[English] 日本語
Yorodumi
- PDB-7pub: Late assembly intermediate of the Trypanosoma brucei mitoribosoma... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7pub
TitleLate assembly intermediate of the Trypanosoma brucei mitoribosomal small subunit
Components
  • 30S Ribosomal protein S17, putative
  • 30S ribosomal protein S8, putative
  • 9S rRNA
  • AKAP7_NLS domain-containing protein
  • Acyl transferase-like protein
  • DNA photolyase, putative
  • ECH_2 domain-containing protein
  • LysM domain-containing protein
  • Protein FYV4, mitochondrial
  • Rhodanese domain-containing protein
  • Ribosomal_S5_C domain-containing protein
  • Sod_Fe_C domain-containing protein
  • Superoxide dismutase, putative
  • Translation initiation factor IF-2, putative
  • Ubiquitin-like domain-containing protein
  • Unk
  • Unk7
  • UnkE
  • UnkF
  • UnkG
  • UnkI
  • UnkK
  • UnkL
  • bS16m
  • bS18m
  • bS21m
  • bS6m
  • mS22
  • mS23
  • mS26
  • mS29
  • mS33
  • mS34
  • mS35
  • mS37
  • mS38
  • mS48
  • mS49
  • mS50
  • mS51
  • mS52
  • mS53
  • mS54
  • mS55
  • mS56
  • mS57
  • mS58
  • mS59
  • mS60
  • mS61
  • mS62
  • mS63
  • mS65
  • mS66
  • mS69
  • mS70
  • mS71
  • mS72
  • mS73
  • mS74
  • mt-SAF22
  • mt-SAF3
  • mt-SAF37
  • mt-SAF38
  • mt-SAF39
  • mt-SAF6
  • 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 / organellar small ribosomal subunit / mitochondrial mRNA editing complex / mitochondrial RNA processing / photoreactive repair / deoxyribodipyrimidine photo-lyase / kinetoplast / deoxyribodipyrimidine photo-lyase activity / thiosulfate-cyanide sulfurtransferase activity / regulation of protein kinase A signaling ...modulation of formation of structure involved in a symbiotic process / organellar small ribosomal subunit / mitochondrial mRNA editing complex / mitochondrial RNA processing / photoreactive repair / deoxyribodipyrimidine photo-lyase / kinetoplast / deoxyribodipyrimidine photo-lyase activity / thiosulfate-cyanide sulfurtransferase activity / regulation of protein kinase A signaling / quorum sensing / translation factor activity, RNA binding / [acyl-carrier-protein] S-malonyltransferase / enoyl-CoA hydratase activity / [acyl-carrier-protein] S-malonyltransferase activity / ciliary plasm / mRNA stabilization / mitochondrial small ribosomal subunit / fatty acid beta-oxidation / superoxide dismutase / protein kinase A regulatory subunit binding / superoxide dismutase activity / RNA processing / translation initiation factor activity / FAD binding / mitochondrion organization / translational initiation / fatty acid biosynthetic process / transferase activity / ribosome / structural constituent of ribosome / translation / DNA repair / GTPase activity / mRNA binding / GTP binding / mitochondrion / DNA binding / RNA binding / nucleoplasm / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Nucleoid-associated protein YbaB-like domain superfamily / : / Protein kinase A anchor protein, nuclear localisation signal domain / AKAP7 2'5' RNA ligase-like domain / Probable Zinc-ribbon domain / Probable Treble clef zinc finger domain / : / Enoyl-CoA hydratase/isomerase domain / : / Enoyl-CoA hydratase/isomerase ...Nucleoid-associated protein YbaB-like domain superfamily / : / Protein kinase A anchor protein, nuclear localisation signal domain / AKAP7 2'5' RNA ligase-like domain / Probable Zinc-ribbon domain / Probable Treble clef zinc finger domain / : / Enoyl-CoA hydratase/isomerase domain / : / Enoyl-CoA hydratase/isomerase / Protein Fyv4 / IGR protein motif / IGR / Translation initiation factor IF-2, domain II / Initiation factor 2 signature. / Translation initiation factor IF-2, bacterial-like / Cyclic phosphodiesterase / 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 / 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. / Pentatricopeptide repeat / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / LysM domain / Rhodanese-like domain / Manganese/iron superoxide dismutase, C-terminal / Manganese/iron superoxide dismutase, C-terminal domain superfamily / Manganese/iron superoxide dismutase, N-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain / LysM domain / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Acyl transferase/acyl hydrolase/lysophospholipase / ClpP/crotonase-like domain superfamily / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Rossmann-like alpha/beta/alpha sandwich fold / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 superfamily / Ubiquitin family / Ribosomal protein S5, C-terminal / Ribosomal protein S5, C-terminal domain / Small GTP-binding protein 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 / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / FLAVIN-ADENINE DINUCLEOTIDE / GUANOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / URIDINE 5'-TRIPHOSPHATE / : / RNA / RNA (> 10) / RNA (> 100) / A-kinase anchor protein 7-like phosphoesterase domain-containing protein ...ADENOSINE-5'-TRIPHOSPHATE / FLAVIN-ADENINE DINUCLEOTIDE / GUANOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / URIDINE 5'-TRIPHOSPHATE / : / RNA / RNA (> 10) / RNA (> 100) / A-kinase anchor protein 7-like phosphoesterase domain-containing protein / DNA photolyase, putative / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Enoyl-CoA hydratase/isomerase domain-containing protein / Uncharacterized protein / Uncharacterized protein / Mitochondrial SSU ribosomal protein / Mitochondrial SSU ribosomal protein / Uncharacterized protein / Probable Zinc-ribbon domain-containing protein / 30S ribosomal protein S8, putative / Uncharacterized protein / Small ribosomal subunit protein mS41 / Uncharacterized protein / Uncharacterized protein / Mitochondrial ribosomal protein S18 / Small ribosomal subunit protein uS5 C-terminal domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Trans-sialidase / [acyl-carrier-protein] S-malonyltransferase / Uncharacterized protein / 30S Ribosomal protein S17, putative / Uncharacterized protein / Target SNARE / Uncharacterized protein / Opioid growth factor receptor (OGFr) conserved domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Pentacotripeptide-repeat region of PRORP domain-containing protein / Uncharacterized protein / Uncharacterized protein / Ribosomal protein S9 / Translation initiation factor IF-2, chloroplastic / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Trichohyalin / Uncharacterized protein / LysM domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Pentacotripeptide-repeat region of PRORP domain-containing protein / Ubiquitin-like domain-containing protein / Uncharacterized protein / Manganese/iron superoxide dismutase C-terminal domain-containing protein / Superoxide dismutase, putative / Rhodanese domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 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 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 20, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
CA: 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
Cq: Superoxide dismutase, putative
Cr: Sod_Fe_C domain-containing protein
Cv: ECH_2 domain-containing protein
DA: mS48
DB: mS49
DC: mS50
DD: mS51
DE: mS52
DF: mS53
DG: mS54
DH: mS55
DI: mS56
DJ: mS57
DK: mS58
DL: mS59
DM: mS60
DN: mS61
DO: mS62
DP: mS63
DQ: AKAP7_NLS domain-containing protein
DR: mS65
DS: mS66
DT: Rhodanese domain-containing protein
DU: Ubiquitin-like domain-containing protein
DV: mS69
DW: mS70
DX: mS71
DY: mS72
DZ: mS73
Da: mS74
F3: mt-SAF3
F6: mt-SAF6
F7: mt-SAF7
F9: mt-SAF9
FO: mt-SAF22
Ff: DNA photolyase, putative
Fg: Acyl transferase-like protein
Fh: mt-SAF37
Fi: mt-SAF38
IA: Translation initiation factor IF-2, putative
IB: mt-SAF39
U6: Unk
U7: Unk7
UE: UnkE
UF: UnkF
UG: UnkG
UI: UnkI
UJ: Unk
UK: UnkK
UL: UnkL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,617,42891
Polymers3,614,70676
Non-polymers2,72315
Water905
1


