7AOI

Trypanosoma brucei mitochondrial ribosome large subunit assembly intermediate

  • Classification: RIBOSOME
  • Organism(s): Trypanosoma brucei
  • Mutation(s): Yes 

  • Deposited: 2020-10-14 Released: 2020-12-02 
  • Deposition Author(s): Tobiasson, V., Gahura, O., Aibara, S., Baradaran, R., Zikova, A., Amunts, A.
  • Funding Organization(s): The Swedish Foundation for Strategic Research, Swedish Research Council, European Research Council (ERC), Knut and Alice Wallenberg Foundation, European Molecular Biology Organization (EMBO), Czech Science Foundation

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 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

Interconnected assembly factors regulate the biogenesis of mitoribosomal large subunit.

Tobiasson, V.Gahura, O.Aibara, S.Baradaran, R.Zikova, A.Amunts, A.

(2021) EMBO J 40: e106292-e106292

  • DOI: 10.15252/embj.2020106292
  • Primary Citation of Related Structures:  
    7AOI

  • PubMed Abstract: 
  • Mitoribosomes consist of ribosomal RNA and protein components, coordinated assembly of which is critical for function. We used mitoribosomes from Trypanosoma brucei with reduced RNA and increased protein mass to provide insights into the biogenesis of the mitoribosomal large subunit ...

    Mitoribosomes consist of ribosomal RNA and protein components, coordinated assembly of which is critical for function. We used mitoribosomes from Trypanosoma brucei with reduced RNA and increased protein mass to provide insights into the biogenesis of the mitoribosomal large subunit. Structural characterization of a stable assembly intermediate revealed 22 assembly factors, some of which have orthologues/counterparts/homologues in mammalian genomes. These assembly factors form a protein network that spans a distance of 180 Å, shielding the ribosomal RNA surface. The central protuberance and L7/L12 stalk are not assembled entirely and require removal of assembly factors and remodeling of the mitoribosomal proteins to become functional. The conserved proteins GTPBP7 and mt-EngA are bound together at the subunit interface in proximity to the peptidyl transferase center. A mitochondrial acyl-carrier protein plays a role in docking the L1 stalk, which needs to be repositioned during maturation. Additional enzymatically deactivated factors scaffold the assembly while the exit tunnel is blocked. Together, this extensive network of accessory factors stabilizes the immature sites and connects the functionally important regions of the mitoribosomal large subunit.


