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- PDB-9hny: Mitoribosomal small subunit in complex with Mettl15 and Mettl17 -

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Basic information

Entry
Database: PDB / ID: 9hny
TitleMitoribosomal small subunit in complex with Mettl15 and Mettl17
Components
  • (Mitochondrial ...) x 6
  • (PPR_long domain-containing ...) x 2
  • 30S ribosomal protein S8
  • 9S RNA
  • ADP-ribosylglycohydrolase
  • Acyl carrier protein
  • Chromosome passenger complex (CPC) protein INCENP N terminal
  • Complex 1 protein (LYR family)
  • Cupin type-1 domain-containing protein
  • DUF4460 domain-containing protein
  • Kinteoplast poly(A) polymerase complex 1 subunit
  • Low molecular weight protein tyrosine phosphatase
  • LysM domain-containing protein
  • Metallo-beta-lactamase domain-containing protein
  • Methyltranfer_dom domain-containing protein
  • Pentacotripeptide-repeat region of PRORP domain-containing protein
  • Potassium voltage-gated channel, putative
  • Probable Zinc-ribbon domain-containing protein
  • Protein FYV4, mitochondrial
  • Rhodanese domain-containing protein
  • Ribosomal protein S9/S16
  • S-adenosyl-methyltransferase mraW-like protein
  • Small ribosomal subunit protein uS5 C-terminal domain-containing protein
  • Trichohyalin
  • UNK-A
  • UNK-B
  • UNK-C
  • UNK-F
  • UNK-G,J
  • UNK-I
  • UNK-K
  • UNK-L
  • UNK-M,Q
  • UNK-N
  • UNK-O
  • UNK-P
  • UNK-Y
  • UNK-d
  • UNK-g
  • UNK-h
  • UNK-k
  • UNK-l
  • Ubiquitin-like domain-containing protein
  • bS16m
  • bS6m
  • mS23
  • mS26
  • mS33
  • mS34
  • mS35
  • mS38
  • mS49
  • mS50
  • mS51
  • mS53
  • mS54
  • mS55
  • mS56
  • mS57
  • mS58
  • mS59
  • mS62
  • mS63
  • mS65
  • mS69
  • mS70
  • mS71
  • mS72
  • mS73
  • mt-SAF10
  • mt-SAF13
  • mt-SAF15
  • mt-SAF16 (P32)
  • mt-SAF17
  • mt-SAF18 (RbfA)
  • mt-SAF21
  • mt-SAF22
  • mt-SAF25
  • mt-SAF28
  • mt-SAF29
  • mt-SAF3
  • mt-SAF30
  • mt-SAF34
  • mt-SAF38
  • mt-SAF7 (KRIPP10)
  • tRNA pseudouridine synthase A-like protein
  • uS11m
  • uS14m
  • uS17m
  • uS19m
  • uS3m
KeywordsRIBOSOME / Mitochondrial ribosome / METTL15 / METTL17 / RbfA / Trypanosoma brucei
Function / homology
Function and homology information