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

-
Components

-
RNA chain , 1 types, 1 molecules CA

#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) / Strain: Tb427.10 / References: GenBank: 13740

+
Protein , 67 types, 67 molecules CCCECFCHCICJCKCLCNCOCPCQCRCSCUCaCbCdCgCiCjCkCmCnCpCqCrCvDADB...

#2: Protein uS3m


Mass: 9070.940 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10
#3: Protein Ribosomal_S5_C domain-containing protein / uS5m


Mass: 50147.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10 / References: UniProt: Q38AX6
#4: Protein bS6m


Mass: 18861.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10 / References: UniProt: Q38BW5
#5: Protein 30S ribosomal protein S8, putative / uS8m


Mass: 32766.459 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10 / References: UniProt: Q388R7
#6: Protein uS9m


Mass: 50201.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10 / References: UniProt: Q57W62
#7: Protein LysM domain-containing protein / uS10m


Mass: 94321.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10 / References: UniProt: Q57Z45
#8: Protein uS11m


Mass: 37925.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10 / References: UniProt: Q389T7
#9: Protein uS12m


Mass: 10421.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10
#10: Protein uS14m


Mass: 19900.014 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10 / References: UniProt: Q580I0
#11: Protein uS15m


Mass: 50401.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10 / References: UniProt: Q4GZ99
#12: Protein bS16m


Mass: 22077.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10 / References: UniProt: Q384N9
#13: Protein 30S Ribosomal protein S17, putative / uS17m


Mass: 35632.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10 / References: UniProt: Q38DP8
#14: Protein bS18m


Mass: 36988.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10 / References: UniProt: Q38AS2
#15: Protein uS19m


Mass: 28364.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10
#16: Protein bS21m


Mass: 23087.889 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10 / References: UniProt: Q580M9
#17: Protein mS22


Mass: 73064.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10 / References: UniProt: Q38DR3
#18: Protein mS23


Mass: 36869.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10
#19: Protein mS26


Mass: 51192.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10 / References: UniProt: Q38DK6
#20: Protein mS29


Mass: 57048.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10
#21: Protein mS33


Mass: 21244.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10 / References: UniProt: Q57WW0
#22: Protein mS34


Mass: 28728.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10 / References: UniProt: Q57UK0
#23: Protein mS35


Mass: 98277.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10 / References: UniProt: Q387C7
#24: Protein mS37


Mass: 24757.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10 / References: UniProt: Q38C96
#25: Protein mS38


Mass: 28240.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10 / References: UniProt: Q57VQ9
#26: Protein Protein FYV4, mitochondrial / mS41


Mass: 22421.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10 / References: UniProt: Q389L3
#27: Protein Superoxide dismutase, putative / mS42


Mass: 29748.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10 / References: UniProt: Q586A1, superoxide dismutase
#28: Protein Sod_Fe_C domain-containing protein / mS43


Mass: 48590.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10 / References: UniProt: Q585I1
#29: Protein ECH_2 domain-containing protein / mS47


Mass: 137898.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10 / References: UniProt: Q383R4
#30: Protein mS48


Mass: 201787.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10 / References: UniProt: Q57UJ2
#31: Protein mS49


Mass: 137234.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10 / References: UniProt: Q586P5
#32: Protein mS50


Mass: 131719.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10 / References: UniProt: Q57YB5
#33: Protein mS51


Mass: 95080.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10 / References: UniProt: Q385L8
#34: Protein mS52


Mass: 84938.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10 / References: UniProt: Q386Q7
#35: Protein mS53


Mass: 75338.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10 / References: UniProt: Q38ET1
#36: Protein mS54


Mass: 72046.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10 / References: UniProt: Q57ZP8
#37: Protein mS55


