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- PDB-7pua: Middle assembly intermediate of the Trypanosoma brucei mitoriboso... -

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Basic information

Entry
Database: PDB / ID: 7pua
TitleMiddle assembly intermediate of the Trypanosoma brucei mitoribosomal small subunit
Components
  • (9S rRNA) x 2
  • 30S Ribosomal protein S17, putative
  • 30S ribosomal protein S8, putative
  • Acyl carrier protein
  • Acyl transferase-like protein, putative
  • DNA photolyase, putative
  • DUF4379 domain-containing protein
  • DUF4460 domain-containing protein
  • LMWPc domain-containing protein
  • LysM domain-containing protein
  • PPR_long domain-containing protein
  • Protein FYV4, mitochondrial
  • Rhodanese domain-containing protein
  • Ribosomal_S5_C domain-containing protein
  • Translation initiation factor IF-2, putative
  • Ubiquitin-like domain-containing protein
  • Unk
  • Unk8
  • UnkC
  • UnkD
  • UnkF
  • UnkG
  • UnkI
  • UnkK
  • UnkP
  • Unka
  • Unkg
  • bS16m
  • bS18m
  • bS21m
  • bS6m
  • mS22
  • mS23
  • mS26
  • mS29
  • mS33
  • mS34
  • mS35
  • mS37
  • mS38
  • mS49
  • mS50
  • mS51
  • mS52
  • mS53
  • mS54
  • mS55
  • mS56
  • mS57
  • mS58
  • mS59
  • mS62
  • mS63
  • mS65
  • mS69
  • mS70
  • mS71
  • mS72
  • mS73
  • mS74
  • mt-SAF21
  • mt-SAF22
  • mt-SAF23
  • mt-SAF27
  • mt-SAF29
  • mt-SAF3
  • mt-SAF31
  • mt-SAF37
  • mt-SAF38
  • mt-SAF39
  • mt-SAF5
  • mt-SAF7
  • mt-SAF9
  • uS11m
  • uS12m
  • uS14m
  • uS15m
  • uS19m
  • uS3m
  • uS9m
KeywordsRIBOSOME / mitoribosome / assembly intermediate / Trypanosoma brucei / small subunit / mt-SSU / SSU
Function / homology
Function and homology information