rRNA (cytosine-N4-)-methyltransferase activity / mitochondrial mRNA editing complex / mitochondrial RNA processing / tRNA pseudouridine synthesis / pseudouridine synthase activity / ATP-activated inward rectifier potassium channel activity / kinetoplast / thiosulfate-cyanide sulfurtransferase activity / rRNA base methylation / response to arsenic-containing substance ...rRNA (cytosine-N4-)-methyltransferase activity / mitochondrial mRNA editing complex / mitochondrial RNA processing / tRNA pseudouridine synthesis / pseudouridine synthase activity / ATP-activated inward rectifier potassium channel activity / kinetoplast / thiosulfate-cyanide sulfurtransferase activity / rRNA base methylation / 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 / iron-sulfur cluster binding / catalytic activity / voltage-gated potassium channel activity / RNA processing / voltage-gated potassium channel complex / methyltransferase activity / mitochondrion organization / potassium ion transport / protein homooligomerization / NAD binding / fatty acid biosynthetic process / NADP binding / ribosome / structural constituent of ribosome / mitochondrial matrix / translation / ribonucleoprotein complex / mRNA binding / mitochondrion / RNA binding / nucleoplasm / metal ion binding / membrane / cytosol / cytoplasm
Similarity search - Function
: / T-cell activation inhibitor, mitochondrial / Domain of unknown function DUF4460 / Domain of unknown function (DUF4460) / Mitochondrial glycoprotein / Mitochondrial glycoprotein superfamily / Mitochondrial glycoprotein / PPR repeat / Probable Zinc-ribbon domain / Probable Treble clef zinc finger domain ...: / T-cell activation inhibitor, mitochondrial / Domain of unknown function DUF4460 / Domain of unknown function (DUF4460) / Mitochondrial glycoprotein / Mitochondrial glycoprotein superfamily / Mitochondrial glycoprotein / PPR repeat / Probable Zinc-ribbon domain / Probable Treble clef zinc finger domain / Pentacotripeptide-repeat region of PRORP / Pentacotripeptide-repeat region of PRORP / Pseudouridine synthase I, TruA / Pseudouridine synthase I, TruA, C-terminal / Pseudouridine synthase I, TruA, alpha/beta domain / tRNA pseudouridine synthase / Ribosomal protein Rsm22-like / : / Mitochondrial small ribosomal subunit Rsm22 / Ribosomal RNA small subunit methyltransferase H / S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain superfamily / MraW methylase family / ADP-ribosylation/Crystallin J1 superfamily / Protein Fyv4 / : / IGR protein motif / IGR / 3-hydroxyisobutyrate dehydrogenase-like, NAD-binding domain / NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase / Phosphotyrosine protein phosphatase I / Phosphotyrosine protein phosphatase I superfamily / Low molecular weight phosphotyrosine protein phosphatase / Low molecular weight phosphatase family / Pseudouridine synthase, catalytic domain superfamily / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / Pentatricopeptide repeat domain / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / 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 / Rhodanese-like domain / LysM domain / LysM domain / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / Metallo-beta-lactamase superfamily / Acyl carrier protein (ACP) / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Phosphopantetheine attachment site / SKP1/BTB/POZ domain superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Ribosomal protein S18 superfamily / Translation elongation factor EF1B/ribosomal protein S6 / Ubiquitin family / Ribosomal protein S5, C-terminal / 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 S11 superfamily / S15/NS1, RNA-binding / Thioredoxin-like 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 / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
ACETYL COENZYME *A / GUANOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / S-ADENOSYLMETHIONINE / IRON/SULFUR CLUSTER / : / RNA / RNA (> 10) / RNA (> 100) / tRNA pseudouridine synthase A-like protein ...ACETYL COENZYME *A / GUANOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / S-ADENOSYLMETHIONINE / IRON/SULFUR CLUSTER / : / RNA / RNA (> 10) / RNA (> 100) / tRNA pseudouridine synthase A-like protein / Paraflagellar rod component / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Trypanosomal VSG domain containing protein / Uncharacterized protein / Uncharacterized protein / 30S ribosomal protein S8 / Small ribosomal subunit protein mS41 / Mitochondrial ribosomal protein S18 / Uncharacterized protein / Low molecular weight protein tyrosine phosphatase / Uncharacterized protein / Ribosomal protein S9/S16 / S-adenosyl-methyltransferase mraW-like protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / DUF4460 domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Probable Zinc-ribbon domain-containing protein / Uncharacterized protein / Uncharacterized protein / Mitochondrial ribosomal protein S15 / Complex 1 protein (LYR family) / Dehydrogenase-like protein / Opioid growth factor receptor (OGFr) conserved domain-containing protein / Mitochondrial glycoprotein / Methyltransferase / Methyltransferase / Kinteoplast poly(A) polymerase complex 1 subunit / ADP-ribosylglycohydrolase / Ribosomal protein S24/S35 mitochondrial conserved domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Mitochondrial SSU ribosomal protein / Uncharacterized protein / Mitochondrial SSU ribosomal protein / Potassium voltage-gated channel, putative / Uncharacterized protein / Uncharacterized protein / Small ribosomal