Mass: 66676.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10 / References: UniProt: Q580V1
#38: Protein mS56


Mass: 47306.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10 / References: UniProt: Q587C2
#39: Protein mS57


Mass: 45956.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10 / References: UniProt: Q584U8
#40: Protein mS58


Mass: 35623.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10 / References: UniProt: Q38BP1
#41: Protein mS59


Mass: 35395.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10 / References: UniProt: Q38BS2
#42: Protein mS60


Mass: 34546.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10 / References: UniProt: Q57XL2
#43: Protein mS61


Mass: 33482.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10 / References: UniProt: Q38D60
#44: Protein mS62


Mass: 32068.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10 / References: UniProt: Q383D1
#45: Protein mS63


Mass: 31922.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10 / References: UniProt: Q38F25
#46: Protein AKAP7_NLS domain-containing protein / mS64


Mass: 30742.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10 / References: UniProt: Q382E8
#47: Protein mS65


Mass: 30617.381 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10 / References: UniProt: Q57UA2
#48: Protein mS66


Mass: 29960.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10 / References: UniProt: Q388L7
#49: Protein Rhodanese domain-containing protein / mS67


Mass: 30096.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10 / References: UniProt: Q586G5
#50: 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: Tb427.10 / References: UniProt: Q582T9
#51: Protein mS69


Mass: 21589.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10 / References: UniProt: Q57UZ6
#52: Protein mS70


Mass: 21247.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10 / References: UniProt: Q383N9
#53: Protein mS71


Mass: 20093.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10 / References: UniProt: Q383G5
#54: Protein mS72


Mass: 19340.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10 / References: UniProt: Q57YD4
#55: Protein mS73


Mass: 11360.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10 / References: UniProt: Q587C4
#56: Protein mS74


Mass: 8203.408 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10
#57: 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: Tb427.10 / References: UniProt: Q38E61
#58: Protein mt-SAF6


Mass: 76781.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10
#59: 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: Tb427.10 / References: UniProt: Q57UW6
#60: Protein mt-SAF9


Mass: 69781.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10 / References: UniProt: Q57YC0
#61: 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: Tb427.10 / References: UniProt: Q389F9
#62: Protein DNA photolyase, putative / mt-SAF35


Mass: 95285.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10
References: UniProt: Q382U6, deoxyribodipyrimidine photo-lyase
#63: Protein Acyl transferase-like protein / mt-SAF36


Mass: 60722.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10 / References: UniProt: Q38DK4
#64: 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: Tb427.10 / References: UniProt: Q38A63
#65: 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: Tb427.10 / References: UniProt: Q57ZP1
#66: Protein Translation initiation factor IF-2, putative / mt-IF-2


Mass: 87113.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10 / References: UniProt: Q57WE3
#67: 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: Tb427.10 / References: UniProt: Q387Q6
#70: Protein UnkE


Mass: 4528.573 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10

-
Protein/peptide , 7 types, 8 molecules U6UJU7UFUGUIUKUL

#68: Protein/peptide Unk


Mass: 1805.216 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10
#69: Protein/peptide Unk7


Mass: 3422.209 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10
#71: Protein/peptide UnkF


Mass: 3337.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10
#72: Protein/peptide UnkG


Mass: 1124.378 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10
#73: Protein/peptide UnkI


Mass: 869.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10
#74: Protein/peptide UnkK


Mass: 273.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10
#75: Protein/peptide UnkL


Mass: 1720.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: Tb427.10

-
Non-polymers , 8 types, 20 molecules

#76: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#77: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#78: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#79: Chemical ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE


Mass: 484.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N2O15P3 / Comment: UTP*YM
#80: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#81: 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
#82: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#83: 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: Late assembly intermediate of the Trypanosoma brucei mitoribosomal small subunit
Type: RIBOSOME / Entity ID: #1-#75 / 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)

-
Processing

EM software
IDNameCategory
4GctfCTF correction
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17391 / Symmetry type: POINT

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more