modulation of formation of structure involved in a symbiotic process / mitochondrial mRNA editing complex / mitochondrial RNA processing / photoreactive repair / deoxyribodipyrimidine photo-lyase / kinetoplast / thiosulfate-cyanide sulfurtransferase activity / deoxyribodipyrimidine photo-lyase activity / quorum sensing / [acyl-carrier-protein] S-malonyltransferase ...modulation of formation of structure involved in a symbiotic process / mitochondrial mRNA editing complex / mitochondrial RNA processing / photoreactive repair / deoxyribodipyrimidine photo-lyase / kinetoplast / thiosulfate-cyanide sulfurtransferase activity / deoxyribodipyrimidine photo-lyase activity / quorum sensing / [acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity / response to arsenic-containing substance / ciliary plasm / ribonuclease P activity / tRNA 5'-leader removal / nuclear lumen / mRNA stabilization / mitochondrial small ribosomal subunit / acyl binding / acyl carrier activity / translation initiation factor activity / FAD binding / NAD binding / fatty acid biosynthetic process / NADP binding / structural constituent of ribosome / ribosome / translation / mitochondrial matrix / ribonucleoprotein complex / GTPase activity / mRNA binding / GTP binding / mitochondrion / DNA binding / RNA binding / cytoplasm / cytosol
Similarity search - Function
T-cell activation inhibitor, mitochondrial / Domain of unknown function DUF4460 / Domain of unknown function (DUF4460) / PPR repeat / Probable Zinc-ribbon domain / Probable Treble clef zinc finger domain / Pentacotripeptide-repeat region of PRORP / Pentacotripeptide-repeat region of PRORP / : / Protein Fyv4 ...T-cell activation inhibitor, mitochondrial / Domain of unknown function DUF4460 / Domain of unknown function (DUF4460) / PPR repeat / Probable Zinc-ribbon domain / Probable Treble clef zinc finger domain / Pentacotripeptide-repeat region of PRORP / Pentacotripeptide-repeat region of PRORP / : / Protein Fyv4 / Small ribosomal subunit protein mS41 SAM domain / IGR protein motif / ADP-ribosylation/Crystallin J1 superfamily / : / IGR / 3-hydroxyisobutyrate dehydrogenase-like, NAD-binding domain / NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase / Translation initiation factor IF-2, domain II / Initiation factor 2 signature. / Translation initiation factor IF-2, bacterial-like / Phosphotyrosine protein phosphatase I / Phosphotyrosine protein phosphatase I superfamily / Low molecular weight phosphotyrosine protein phosphatase / Low molecular weight phosphatase family / Cryptochrome/DNA photolyase class 1 / Cryptochrome/DNA photolyase, FAD-binding domain / FAD binding domain of DNA photolyase / : / Elongation factor G domain 2 / Translation initiation factor IF- 2 / Translation initiation factor IF-2, domain 3 superfamily / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / Pentatricopeptide repeat domain / DNA photolyase, N-terminal / Cryptochrome/photolyase, N-terminal domain superfamily / DNA photolyase / Photolyase/cryptochrome alpha/beta domain profile. / Cryptochrome/DNA photolyase, FAD-binding domain-like superfamily / Pentatricopeptide (PPR) repeat profile. / Ribosomal protein S23/S29, mitochondrial / Mitochondrial ribosomal death-associated protein 3 / Pentatricopeptide repeat / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / LysM domain / Rhodanese-like domain / LysM domain / 6-phosphogluconate dehydrogenase, domain 2 / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / Acyl transferase/acyl hydrolase/lysophospholipase / Acyl carrier protein (ACP) / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Rossmann-like alpha/beta/alpha sandwich fold / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 superfamily / Ubiquitin family / Ribosomal protein S5, C-terminal / Small GTP-binding protein domain / Ribosomal protein S5, C-terminal domain / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / Tetratricopeptide-like helical domain superfamily / Ubiquitin domain profile. / Ubiquitin-like domain / Ribosomal protein S9 / Ribosomal protein S9/S16 / Ribosomal protein S17/S11 / Ribosomal protein S17 / Ribosomal protein S11 superfamily / S15/NS1, RNA-binding / Translation protein, beta-barrel domain superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ubiquitin-like domain superfamily / Ribosomal protein S5 domain 2-type fold / NAD(P)-binding domain superfamily / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / GUANOSINE-5'-DIPHOSPHATE / Chem-PM8 / PHOSPHATE ION / : / RNA / RNA (> 10) / RNA (> 100) / Trypanosomal VSG domain containing protein ...ADENOSINE-5'-TRIPHOSPHATE / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / GUANOSINE-5'-DIPHOSPHATE / Chem-PM8 / PHOSPHATE ION / : / RNA / RNA (> 10) / RNA (> 100) / Trypanosomal VSG domain containing protein / Uncharacterized protein / Mitochondrial RNA binding complex 1 subunit / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / PROP1-like PPR domain-containing protein / Uncharacterized protein / Dehydrogenase-like protein / Ubiquitin-like domain-containing protein / Ribosomal protein S23 mitochondrial conserved domain-containing protein / Uncharacterized protein / Uncharacterized protein / T. brucei spp.-specific protein / LysM domain-containing protein / Trichohyalin / Translation initiation factor IF-2, chloroplastic / Opioid growth factor receptor (OGFr) conserved domain-containing protein / Uncharacterized protein / 30S Ribosomal protein S17, putative / [acyl-carrier-protein] S-malonyltransferase / 30S ribosomal protein S8, putative / T. brucei spp.-specific protein / T. brucei spp.-specific protein / Small ribosomal subunit protein uS5 C-terminal domain-containing protein / Mitochondrial ribosomal protein S18 / Uncharacterized protein / T. brucei spp.-specific protein / ADP-ribosylglycohydrolase / DNA photolyase, putative / Kinteoplast poly(A) polymerase complex 1 subunit / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Mitochondrial SSU ribosomal protein / Mitochondrial SSU ribosomal protein / Uncharacterized protein / Small ribosomal subunit protein mS41 / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Target SNARE / Phosphotyrosine protein phosphatase I domain-containing protein / DUF4460 domain-containing protein / Uncharacterized protein / Uncharacterized protein / Pentacotripeptide-repeat region of PRORP domain-containing protein / Uncharacterized protein / Uncharacterized protein / Ribosomal protein S9 / Uncharacterized protein / Acyl carrier protein / Uncharacterized protein / Pentacotripeptide-repeat region of PRORP domain-containing protein / Uncharacterized protein / Uncharacterized protein / Treble clef zinc finger domain-containing protein / Succinate dehydrogenase assembly factor 3, mitochondrial / Uncharacterized protein / Small ribosomal subunit protein mS29 / Rhodanese domain-containing protein / Uncharacterized protein
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsLenarcic, T. / Leibundgut, M. / Saurer, M. / Ramrath, D.J.F. / Fluegel, T. / Boehringer, D. / Ban, N.
Funding support Switzerland, 3items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_182341 Switzerland
European Molecular Biology Organization (EMBO)1074-2019 Switzerland
Swiss National Science Foundation182880 Switzerland
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: Mitoribosomal small subunit maturation involves formation of initiation-like complexes.
Authors: Tea Lenarčič / Moritz Niemann / David J F Ramrath / Salvatore Calderaro / Timo Flügel / Martin Saurer / Marc Leibundgut / Daniel Boehringer / Céline Prange / Elke K Horn / André Schneider / Nenad Ban /
Abstract: Mitochondrial ribosomes (mitoribosomes) play a central role in synthesizing mitochondrial inner membrane proteins responsible for oxidative phosphorylation. Although mitoribosomes from different ...Mitochondrial ribosomes (mitoribosomes) play a central role in synthesizing mitochondrial inner membrane proteins responsible for oxidative phosphorylation. Although mitoribosomes from different organisms exhibit considerable structural variations, recent insights into mitoribosome assembly suggest that mitoribosome maturation follows common principles and involves a number of conserved assembly factors. To investigate the steps involved in the assembly of the mitoribosomal small subunit (mt-SSU) we determined the cryoelectron microscopy structures of middle and late assembly intermediates of the mitochondrial small subunit (mt-SSU) at 3.6- and 3.7-Å resolution, respectively. We identified five additional assembly factors that together with the mitochondrial initiation factor 2 (mt-IF-2) specifically interact with functionally important regions of the rRNA, including the decoding center, thereby preventing premature mRNA or large subunit binding. Structural comparison of assembly intermediates with mature mt-SSU combined with RNAi experiments suggests a noncanonical role of mt-IF-2 and a stepwise assembly process, where modular exchange of ribosomal proteins and assembly factors together with mt-IF-2 ensure proper 9S rRNA folding and protein maturation during the final steps of assembly.
History
DepositionSep 29, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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  • Deposited structure unit
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Structure viewerMolecule:
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Assembly