subunit protein uS5 C-terminal domain-containing protein / Uncharacterized protein / Uncharacterized protein / Methyltransferase domain-containing protein / Uncharacterized protein / Uncharacterized protein / Target SNARE / Uncharacterized protein / PROP1-like PPR domain-containing protein / Uncharacterized protein / Pentacotripeptide-repeat region of PRORP domain-containing protein / Glutaredoxin domain-containing protein / JmjC domain-containing protein / Acyl carrier protein / Metallo-beta-lactamase domain-containing protein / Mitochondrial glycoprotein-like protein / Uncharacterized protein / Trichohyalin / Pentacotripeptide-repeat region of PRORP domain-containing protein / LysM domain-containing protein / Uncharacterized protein / Pentacotripeptide-repeat region of PRORP domain-containing protein / Ubiquitin-like domain-containing protein / Uncharacterized protein / Uncharacterized protein / Chromosomal passenger protein / Small ribosomal subunit protein mS29 / Rhodanese domain-containing protein / Uncharacterized protein / Uncharacterized protein
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsZgadzay, Y. / Aibara, S. / Gahura, O. / Amunts, A.
Funding supportEuropean Union, Sweden, 2items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-2018-StG-805230European Union
Knut and Alice Wallenberg Foundation2018.0080 Sweden
CitationJournal: bioRxiv / Year: 2025
Title: Mettl15-Mettl17 modulates the transition from early to late pre-mitoribosome.
Authors: Yury Zgadzay / Claudio Mirabello / George Wanes / Tomáš Pánek / Prashant Chauhan / Björn Nystedt / Alena Zíková / Paul C Whitford / Ondřej Gahura / Alexey Amunts /
Abstract: The assembly of the mitoribosomal small subunit involves folding and modification of rRNA, and its association with mitoribosomal proteins. This process is assisted by a dynamic network of assembly ...The assembly of the mitoribosomal small subunit involves folding and modification of rRNA, and its association with mitoribosomal proteins. This process is assisted by a dynamic network of assembly factors. Conserved methyltransferases Mettl15 and Mettl17 act on the solvent-exposed surface of rRNA. Binding of Mettl17 is associated with the early assembly stage, whereas Mettl15 is involved in the late stage, but the mechanism of transition between the two was unclear. Here, we integrate structural data from with mammalian homologs and molecular dynamics simulations. We reveal how the interplay of Mettl15 and Mettl17 in intermediate steps links the distinct stages of small subunit assembly. The analysis suggests a model wherein Mettl17 acts as a platform for Mettl15 recruitment. Subsequent release of Mettl17 allows a conformational change of Mettl15 for substrate recognition. Upon methylation, Mettl15 adopts a loosely bound state which ultimately leads to its replacement by initiation factors, concluding the assembly. Together, our results indicate that assembly factors Mettl15 and Mettl17 cooperate to regulate the biogenesis process, and present a structural data resource for understanding molecular adaptations of assembly factors in mitoribosome.
History
DepositionDec 11, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
CA: 9S RNA
CC: uS3m
CE: Small ribosomal subunit protein uS5 C-terminal domain-containing protein
CF: bS6m
CH: 30S ribosomal protein S8
CI: Ribosomal protein S9/S16
CJ: LysM domain-containing protein
CK: uS11m
CN: uS14m
CO: Mitochondrial ribosomal protein S15
CP: bS16m
CQ: uS17m
CR: Mitochondrial ribosomal protein S18
CS: uS19m
Ca: Chromosome passenger complex (CPC) protein INCENP N terminal
Cb: mS23
Cd: mS26
Cg: Mitochondrial SSU ribosomal protein 29
Ci: mS33
Cj: mS34
Ck: mS35
Cn: mS38
Cp: Protein FYV4, mitochondrial
DB: mS49
DC: mS50
DD: mS51
DE: Mitochondrial SSU ribosomal protein
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
F1: Mitochondrial small ribosomal subunit Rsm22
F2: Pentacotripeptide-repeat region of PRORP domain-containing protein
F3: mt-SAF3
F4: Methyltranfer_dom domain-containing protein
F5: Kinteoplast poly(A) polymerase complex 1 subunit
F6: DUF4460 domain-containing protein
F7: mt-SAF7 (KRIPP10)
F8: Cupin type-1 domain-containing protein
F9: Trichohyalin
FA: mt-SAF10
FB: tRNA pseudouridine synthase A-like protein
FC: tRNA pseudouridine synthase A-like protein
FD: PPR_long domain-containing protein
FE: mt-SAF13
FF: S-adenosyl-methyltransferase mraW-like protein
FG: mt-SAF15
FH: mt-SAF16 (P32)
FI: mt-SAF17
FJ: mt-SAF18 (RbfA)
FK: Mitochondrial glycoprotein
FL: Metallo-beta-lactamase domain-containing protein
FM: mt-SAF21
FN: mt-SAF21
FO: mt-SAF22
FP: ADP-ribosylglycohydrolase
FQ: Potassium voltage-gated channel, putative
FR: Potassium voltage-gated channel, putative
FS: Potassium voltage-gated channel, putative
FT: Potassium voltage-gated channel, putative
FU: Potassium voltage-gated channel, putative
FV: mt-SAF25
FW: Low molecular weight protein tyrosine phosphatase
FX: PPR_long domain-containing protein
FY: mt-SAF28
FZ: mt-SAF29
Fa: mt-SAF30
Fb: Complex 1 protein (LYR family)
Fc: Acyl carrier protein
Fd: Probable Zinc-ribbon domain-containing protein
Fe: mt-SAF34
Fi: mt-SAF38
UA: UNK-A
UB: UNK-B
UC: UNK-C
UF: UNK-F
UG: UNK-G,J
UI: UNK-I
UJ: UNK-G,J
UK: UNK-K
UL: UNK-L
UM: UNK-M,Q
UN: UNK-N
UO: UNK-O
UP: UNK-P
UQ: UNK-M,Q
UY: UNK-Y
Ud: UNK-d
Ug: UNK-g
Uh: UNK-h
Uk: UNK-k
Ul: UNK-l
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,346,236116
Polymers4,343,374105
Non-polymers2,86211
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 1 types, 1 molecules CA