    Organizational Affiliation

    Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
bL28mA [auth A1]217Trypanosoma bruceiMutation(s): 0 
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Find proteins for A0A3L6L6A9 (Trypanosoma brucei equiperdum)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
uL29mB [auth A2]463Trypanosoma bruceiMutation(s): 0 
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Find proteins for Q38EM7 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
uL30mC [auth A3]150Trypanosoma bruceiMutation(s): 1 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
bL32mD [auth A5]55Trypanosoma bruceiMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
bL33mE [auth A8]142Trypanosoma bruceiMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L3 mitochondrial, putativeG [auth AE]367Trypanosoma bruceiMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L4/L1 familyH [auth AF]442Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL_L9 domain-containing proteinI [auth AI]212Trypanosoma bruceiMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L11,uL11mJ [auth AK]278Trypanosoma bruceiMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13K [auth AN]171Trypanosoma bruceiMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal_L18e/L15P domain-containing proteinL [auth AP]354Trypanosoma bruceiMutation(s): 0 
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Entity ID: 13
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50S ribosomal protein L17M [auth AR]256Trypanosoma bruceiMutation(s): 1 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
bL19mN [auth AT]138Trypanosoma bruceiMutation(s): 0 
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Find proteins for A0A3L6LD66 (Trypanosoma brucei equiperdum)
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
bL20mO [auth AU]196Trypanosoma bruceiMutation(s): 0 
UniProt
Find proteins for A0A3L6KV21 (Trypanosoma brucei equiperdum)
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L21P [auth AV]180Trypanosoma bruceiMutation(s): 0 
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Entity ID: 17
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Ribosomal protein L22p/L17eQ [auth AW]277Trypanosoma bruceiMutation(s): 0 
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Entity ID: 18
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Ribosomal protein L23R [auth AX]165Trypanosoma bruceiMutation(s): 1 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
uL24mS [auth AY]340Trypanosoma bruceiMutation(s): 1 
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Find proteins for C9ZK52 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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Entity ID: 20
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mL41T [auth Ae]116Trypanosoma bruceiMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
mL42U [auth Af]133Trypanosoma bruceiMutation(s): 0 
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Entity ID: 22
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Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain containing proteinV [auth Ag]185Trypanosoma bruceiMutation(s): 0 
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Entity ID: 23
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mL49W [auth Al]182Trypanosoma bruceiMutation(s): 0 
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Entity ID: 24
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mL52X [auth Ao]133Trypanosoma bruceiMutation(s): 0 
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Entity ID: 25
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mL53Y [auth Ap]288Trypanosoma bruceiMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
mL63Z [auth At]145Trypanosoma bruceiMutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
mL64,mL64AA [auth Av]197Trypanosoma bruceiMutation(s): 1 
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Find proteins for A0A3L6KTC7 (Trypanosoma brucei equiperdum)
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Entity ID: 28
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mL67BA798Trypanosoma bruceiMutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
mL68,mL68,mL68CA [auth BB]371Trypanosoma bruceiMutation(s): 0 
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Find proteins for A0A3L6KX69 (Trypanosoma brucei equiperdum)
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
mL70DA [auth BD]417Trypanosoma bruceiMutation(s): 0 
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Entity ID: 31
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mL71EA [auth BE]438Trypanosoma bruceiMutation(s): 0 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
Tetratricopeptide repeatFA [auth BF]421Trypanosoma bruceiMutation(s): 0 
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Entity ID: 33
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mL74GA [auth BH]225Trypanosoma bruceiMutation(s): 0 
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Entity ID: 34
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Mitochondrial RNA binding complex 1 subunitHA [auth BI]323Trypanosoma bruceiMutation(s): 1 
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Entity ID: 35
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mL76IA [auth BJ]161Trypanosoma bruceiMutation(s): 0 
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Entity ID: 36
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Chaperone protein DNAj, putative,mL77,Chaperone protein DNAj, putativeJA [auth BK]273Trypanosoma bruceiMutation(s): 1 
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
mL78KA [auth BL]276Trypanosoma bruceiMutation(s): 0 
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
mL80LA [auth BN]214Trypanosoma bruceiMutation(s): 0 
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Entity ID: 39
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mL81MA [auth BO]227Trypanosoma bruceiMutation(s): 0 
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Entity ID: 40
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Peptidyl-prolyl cis-trans isomeraseNA [auth BQ]185Trypanosoma bruceiMutation(s): 0 
EC: 5.2.1.8
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Entity ID: 41
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mL84OA [auth BR]195Trypanosoma bruceiMutation(s): 0 
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Entity ID: 42
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mL85PA [auth BS]144Trypanosoma bruceiMutation(s): 0 
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Entity ID: 43
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mL86QA [auth BT]167Trypanosoma bruceiMutation(s): 0 
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Entity ID: 44
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mL87RA [auth BU]82Trypanosoma bruceiMutation(s): 0 
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Entity ID: 45
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mL89SA [auth BW]187Trypanosoma bruceiMutation(s): 0 
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Entity ID: 46
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LIM domain containing protein,mL90TA [auth BX]116Trypanosoma bruceiMutation(s): 0 
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Entity ID: 47
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Peptidyl-prolyl cis-trans isomeraseUA [auth BZ]189Trypanosoma bruceiMutation(s): 0 
EC: 5.2.1.8
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Entity ID: 48
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mL93VA [auth Ba]135Trypanosoma bruceiMutation(s): 0 
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Entity ID: 49
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mL94WA [auth Bb]103Trypanosoma bruceiMutation(s): 0 
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Entity ID: 50
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mL95XA [auth Bc]137Trypanosoma bruceiMutation(s): 0 
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Entity ID: 51
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mL98YA [auth Bf]86Trypanosoma bruceiMutation(s): 0 