Deposited unit
CA: 9S rRNA
CB: 9S rRNA
CC: uS3m
CE: Ribosomal_S5_C domain-containing protein
CF: bS6m
CH: 30S ribosomal protein S8, putative
CI: uS9m
CJ: LysM domain-containing protein
CK: uS11m
CL: uS12m
CN: uS14m
CO: uS15m
CP: bS16m
CQ: 30S Ribosomal protein S17, putative
CR: bS18m
CS: uS19m
CU: bS21m
Ca: mS22
Cb: mS23
Cd: mS26
Cg: mS29
Ci: mS33
Cj: mS34
Ck: mS35
Cm: mS37
Cn: mS38
Cp: Protein FYV4, mitochondrial
DB: mS49
DC: mS50
DD: mS51
DE: mS52
DF: mS53
DG: mS54
DH: mS55
DI: mS56
DJ: mS57
DK: mS58
DL: mS59
DO: mS62
DP: mS63
DR: mS65
DT: Rhodanese domain-containing protein
DU: Ubiquitin-like domain-containing protein
DV: mS69
DW: mS70
DX: mS71
DY: mS72
DZ: mS73
Da: mS74
F2: PPR_long domain-containing protein
F3: mt-SAF3
F5: mt-SAF5
F6: DUF4460 domain-containing protein
F7: mt-SAF7
F9: mt-SAF9
FM: mt-SAF21
FN: mt-SAF21
FO: mt-SAF22
FP: mt-SAF23
FW: LMWPc domain-containing protein
FX: mt-SAF27
FZ: mt-SAF29
Fb: mt-SAF31
Fc: Acyl carrier protein
Fd: DUF4379 domain-containing protein
Ff: DNA photolyase, putative
Fg: Acyl transferase-like protein, putative
Fh: mt-SAF37
Fi: mt-SAF38
IA: Translation initiation factor IF-2, putative
IB: mt-SAF39
U8: Unk8
UC: UnkC
UD: UnkD
UF: UnkF
UG: UnkG
UI: UnkI
UK: UnkK
UM: Unk
UN: Unk
UP: UnkP
UQ: Unk
Ua: Unka
Ug: Unkg
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,540,31798
Polymers3,537,65784
Non-polymers2,66014
Water905
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 2 types, 2 molecules CACB

#1: RNA chain 9S rRNA


Mass: 198441.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: GenBank: 13740
#2: RNA chain 9S rRNA


Mass: 919.620 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote)

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Protein , 69 types, 70 molecules CCCECFCHCICJCKCLCNCOCPCQCRCSCUCaCbCdCgCiCjCkCmCnCpDBDCDDDEDF...