#1: RNA chain 9S RNA


Mass: 198135.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: GenBank: X02547.1

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Protein , 74 types, 80 molecules CCCECFCHCICJCKCNCPCQCSCaCbCdCiCjCkCnCpDBDCDDDFDGDHDIDJDKDLDO...

#2: Protein uS3m


Mass: 9070.940 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote)
#3: Protein Small ribosomal subunit protein uS5 C-terminal domain-containing protein


Mass: 50119.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / 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 (eukaryote) / References: UniProt: Q38BW5
#5: Protein 30S ribosomal protein S8


Mass: 32766.459 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6KZN8
#6: Protein Ribosomal protein S9/S16


Mass: 50229.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6L332
#7: Protein LysM domain-containing protein


Mass: 94389.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q57Z45
#8: Protein uS11m


Mass: 37953.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q389T7
#9: Protein uS14m


Mass: 18956.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6L312
#11: Protein bS16m


Mass: 22077.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q384N9
#12: Protein uS17m


Mass: 39012.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote)
#14: Protein uS19m


Mass: 28364.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote)
#15: Protein Chromosome passenger complex (CPC) protein INCENP N terminal


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


Mass: 35358.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6L708
#17: Protein mS26


Mass: 51136.684 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6L151
#19: Protein mS33


Mass: 21244.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6LBN2
#20: Protein mS34


Mass: 28728.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6LCQ0
#21: Protein mS35


Mass: 98361.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q387C7
#22: Protein mS38


Mass: 28240.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6L7V5
#23: Protein Protein FYV4, mitochondrial


Mass: 22421.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6L0Z8
#24: Protein mS49


Mass: 137108.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q586P5
#25: Protein mS50


Mass: 131751.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q57YB5
#26: Protein mS51


Mass: 95099.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q385L8
#28: Protein mS53


Mass: 75251.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q38ET1
#29: Protein mS54


Mass: 72046.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6L8G2
#30: Protein mS55


Mass: 66756.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q580V1
#31: Protein mS56


Mass: 47248.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q587C2
#32: Protein mS57


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


Mass: 35663.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q38BP1
#34: Protein mS59


Mass: 35395.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6KXC4
#35: Protein mS62


Mass: 32068.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6KX59
#36: Protein mS63


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


Mass: 30680.365 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q57UA2
#38: Protein Rhodanese domain-containing protein


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


Mass: 26458.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q582T9
#40: Protein mS69


Mass: 21619.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6L4I3
#41: Protein mS70


Mass: 21277.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q383N9
#42: Protein mS71


Mass: 20093.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6KVH3
#43: Protein mS72


Mass: 19317.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6L8T2
#44: Protein mS73


Mass: 11360.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6L904
#46: Protein Pentacotripeptide-repeat region of PRORP domain-containing protein


Mass: 116103.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q4GYS4
#47: Protein mt-SAF3


Mass: 106621.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q38E61
#48: Protein Methyltranfer_dom domain-containing protein


Mass: 91520.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q38BY6
#49: Protein Kinteoplast poly(A) polymerase complex 1 subunit


Mass: 86901.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q381K1
#50: Protein DUF4460 domain-containing protein


Mass: 76781.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6L7Z3
#51: Protein mt-SAF7 (KRIPP10)


Mass: 76635.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q57UW6
#52: Protein Cupin type-1 domain-containing protein


Mass: 76474.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q57W22
#53: Protein Trichohyalin


Mass: 69816.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q57YC0
#54: Protein mt-SAF10


Mass: 69311.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q386U1
#55: Protein tRNA pseudouridine synthase A-like protein


Mass: 65949.203 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A1G4II72
#57: Protein mt-SAF13


Mass: 63690.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: D0A7Q0
#58: Protein S-adenosyl-methyltransferase mraW-like protein


Mass: 53320.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6L433
#59: Protein mt-SAF15


