› 6sga

Electron Microscopy
3.1Å resolution

Body domain of the mt-SSU assemblosome from Trypanosoma brucei

Released:
DOI: 10.2210/pdb6sga/pdb
PDB entry 6sga coloured by chain, front view.
PDB entry 6sga coloured by chain, side view.
PDB entry 6sga coloured by chain, top view.
Source organism: Trypanosoma brucei brucei
Primary publication:
Mitoribosomal small subunit biogenesis in trypanosomes involves an extensive assembly machinery.
Saurer M, Ramrath DJF, Niemann M, Calderaro S, Prange C, Mattei S, Scaiola A, Leitner A, Bieri P, Horn EK, Leibundgut M, Boehringer D, Schneider A, Ban N
Science 365 1144-1149 (2019)
PMID: 31515389
Related structures: EMD-10177

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 72-mer (preferred)
PDBe Complex ID:
PDB-CPX-167461 (preferred)
Entry contents:
61 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (62 distinct):
uS5m Chain: CE
Molecule details ›
Chain: CE
Length: 435 amino acids
Theoretical weight: 50.15 KDa
Source organism: Trypanosoma brucei brucei
bS6m Chain: CF
Molecule details ›
Chain: CF
Length: 160 amino acids
Theoretical weight: 18.86 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q38BW5 (Residues: 1-160; Coverage: 100%)
Gene name: Tb10.70.4850
uS8m Chain: CH
Molecule details ›
Chain: CH
Length: 282 amino acids
Theoretical weight: 32.77 KDa
Source organism: Trypanosoma brucei brucei
uS11m Chain: CK
Molecule details ›
Chain: CK
Length: 326 amino acids
Theoretical weight: 37.95 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q389T7 (Residues: 1-326; Coverage: 100%)
Gene name: Tb10.406.0510
uS15m Chain: CO
Molecule details ›
Chain: CO
Length: 429 amino acids
Theoretical weight: 50.4 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q4GZ99 (Residues: 1-429; Coverage: 100%)
Gene name: TB927.1.1200
bS16m Chain: CP
Molecule details ›
Chain: CP
Length: 188 amino acids
Theoretical weight: 22.08 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q384N9 (Residues: 1-188; Coverage: 100%)
Gene name: Tb11.02.5670
uS17m Chain: CQ
Molecule details ›
Chain: CQ
Length: 336 amino acids
Theoretical weight: 39.01 KDa
Source organism: Trypanosoma brucei brucei
bS18m Chain: CR
Molecule details ›
Chain: CR
Length: 320 amino acids
Theoretical weight: 36.99 KDa
Source organism: Trypanosoma brucei brucei
mS22 Chain: Ca
Molecule details ›
Chain: Ca
Length: 602 amino acids
Theoretical weight: 73.06 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q38DR3 (Residues: 1-602; Coverage: 100%)
Gene name: Tb09.211.2430
mS23 Chain: Cb
Molecule details ›
Chain: Cb
Length: 311 amino acids
Theoretical weight: 35.36 KDa
Source organism: Trypanosoma brucei brucei
mS26 Chain: Cd
Molecule details ›
Chain: Cd
Length: 440 amino acids
Theoretical weight: 51.14 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q38DK6 (Residues: 1-440; Coverage: 100%)
Gene name: Tb09.211.3000
mS34 Chain: Cj
Molecule details ›
Chain: Cj
Length: 257 amino acids
Theoretical weight: 28.73 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q57UK0 (Residues: 1-257; Coverage: 100%)
Gene names: Tb08.5H5.370, Tb927.8.5280
mS38 Chain: Cn
Molecule details ›
Chain: Cn
Length: 250 amino acids
Theoretical weight: 28.24 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q57VQ9 (Residues: 1-250; Coverage: 100%)
Gene names: Tb07.29K4.740, Tb927.7.630
Small ribosomal subunit protein mS41 Chain: Cp
Molecule details ›
Chain: Cp
Length: 187 amino acids
Theoretical weight: 22.42 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q389L3 (Residues: 1-187; Coverage: 100%)
Gene name: Tb10.26.0750
mS51 (KRIPP1) Chain: DD
Molecule details ›
Chain: DD
Length: 812 amino acids
Theoretical weight: 95.08 KDa
Source organism: Trypanosoma brucei brucei
mS56 Chain: DI
Molecule details ›
Chain: DI
Length: 407 amino acids
Theoretical weight: 47.31 KDa
Source organism: Trypanosoma brucei brucei
mS59 Chain: DL
Molecule details ›
Chain: DL
Length: 307 amino acids
Theoretical weight: 35.4 KDa
Source organism: Trypanosoma brucei brucei
mS62 (KRIPP14) Chain: DO
Molecule details ›
Chain: DO
Length: 282 amino acids
Theoretical weight: 32.07 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q383D1 (Residues: 1-282; Coverage: 100%)
Gene name: Tb11.01.3300
mS63 (KRIPP16) Chain: DP
Molecule details ›
Chain: DP
Length: 274 amino acids
Theoretical weight: 31.92 KDa
Source organism: Trypanosoma brucei brucei
mS65 Chain: DR
Molecule details ›
Chain: DR
Length: 270 amino acids
Theoretical weight: 30.62 KDa
Source organism: Trypanosoma brucei brucei
mS68 Chain: DU
Molecule details ›
Chain: DU
Length: 228 amino acids
Theoretical weight: 26.47 KDa
Source organism: Trypanosoma brucei brucei
mS73 Chain: DZ
Molecule details ›
Chain: DZ
Length: 94 amino acids
Theoretical weight: 11.36 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q587C4 (Residues: 1-94; Coverage: 100%)