#3: Protein uS3m


Mass: 9070.940 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote)
#4: Protein Ribosomal_S5_C domain-containing protein


Mass: 50147.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: MHOM/CI/86/DAL972 / References: UniProt: D0A335
#5: Protein bS6m


Mass: 18861.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q38BW5
#6: Protein 30S ribosomal protein S8, putative


Mass: 32766.459 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: MHOM/CI/86/DAL972 / References: UniProt: C9ZZU9
#7: Protein uS9m


Mass: 50201.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q57W62
#8: Protein LysM domain-containing protein


Mass: 94321.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: MHOM/CI/86/DAL972 / References: UniProt: C9ZPU0
#9: Protein uS11m


Mass: 37925.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q389T7
#10: Protein uS12m


Mass: 10421.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote)
#11: Protein uS14m


Mass: 19900.014 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q580I0
#12: Protein uS15m


Mass: 50401.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q4GZ99
#13: Protein bS16m


Mass: 22077.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q384N9
#14: Protein 30S Ribosomal protein S17, putative


Mass: 35632.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: MHOM/CI/86/DAL972 / References: UniProt: C9ZYU9
#15: Protein bS18m


Mass: 36988.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: MHOM/CI/86/DAL972 / References: UniProt: D0A3A4
#16: Protein uS19m


Mass: 28364.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: A0A3L6L621
#17: Protein bS21m


Mass: 23087.889 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q580M9
#18: Protein mS22


Mass: 73064.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q38DR3
#19: Protein mS23


Mass: 36869.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: MHOM/CI/86/DAL972 / References: UniProt: C9ZNU0
#20: Protein mS26


Mass: 51192.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q38DK6
#21: Protein mS29


Mass: 57048.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q585C2
#22: Protein mS33


Mass: 21244.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q57WW0
#23: Protein mS34


Mass: 28728.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q57UK0
#24: Protein mS35


Mass: 98277.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q387C7
#25: Protein mS37


Mass: 24757.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q38C96
#26: Protein mS38


Mass: 28240.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q57VQ9
#27: Protein Protein FYV4, mitochondrial


Mass: 22421.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q389L3
#28: Protein mS49


Mass: 137234.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: MHOM/CI/86/DAL972 / References: UniProt: C9ZJE4
#29: Protein mS50


Mass: 131719.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: A0A3L6L3Q2
#30: Protein mS51


Mass: 93661.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: MHOM/CI/86/DAL972 / References: UniProt: D0A752
#31: Protein mS52


Mass: 84938.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q386Q7
#32: Protein mS53


Mass: 75338.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: MHOM/CI/86/DAL972 / References: UniProt: C9ZXX4
#33: Protein mS54


Mass: 72046.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: MHOM/CI/86/DAL972 / References: UniProt: C9ZNY4
#34: Protein mS55


Mass: 66676.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: A0A3L6LGC8
#35: Protein mS56


Mass: 47306.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: A0A3L6L6C6
#36: Protein mS57


Mass: 45956.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q584U8
#37: Protein mS58


Mass: 35651.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: A0A3L6L3U6
#38: Protein mS59


Mass: 35395.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: MHOM/CI/86/DAL972 / References: UniProt: D0A232
#39: Protein mS62


Mass: 32068.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q383D1
#40: Protein mS63


Mass: 31922.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: MHOM/CI/86/DAL972 / References: UniProt: C9ZXR0
#41: Protein mS65


Mass: 30617.381 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: MHOM/CI/86/DAL972 / References: UniProt: C9ZPP1
#42: Protein Rhodanese domain-containing protein


Mass: 30096.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q586G5
#43: Protein Ubiquitin-like domain-containing protein


Mass: 26472.807 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: MHOM/CI/86/DAL972 / References: UniProt: C9ZKC1
#44: Protein mS69


Mass: 21589.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q57UZ6
#45: Protein mS70


