6SGA

Body domain of the mt-SSU assemblosome from Trypanosoma brucei

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 1.2 of the entry. See complete history. 


Literature

Mitoribosomal small subunit biogenesis in trypanosomes involves an extensive assembly machinery.

Saurer, M., Ramrath, D.J.F., Niemann, M., Calderaro, S., Prange, C., Mattei, S., Scaiola, A., Leitner, A., Bieri, P., Horn, E.K., Leibundgut, M., Boehringer, D., Schneider, A., Ban, N.

(2019) Science 365: 1144-1149

  • DOI: https://doi.org/10.1126/science.aaw5570
  • Primary Citation of Related Structures:  
    6SG9, 6SGA, 6SGB

  • PubMed Abstract: 

    Mitochondrial ribosomes (mitoribosomes) are large ribonucleoprotein complexes that synthesize proteins encoded by the mitochondrial genome. An extensive cellular machinery responsible for ribosome assembly has been described only for eukaryotic cytosolic ribosomes. Here we report that the assembly of the small mitoribosomal subunit in Trypanosoma brucei involves a large number of factors and proceeds through the formation of assembly intermediates, which we analyzed by using cryo-electron microscopy. One of them is a 4-megadalton complex, referred to as the small subunit assemblosome, in which we identified 34 factors that interact with immature ribosomal RNA (rRNA) and recognize its functionally important regions. The assembly proceeds through large-scale conformational changes in rRNA coupled with successive incorporation of mitoribosomal proteins, providing an example for the complexity of the ribosomal assembly process in mitochondria.

    • Organizational Affiliation: 

    Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, CH-8093 Zurich, Switzerland.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
uS5mA [auth CE]435Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
bS6mB [auth CF]160Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q38BW5 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
uS8mC [auth CH]282Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
uS11mD [auth CK]326Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q389T7 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
uS15mE [auth CO]429Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
bS16mF [auth CP]188Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
uS17mG [auth CQ]336Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
bS18mH [auth CR]320Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
mS22I [auth Ca]602Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q38DR3 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
mS23J [auth Cb]311Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
mS26K [auth Cd]440Trypanosoma brucei 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: 12
MoleculeChains Sequence LengthOrganismDetailsImage
mS34L [auth Cj]257Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q57UK0 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
mS38M [auth Cn]250Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
mS41N [auth Cp]187Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
mS51 (KRIPP1)O [auth DD]812Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
mS56P [auth DI]407Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
mS59Q [auth DL]307Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
mS62 (KRIPP14)R [auth DO]282Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
mS63 (KRIPP16)S [auth DP]274Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
mS65T [auth DR]270Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
mS68U [auth DU]228Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
mS73V [auth DZ]94Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q587C4 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
mt-SAF2 (KRIPP2)W [auth F2]1,024Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
mt-SAF3X [auth F3]966Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q38E61 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
mt-SAF5Y [auth F5]754Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
mt-SAF6Z [auth F6]676Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q38FQ8 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
mt-SAF7 (KRIPP10)AA [auth F7]679Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
mt-SAF8BA [auth F8]726Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
mt-SAF9CA [auth F9]608Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
mt-SAF10DA [auth FA]642Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
mt-SAF11EA [auth FB],
FA [auth FC]		579Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
mt-SAF13GA [auth FE]553Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
mt-SAF18HA [auth FJ]362Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
mt-SAF21IA [auth FM],
JA [auth FN]		370Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
mt-SAF22 (KRIPP17)KA [auth FO]334Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
mt-SAF23LA [auth FP]349Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
mt-SAF24MA [auth FQ],
NA [auth FR],
OA [auth FS],
PA [auth FT],
QA [auth FU]		307Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q387P8 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
mt-SAF26RA [auth FW]263Trypanosoma brucei bruceiMutation(s): 0 
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Find proteins for Q38FI3 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
mt-SAF27SA [auth FX]239Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
mt-SAF28TA [auth FY]188Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
mt-SAF29UA [auth FZ]178Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
mt-SAF30VA [auth Fa]171Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
mt-SAF31WA [auth Fb]151Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q581U4 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
mt-SAF32XA [auth Fc]148Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q57WW9 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
mt-SAF33YA [auth Fd]143Trypanosoma brucei bruceiMutation(s): 0 
UniProt
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
UNK-AZA [auth UA]21Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
UNK-BAB [auth UB]27Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
UNK-CBB [auth UC]10Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
UNK-D, UNK-M, UNK-QCB [auth UD],
KB [auth UM],
OB [auth UQ]		9Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
UNK-E, UNK-PDB [auth UE],
NB [auth UP]		45Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
UNK-FEB [auth UF]11Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
UNK-GFB [auth UG]17Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
UNK-HGB [auth UH]5Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
UNK-I, UNK-MHB [auth UI],
LB [auth UN]		8Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
UNK-JIB [auth UJ]16Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
UNK-LJB [auth UL]22Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
UNK-OMB [auth UO]30Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
UNK-UPB [auth UU]24Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
UNK-IQB [auth UY]468Trypanosoma brucei bruceiMutation(s): 0 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
mt-SAF1 (RSM22)SB [auth F1]1,041Trypanosoma brucei bruceiMutation(s): 0 
UniProt
Find proteins for Q385R2 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Go to UniProtKB:  Q385R2
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UniProt GroupQ385R2
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
mt-SAF14TB [auth FF]474Trypanosoma brucei bruceiMutation(s): 0 
EC: 2.1.1
UniProt
Find proteins for Q57W60 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Go to UniProtKB:  Q57W60
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UniProt GroupQ57W60
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Entity ID: 60
MoleculeChains LengthOrganismImage
9S rRNARB [auth CA]474Trypanosoma brucei brucei
Sequence Annotations
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PM8
Query on PM8
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XB [auth FcA]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
PO4
Query on PO4
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VB [auth FWA]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN
Query on ZN
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YB [auth FdA]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
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AC [auth CAB],
UB [auth FPA],
WB [auth FWB],
ZB [auth CAA]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

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: 2019-09-18
    Type: Initial release
  • Version 1.1: 2019-09-25
    Changes: Data collection, Database references
  • Version 1.2: 2024-11-13
    Changes: Data collection, Database references, Derived calculations, Structure summary