishmania tarentolaeMutation(s): 0 
EC: 5.2.1.8
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Entity ID: 55
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LIM zinc-binding domain-containing proteinCB [auth Ax]216Leishmania tarentolaeMutation(s): 0 
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Entity ID: 56
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DNAj-like proteinDB [auth BS]416Leishmania tarentolaeMutation(s): 0 
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Entity ID: 57
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SpoU_methylase domain-containing proteinFB [auth BX], EB [auth BY]569Leishmania tarentolaeMutation(s): 0 
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Entity ID: 58
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Pseudouridylate synthase-like proteinGB [auth BZ]413Leishmania tarentolaeMutation(s): 0 
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Entity ID: 59
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Acyl carrier proteinHB [auth CC]150Leishmania tarentolaeMutation(s): 0 
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Entity ID: 60
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L0R8F8IB [auth CD]126Leishmania tarentolaeMutation(s): 0 
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Entity ID: 61
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G domain-containing proteinJB [auth BT]464Leishmania tarentolaeMutation(s): 0 
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Entity ID: 62
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GTPase DerKB [auth BU]497Leishmania tarentolaeMutation(s): 0 
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Find proteins for Q4Q9G4 (Leishmania major)
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Entity ID: 63
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DEAD/DEAH box helicase-like proteinLB [auth BW]776Leishmania tarentolaeMutation(s): 0 
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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetailsImage
G domain-containing proteinMB [auth BV]787Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for Q4Q4X0 (Leishmania major)
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Entity ID: 65
MoleculeChainsSequence LengthOrganismDetailsImage
mL78NB [auth U7]40Leishmania tarentolaeMutation(s): 0 
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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetailsImage
U6OB [auth U6]187Leishmania tarentolaeMutation(s): 0 
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Entity ID: 67
MoleculeChainsSequence LengthOrganismDetailsImage
U1PB [auth U1]46Leishmania tarentolaeMutation(s): 0 
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Entity ID: 68
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U3QB [auth U3]75Leishmania tarentolaeMutation(s): 0 
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Entity ID: 69
MoleculeChainsSequence LengthOrganismDetailsImage
U4RB [auth U4]136Leishmania tarentolaeMutation(s): 0 
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Entity ID: 70
MoleculeChainsSequence LengthOrganismDetailsImage
U5SB [auth U5]94Leishmania tarentolaeMutation(s): 0 
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Entity ID: 71
MoleculeChainsSequence LengthOrganismDetailsImage
mL78TB [auth BR]301Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A504XZ90 (Leishmania donovani)
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Entity ID: 72
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U2UB [auth U2]37Leishmania tarentolaeMutation(s): 0 
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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetailsImage
U8ZB [auth U8]59Leishmania tarentolaeMutation(s): 0 
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Entity ID: 73
MoleculeChainsLengthOrganismImage
Ribosomal RNAVB [auth 1]19000Leishmania tarentolae
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  • Entity ID: 74
    MoleculeChainsLengthOrganismImage
    R1WB [auth R1]3Leishmania tarentolae
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    Entity ID: 75
    MoleculeChainsLengthOrganismImage
    R2XB [auth R2]35Leishmania tarentolae
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    • Entity ID: 76
      MoleculeChainsLengthOrganismImage
      R5YB [auth R5]5Leishmania tarentolae
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      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      GTP (Subject of Investigation/LOI)
      Query on GTP

      Download Ideal Coordinates CCD File 
      AC [auth BU]GUANOSINE-5'-TRIPHOSPHATE
      C10 H16 N5 O14 P3
      XKMLYUALXHKNFT-UUOKFMHZSA-N
       Ligand Interaction
      ATP (Subject of Investigation/LOI)
      Query on ATP

      Download Ideal Coordinates CCD File 
      BC [auth BW]ADENOSINE-5'-TRIPHOSPHATE
      C10 H16 N5 O13 P3
      ZKHQWZAMYRWXGA-KQYNXXCUSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: ELECTRON MICROSCOPY
      • Resolution: 3.40 Å
      • Aggregation State: PARTICLE 
      • Reconstruction Method: SINGLE PARTICLE 

      Structure Validation

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      Entry History & Funding Information

      Deposition Data


      Funding OrganizationLocationGrant Number
      European Research Council (ERC)France--

      Revision History  (Full details and data files)

      • Version 1.0: 2021-04-28
        Type: Initial release