Mass: 21247.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: MHOM/CI/86/DAL972 / References: UniProt: D0A8P6
#46: Protein mS71


Mass: 20093.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q383G5
#47: Protein mS72


Mass: 19340.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q57YD4
#48: Protein mS73


Mass: 11360.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q587C4
#49: Protein mS74


Mass: 8203.408 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: A0A3L6KY67
#50: Protein PPR_long domain-containing protein


Mass: 116189.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: MHOM/CI/86/DAL972 / References: UniProt: C9ZIL7
#51: Protein mt-SAF3


Mass: 106621.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q38E61
#52: Protein mt-SAF5


Mass: 86949.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: MHOM/CI/86/DAL972 / References: UniProt: D0AAF7
#53: Protein DUF4460 domain-containing protein


Mass: 76781.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q38FQ8
#54: Protein mt-SAF7


Mass: 76675.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q57UW6
#55: Protein mt-SAF9


Mass: 69652.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: MHOM/CI/86/DAL972 / References: UniProt: C9ZSL5
#56: Protein mt-SAF21


Mass: 39638.848 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: MHOM/CI/86/DAL972 / References: UniProt: C9ZJW2
#57: Protein mt-SAF22


Mass: 39132.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q389F9
#58: Protein mt-SAF23


Mass: 38240.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: MHOM/CI/86/DAL972 / References: UniProt: D0A963
#59: Protein LMWPc domain-containing protein


Mass: 30538.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q38FI3
#60: Protein mt-SAF27


Mass: 26936.748 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q57YK5
#61: Protein mt-SAF29


Mass: 20048.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: A0A3L6KWY8
#62: Protein mt-SAF31


Mass: 17673.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q581U4
#63: Protein Acyl carrier protein


Mass: 16550.807 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q57WW9
#64: Protein DUF4379 domain-containing protein


Mass: 16291.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q581T4
#65: Protein DNA photolyase, putative


Mass: 95285.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: MHOM/CI/86/DAL972
References: UniProt: D0A9A9, deoxyribodipyrimidine photo-lyase
#66: Protein Acyl transferase-like protein, putative


Mass: 60722.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: MHOM/CI/86/DAL972 / References: UniProt: C9ZYZ4
#67: Protein mt-SAF37


Mass: 37009.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / References: UniProt: Q38A63
#68: Protein mt-SAF38


Mass: 69516.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: MHOM/CI/86/DAL972 / References: UniProt: C9ZNX5
#69: Protein Translation initiation factor IF-2, putative


Mass: 87113.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: MHOM/CI/86/DAL972 / References: UniProt: C9ZSN7
#70: Protein mt-SAF39


Mass: 89639.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: MHOM/CI/86/DAL972 / References: UniProt: D0A0V4
#81: Protein Unkg


Mass: 23081.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote)

-
Protein/peptide , 10 types, 12 molecules U8UCUDUFUGUIUKUMUNUQUPUa

#71: Protein/peptide Unk8


Mass: 2571.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote)
#72: Protein/peptide UnkC


Mass: 783.958 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote)
#73: Protein/peptide UnkD


Mass: 1224.470 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote)
#74: Protein/peptide UnkF


Mass: 3081.790 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote)
#75: Protein/peptide UnkG


Mass: 1459.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote)
#76: Protein/peptide UnkI


Mass: 528.644 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote)
#77: Protein/peptide UnkK


Mass: 2060.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote)
#78: Protein/peptide Unk


Mass: 698.854 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote)
#79: Protein/peptide UnkP


Mass: 2741.370 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote)
#80: Protein/peptide Unka


Mass: 869.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote)

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Non-polymers , 8 types, 19 molecules

#82: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: Mg
#83: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#84: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#85: Chemical ChemComp-PM8 / S-(2-{[N-(2-HYDROXY-4-{[HYDROXY(OXIDO)PHOSPHINO]OXY}-3,3-DIMETHYLBUTANOYL)-BETA-ALANYL]AMINO}ETHYL) DECANETHIOATE


Mass: 496.598 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H41N2O7PS
#86: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#87: Chemical ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H35N9O15P2
#88: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#89: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Middle assembly intermediate of the Trypanosoma brucei mitoribosomal small subunit
Type: RIBOSOME / Entity ID: #1-#81 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Trypanosoma brucei brucei (eukaryote)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 98 % / Chamber temperature: 277 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameCategory
4GctfCTF correction
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 38531 / Symmetry type: POINT

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