9HNY | pdb_00009hny

Mitoribosomal small subunit in complex with Mettl15 and Mettl17


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 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

Mettl15-Mettl17 modulates the transition from early to late pre-mitoribosome.

Zgadzay, Y.Mirabello, C.Wanes, G.Panek, T.Chauhan, P.Nystedt, B.Zikova, A.Whitford, P.C.Gahura, O.Amunts, A.

(2025) bioRxiv 

  • DOI: https://doi.org/10.1101/2024.12.18.629302
  • Primary Citation of Related Structures:  
    9HNY

  • PubMed Abstract: 

    The assembly of the mitoribosomal small subunit involves folding and modification of rRNA, and its association with mitoribosomal proteins. This process is assisted by a dynamic network of assembly factors. Conserved methyltransferases Mettl15 and Mettl17 act on the solvent-exposed surface of rRNA. Binding of Mettl17 is associated with the early assembly stage, whereas Mettl15 is involved in the late stage, but the mechanism of transition between the two was unclear. Here, we integrate structural data from Trypanosoma brucei with mammalian homologs and molecular dynamics simulations. We reveal how the interplay of Mettl15 and Mettl17 in intermediate steps links the distinct stages of small subunit assembly. The analysis suggests a model wherein Mettl17 acts as a platform for Mettl15 recruitment. Subsequent release of Mettl17 allows a conformational change of Mettl15 for substrate recognition. Upon methylation, Mettl15 adopts a loosely bound state which ultimately leads to its replacement by initiation factors, concluding the assembly. Together, our results indicate that assembly factors Mettl15 and Mettl17 cooperate to regulate the biogenesis process, and present a structural data resource for understanding molecular adaptations of assembly factors in mitoribosome.


  • Organizational Affiliation
    • Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, University of Strasbourg, Illkirch, France.

Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
uS3mB [auth CC]74Trypanosoma bruceiMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS5 C-terminal domain-containing proteinC [auth CE]435Trypanosoma bruceiMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
bS6mD [auth CF]160Trypanosoma bruceiMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8E [auth CH]282Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S9/S16F [auth CI]443Trypanosoma bruceiMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
LysM domain-containing proteinG [auth CJ]817Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
uS11mH [auth CK]326Trypanosoma bruceiMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
uS14mI [auth CN]158Trypanosoma bruceiMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S15J [auth CO]429Trypanosoma bruceiMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
bS16mK [auth CP]188Trypanosoma bruceiMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
uS17mL [auth CQ]336Trypanosoma bruceiMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ribosomal protein S18M [auth CR]320Trypanosoma bruceiMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
uS19mN [auth CS]244Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Chromosome passenger complex (CPC) protein INCENP N terminalO [auth Ca]602Trypanosoma bruceiMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
mS23P [auth Cb]311Trypanosoma bruceiMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
mS26Q [auth Cd]440Trypanosoma bruceiMutation(s): 0 
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Find proteins for Q38DK6 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial SSU ribosomal protein 29R [auth Cg]490Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
mS33S [auth Ci]181Trypanosoma bruceiMutation(s): 0 
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Find proteins for Q57WW0 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
mS34T [auth Cj]257Trypanosoma bruceiMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
mS35U [auth Ck]874Trypanosoma bruceiMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
mS38V [auth Cn]250Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Protein FYV4, mitochondrialW [auth Cp]187Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
mS49X [auth DB]1,181Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
mS50Y [auth DC]1,165Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
mS51Z [auth DD]812Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial SSU ribosomal proteinAA [auth DE]747Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
mS53BA [auth DF]666Trypanosoma bruceiMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
mS54CA [auth DG]631Trypanosoma bruceiMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
mS55DA [auth DH]581Trypanosoma bruceiMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
mS56EA [auth DI]407Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
mS57FA [auth DJ]396Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
mS58GA [auth DK]324Trypanosoma bruceiMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
mS59HA [auth DL]307Trypanosoma bruceiMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
mS62IA [auth DO]282Trypanosoma bruceiMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
mS63JA [auth DP]274Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
mS65KA [auth DR]270Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Rhodanese domain-containing proteinLA [auth DT]247Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-like domain-containing proteinMA [auth DU]228Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
mS69NA [auth DV]183Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
mS70OA [auth DW]179Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
mS71PA [auth DX]169Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
mS72QA [auth DY]163Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
mS73RA [auth DZ]94Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial small ribosomal subunit Rsm22SA [auth F1]1,041Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Pentacotripeptide-repeat region of PRORP domain-containing proteinTA [auth F2]1,024Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
mt-SAF3UA [auth F3]966Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Methyltranfer_dom domain-containing proteinVA [auth F4]811Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Kinteoplast poly(A) polymerase complex 1 subunitWA [auth F5]754Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
DUF4460 domain-containing proteinXA [auth F6]676Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
mt-SAF7 (KRIPP10)YA [auth F7]679Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Cupin type-1 domain-containing proteinZA [auth F8]726Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
TrichohyalinAB [auth F9]608Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
mt-SAF10BB [auth FA]642Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA pseudouridine synthase A-like proteinCB [auth FB],
DB [auth FC]
588Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
PPR_long domain-containing proteinEB [auth FD]579Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
mt-SAF13FB [auth FE]553Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
S-adenosyl-methyltransferase mraW-like proteinGB [auth FF]474Trypanosoma bruceiMutation(s): 0 
EC: 2.1.1
UniProt
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
mt-SAF15HB [auth FG]463Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
mt-SAF16 (P32)IB [auth FH]457Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
mt-SAF17JB [auth FI]445Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
mt-SAF18 (RbfA)KB [auth FJ]362Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial glycoproteinLB [auth FK]372Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
Metallo-beta-lactamase domain-containing proteinMB [auth FL]353Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
mt-SAF21NB [auth FM],
OB [auth FN]
370Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
mt-SAF22PB [auth FO]334Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
ADP-ribosylglycohydrolaseQB [auth FP]349Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
Potassium voltage-gated channel, putativeRB [auth FQ],
SB [auth FR],
TB [auth FS],
UB [auth FT],
VB [auth FU]
307Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
mt-SAF25WB [auth FV]264Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
Low molecular weight protein tyrosine phosphataseXB [auth FW]263Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
PPR_long domain-containing proteinYB [auth FX]239Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
mt-SAF28ZB [auth FY]189Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
mt-SAF29AC [auth FZ]178Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
mt-SAF30BC [auth Fa]171Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
Complex 1 protein (LYR family)CC [auth Fb]151Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl carrier proteinDC [auth Fc]148Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
Probable Zinc-ribbon domain-containing proteinEC [auth Fd]143Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
mt-SAF34FC [auth Fe]123Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
mt-SAF38GC [auth Fi]629Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 80
MoleculeChains Sequence LengthOrganismDetailsImage
UNK-AHC [auth UA]27Trypanosoma bruceiMutation(s): 0 
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Entity ID: 81
MoleculeChains Sequence LengthOrganismDetailsImage
UNK-BIC [auth UB]6Trypanosoma bruceiMutation(s): 0 
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Entity ID: 82
MoleculeChains Sequence LengthOrganismDetailsImage
UNK-CJC [auth UC]10Trypanosoma bruceiMutation(s): 0 
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Entity ID: 83
MoleculeChains Sequence LengthOrganismDetailsImage
UNK-FKC [auth UF]11Trypanosoma bruceiMutation(s): 0 
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Entity ID: 84
MoleculeChains Sequence LengthOrganismDetailsImage
UNK-G,JLC [auth UG],
NC [auth UJ]
16Trypanosoma bruceiMutation(s): 0 
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Entity ID: 85
MoleculeChains Sequence LengthOrganismDetailsImage
UNK-IMC [auth UI]8Trypanosoma bruceiMutation(s): 0 
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Entity ID: 86
MoleculeChains Sequence LengthOrganismDetailsImage
UNK-KOC [auth UK]24Trypanosoma bruceiMutation(s): 0 
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Entity ID: 87
MoleculeChains Sequence LengthOrganismDetailsImage
UNK-LPC [auth UL]22Trypanosoma bruceiMutation(s): 0 
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Entity ID: 88
MoleculeChains Sequence LengthOrganismDetailsImage
UNK-M,QQC [auth UM],
UC [auth UQ]
9Trypanosoma bruceiMutation(s): 0 
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Entity ID: 89
MoleculeChains Sequence LengthOrganismDetailsImage
UNK-NRC [auth UN]7Trypanosoma bruceiMutation(s): 0 
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Entity ID: 90
MoleculeChains Sequence LengthOrganismDetailsImage
UNK-OSC [auth UO]30Trypanosoma bruceiMutation(s): 0 
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Entity ID: 91
MoleculeChains Sequence LengthOrganismDetailsImage
UNK-PTC [auth UP]45Trypanosoma bruceiMutation(s): 0 
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Entity ID: 92
MoleculeChains Sequence LengthOrganismDetailsImage
UNK-YVC [auth UY]85Trypanosoma bruceiMutation(s): 0 
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Entity ID: 93
MoleculeChains Sequence LengthOrganismDetailsImage
UNK-dWC [auth Ud]59Trypanosoma bruceiMutation(s): 0 
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Entity ID: 94
MoleculeChains Sequence LengthOrganismDetailsImage
UNK-gXC [auth Ug]167Trypanosoma bruceiMutation(s): 0 
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Entity ID: 95
MoleculeChains Sequence LengthOrganismDetailsImage
UNK-hYC [auth Uh]263Trypanosoma bruceiMutation(s): 0 
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Entity ID: 96
MoleculeChains Sequence LengthOrganismDetailsImage
UNK-kZC [auth Uk]31Trypanosoma bruceiMutation(s): 0 
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Entity ID: 97
MoleculeChains Sequence LengthOrganismDetailsImage
UNK-lAD [auth Ul]14Trypanosoma bruceiMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
9S RNAA [auth CA]620Trypanosoma brucei
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Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ACO
Query on ACO

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FD [auth F3]ACETYL COENZYME *A
C23 H38 N7 O17 P3 S
ZSLZBFCDCINBPY-ZSJPKINUSA-N
GTP
Query on GTP

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BD [auth Cg]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
SAM (Subject of Investigation/LOI)
Query on SAM

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ED [auth F1],
GD [auth FF]
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

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DD [auth F1]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
PO4
Query on PO4

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JD [auth FW]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN
Query on ZN

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HD [auth FG],
ID [auth FL],
KD [auth Fd],
LD [auth Fe]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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CD [auth Cg]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19rc4_4035:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European UnionERC-2018-StG-805230
Knut and Alice Wallenberg FoundationSweden2018.0080

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-26
    Type: Initial release