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mL99ZA [auth Bg]82Trypanosoma bruceiMutation(s): 0 
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Find proteins for A0A3L6LDF0 (Trypanosoma brucei equiperdum)
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetailsImage
mL100,mL100AB [auth Bh]92Trypanosoma bruceiMutation(s): 0 
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Entity ID: 54
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UNK1BB [auth UA]46Trypanosoma bruceiMutation(s): 0 
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
UNK2CB [auth UB]9Trypanosoma bruceiMutation(s): 0 
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetailsImage
UNK3DB [auth UC]14Trypanosoma bruceiMutation(s): 0 
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Entity ID: 57
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UNK4EB [auth UD]8Trypanosoma bruceiMutation(s): 0 
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetailsImage
UNK5FB [auth UE]12Trypanosoma bruceiMutation(s): 0 
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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetailsImage
UNK6/mt-LAF15_2GB [auth UF]139Trypanosoma bruceiMutation(s): 0 
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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetailsImage
UNK7HB [auth UG]19Trypanosoma bruceiMutation(s): 0 
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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetailsImage
UNK8IB [auth UH]17Trypanosoma bruceiMutation(s): 0 
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Entity ID: 62
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UNK9JB [auth UI]39Trypanosoma bruceiMutation(s): 0 
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Entity ID: 63
MoleculeChainsSequence LengthOrganismDetailsImage
UNK10KB [auth UJ]25Trypanosoma bruceiMutation(s): 0 
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Entity ID: 64
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UNK11LB [auth UK]47Trypanosoma bruceiMutation(s): 0 
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Entity ID: 65
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mt-LAF7,mt-LAF7MB [auth XA]155Trypanosoma bruceiMutation(s): 0 
UniProt
Find proteins for Q387S8 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 66
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DEAD-box helicase, putative,mt-LAF2NB [auth XB]668Trypanosoma bruceiMutation(s): 0 
UniProt
Find proteins for D0A9G9 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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Entity ID: 67
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mt-LAF4OB [auth XC]616Trypanosoma bruceiMutation(s): 0 
UniProt
Find proteins for D0A7A5 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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Entity ID: 68
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Acyl carrier proteinPB [auth XD], QB [auth XE]83Trypanosoma bruceiMutation(s): 0 
UniProt
Find proteins for Q57WW9 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 69
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mt-LAF15_1RB [auth XF]198Trypanosoma bruceiMutation(s): 0 
UniProt
Find proteins for A0A3L6LB16 (Trypanosoma brucei equiperdum)
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Entity ID: 70
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50S ribosomal protein L14SB [auth XG]170Trypanosoma bruceiMutation(s): 0 
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Entity ID: 71
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mt-LAF8TB [auth XH]533Trypanosoma bruceiMutation(s): 0 
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Entity ID: 72
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mt-LAF14UB [auth XI]703Trypanosoma bruceiMutation(s): 0 
UniProt
Find proteins for Q57U79 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 73
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RNA uridylyltransferaseVB [auth XJ]150Trypanosoma bruceiMutation(s): 0 
EC: 2.7.7.52
UniProt
Find proteins for A0A3L6L766 (Trypanosoma brucei equiperdum)
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Entity ID: 74
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GTP-binding protein, putative,mt-EngAWB [auth XL]528Trypanosoma bruceiMutation(s): 0 
UniProt
Find proteins for C9ZS56 (Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972))
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Entity ID: 75
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Complex1-LYR-likeXB [auth XM]91Trypanosoma bruceiMutation(s): 0 
UniProt
Find proteins for A0A3L6L7X4 (Trypanosoma brucei equiperdum)
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Entity ID: 76
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mt-LAF12YB [auth XN]620Trypanosoma bruceiMutation(s): 0 
UniProt
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Entity ID: 77
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SpoU rRNA Methylase familyZB [auth XO]428Trypanosoma bruceiMutation(s): 0 
UniProt
Find proteins for A0A3L6L241 (Trypanosoma brucei equiperdum)
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Entity ID: 78
MoleculeChainsSequence LengthOrganismDetailsImage
Pseudouridylate synthase, putativeAC [auth XP]371Trypanosoma bruceiMutation(s): 0 
UniProt
Find proteins for Q38FJ3 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 79
MoleculeChainsSequence LengthOrganismDetailsImage
GTP-binding proteinBC [auth XQ]305Trypanosoma bruceiMutation(s): 0 
UniProt
Find proteins for A0A3L6L0D5 (Trypanosoma brucei equiperdum)
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Entity ID: 80
MoleculeChainsSequence LengthOrganismDetailsImage
Lipase (Class 3)CC [auth XR]161Trypanosoma bruceiMutation(s): 0 
UniProt
Find proteins for A0A3L6L1Y4 (Trypanosoma brucei equiperdum)
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Entity ID: 81
MoleculeChainsSequence LengthOrganismDetailsImage
mL101DC [auth XS]182Trypanosoma bruceiMutation(s): 0 
UniProt
Find proteins for Q4GZ80 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
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Entity ID: 82
MoleculeChainsSequence LengthOrganismDetailsImage
mt-LAF19EC [auth XT]97Trypanosoma bruceiMutation(s): 0 
UniProt
Find proteins for A0A3L6KWY9 (Trypanosoma brucei equiperdum)
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Entity ID: 6
MoleculeChainsLengthOrganismImage
mt-LSU rRNAF [auth AA]758Trypanosoma brucei
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Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD (Subject of Investigation/LOI)
Query on NAD

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GC [auth Av]NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
GTP (Subject of Investigation/LOI)
Query on GTP

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NC [auth XL], OC [auth XL]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
ADP (Subject of Investigation/LOI)
Query on ADP

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MC [auth XB]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
FES
Query on FES

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FC [auth A5]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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HC [auth BX], IC [auth BX], JC [auth Bh], KC [auth XA]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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LC [auth XB]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
4HH
Query on 4HH
PB [auth XD], QB [auth XE]L-PEPTIDE LINKINGC14 H28 N3 O9 P SSER
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The Swedish Foundation for Strategic ResearchSwedenFFL15:0325
Swedish Research CouncilSwedenNT_2015-04107
European Research Council (ERC)SwedenERC-2018-StG-805230
Knut and Alice Wallenberg FoundationSweden2018.0080
European Molecular Biology Organization (EMBO)SwedenEMBO Young Investigator Program to A.A
Czech Science FoundationCzech Republic18-17529S

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-02
    Type: Initial release
  • Version 1.1: 2021-02-24
    Changes: Database references
  • Version 1.2: 2021-03-24
    Changes: Database references