Mass: 53273.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6KUN2
#60: Protein mt-SAF16 (P32)


Mass: 50911.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: D0A6K1
#61: Protein mt-SAF17


Mass: 50147.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6KSV0
#62: Protein mt-SAF18 (RbfA)


Mass: 42538.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q383L9
#64: Protein Metallo-beta-lactamase domain-containing protein


Mass: 40369.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q57XC4
#65: Protein mt-SAF21


Mass: 39610.793 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: C9ZJW2
#66: Protein mt-SAF22


Mass: 39132.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q389F9
#67: Protein ADP-ribosylglycohydrolase


Mass: 38307.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q382Z4
#68: Protein
Potassium voltage-gated channel, putative


Mass: 34648.047 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q387P8
#69: Protein mt-SAF25


Mass: 29470.537 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q38C60
#70: Protein Low molecular weight protein tyrosine phosphatase


Mass: 30538.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6L1H2
#72: Protein mt-SAF28


Mass: 21581.822 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q584U9
#73: Protein mt-SAF29


Mass: 20048.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6KWY8
#74: Protein mt-SAF30


Mass: 19687.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q57VU7
#75: Protein Complex 1 protein (LYR family)


Mass: 17673.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6LFP2
#76: Protein Acyl carrier protein


Mass: 16550.807 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q57WW9
#77: Protein Probable Zinc-ribbon domain-containing protein


Mass: 16291.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6L9W2
#78: Protein mt-SAF34


Mass: 14862.911 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6KU34
#79: Protein mt-SAF38


Mass: 69573.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q57ZP1
#92: Protein UNK-Y


Mass: 7251.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote)
#93: Protein UNK-d


Mass: 5039.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote)
#94: Protein UNK-g


Mass: 14230.525 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote)
#95: Protein UNK-h


Mass: 22400.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote)

-
Mitochondrial ... , 6 types, 6 molecules COCRCgDEF1FK

#10: Protein Mitochondrial ribosomal protein S15


Mass: 50401.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6LDF7
#13: Protein Mitochondrial ribosomal protein S18


Mass: 36988.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: A0A3L6L122
#18: Protein Mitochondrial SSU ribosomal protein 29


Mass: 56334.035 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q585C2
#27: Protein Mitochondrial SSU ribosomal protein


Mass: 84998.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q386Q7
#45: Protein Mitochondrial small ribosomal subunit Rsm22


Mass: 119799.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: D0A703
#63: Protein Mitochondrial glycoprotein


Mass: 41236.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q57XS8

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PPR long domain-containing ... , 2 types, 2 molecules FDFX

#56: Protein PPR_long domain-containing protein


Mass: 65049.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q583U2
#71: Protein PPR_long domain-containing protein


Mass: 26936.748 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q57YK5

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Protein/peptide , 14 types, 16 molecules UAUBUCUFUGUJUIUKULUMUQUNUOUPUkUl

#80: Protein/peptide UNK-A


Mass: 2315.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote)
#81: Protein/peptide UNK-B


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


Mass: 869.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote)
#83: Protein/peptide UNK-F


Mass: 954.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote)
#84: Protein/peptide UNK-G,J


Mass: 1379.692 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote)
#85: Protein/peptide UNK-I


Mass: 698.854 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote)
#86: Protein/peptide UNK-K


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


Mass: 1890.321 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote)
#88: Protein/peptide UNK-M,Q


Mass: 783.958 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote)
#89: Protein/peptide UNK-N


Mass: 613.749 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote)
#90: Protein/peptide UNK-O


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


Mass: 3847.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote)
#96: Protein/peptide UNK-k


Mass: 2656.265 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote)
#97: Protein/peptide UNK-l


Mass: 1209.482 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote)

-
Non-polymers , 7 types, 11 molecules

#98: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#99: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#100: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#101: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#102: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#103: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#104: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Mitoribosomal small subunit in complex with Mettl15 and Mettl17
Type: RIBOSOME / Entity ID: #1-#97 / Source: NATURAL
Source (natural)Organism: Trypanosoma brucei (eukaryote)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DARK FIELD / Nominal defocus max: 3200 nm / Nominal defocus min: 2000 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

-
Processing

EM softwareName: PHENIX / Version: 1.19rc4_4035: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 104838 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003239492
ELECTRON MICROSCOPYf_angle_d0.531326708
ELECTRON MICROSCOPYf_dihedral_angle_d9.26637026
ELECTRON MICROSCOPYf_chiral_restr0.03735869
ELECTRON MICROSCOPYf_plane_restr0.00440718

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