Gene names: Tb06.26G9.560, Tb927.6.4580
mt-SAF2 (KRIPP2) Chain: F2
Molecule details ›
Chain: F2
Length: 1024 amino acids
Theoretical weight: 116.19 KDa
Source organism: Trypanosoma brucei brucei
Target SNARE Chain: F3
Molecule details ›
Chain: F3
Length: 966 amino acids
Theoretical weight: 106.62 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q38E61 (Residues: 1-966; Coverage: 100%)
Gene name: Tb09.211.0950
mt-SAF5 Chain: F5
Molecule details ›
Chain: F5
Length: 754 amino acids
Theoretical weight: 86.95 KDa
Source organism: Trypanosoma brucei brucei
DUF4460 domain-containing protein Chain: F6
Molecule details ›
Chain: F6
Length: 676 amino acids
Theoretical weight: 76.78 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q38FQ8 (Residues: 1-676; Coverage: 100%)
Gene name: Tb09.160.1280
Sequence domains: Domain of unknown function (DUF4460)
Pentacotripeptide-repeat region of PRORP domain-containing protein Chain: F7
Molecule details ›
Chain: F7
Length: 679 amino acids
Theoretical weight: 76.68 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q57UW6 (Residues: 1-679; Coverage: 100%)
Gene names: Tb08.4A8.560, Tb927.8.4860
mt-SAF8 Chain: F8
Molecule details ›
Chain: F8
Length: 726 amino acids
Theoretical weight: 76.73 KDa
Source organism: Trypanosoma brucei brucei
mt-SAF9 Chain: F9
Molecule details ›
Chain: F9
Length: 608 amino acids
Theoretical weight: 69.78 KDa
Source organism: Trypanosoma brucei brucei
mt-SAF10 Chain: FA
Molecule details ›
Chain: FA
Length: 642 amino acids
Theoretical weight: 69.31 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q386U1 (Residues: 1-642; Coverage: 100%)
Gene name: Tb11.18.0009
mt-SAF11 Chains: FB, FC
Molecule details ›
Chains: FB, FC
Length: 579 amino acids
Theoretical weight: 64.92 KDa
Source organism: Trypanosoma brucei brucei
mt-SAF13 Chain: FE
Molecule details ›
Chain: FE
Length: 553 amino acids
Theoretical weight: 63.69 KDa
Source organism: Trypanosoma brucei brucei
mt-SAF18 Chain: FJ
Molecule details ›
Chain: FJ
Length: 362 amino acids
Theoretical weight: 42.51 KDa
Source organism: Trypanosoma brucei brucei
mt-SAF21 Chains: FM, FN
Molecule details ›
Chains: FM, FN
Length: 370 amino acids
Theoretical weight: 39.61 KDa
Source organism: Trypanosoma brucei brucei
mt-SAF22 (KRIPP17) Chain: FO
Molecule details ›
Chain: FO
Length: 334 amino acids
Theoretical weight: 39.13 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q389F9 (Residues: 1-334; Coverage: 100%)
Gene name: Tb10.26.0050
mt-SAF23 Chain: FP
Molecule details ›
Chain: FP
Length: 349 amino acids
Theoretical weight: 38.24 KDa
Source organism: Trypanosoma brucei brucei
Potassium channel tetramerisation-type BTB domain-containing protein Chains: FQ, FR, FS, FT, FU
Molecule details ›
Chains: FQ, FR, FS, FT, FU
Length: 307 amino acids
Theoretical weight: 34.65 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q387P8 (Residues: 1-307; Coverage: 100%)
Gene name: Tb10.61.0090
Sequence domains: BTB/POZ domain
Phosphotyrosine protein phosphatase I domain-containing protein Chain: FW
Molecule details ›
Chain: FW
Length: 263 amino acids
Theoretical weight: 30.54 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q38FI3 (Residues: 1-263; Coverage: 100%)
Gene name: Tb09.160.2100
Sequence domains: Low molecular weight phosphotyrosine protein phosphatase
Pentacotripeptide-repeat region of PRORP domain-containing protein Chain: FX
Molecule details ›
Chain: FX
Length: 239 amino acids
Theoretical weight: 26.94 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q57YK5 (Residues: 1-239; Coverage: 100%)
Gene names: Tb08.11J15.790, Tb927.8.6040
Sequence domains: Pentatricopeptide repeat domain
mt-SAF28 Chain: FY
Molecule details ›
Chain: FY
Length: 188 amino acids
Theoretical weight: 21.47 KDa
Source organism: Trypanosoma brucei brucei
mt-SAF29 Chain: FZ
Molecule details ›
Chain: FZ
Length: 178 amino acids
Theoretical weight: 20.05 KDa
Source organism: Trypanosoma brucei brucei
Glutaredoxin domain-containing protein Chain: Fa
Molecule details ›
Chain: Fa
Length: 171 amino acids
Theoretical weight: 19.66 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q57VU7 (Residues: 1-171; Coverage: 100%)
Gene names: Tb07.29K4.100, Tb927.7.1010
Succinate dehydrogenase assembly factor 3, mitochondrial Chain: Fb
Molecule details ›
Chain: Fb
Length: 151 amino acids
Theoretical weight: 17.67 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q581U4 (Residues: 1-151; Coverage: 100%)
Gene names: Tb04.2L9.550, Tb927.4.1370
Acyl carrier protein Chain: Fc
Molecule details ›
Chain: Fc
Length: 148 amino acids
Theoretical weight: 16.55 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q57WW9 (Residues: 1-148; Coverage: 100%)
Gene names: Tb03.27F10.580, Tb927.3.860
Sequence domains: Phosphopantetheine attachment site
Probable Zinc-ribbon domain-containing protein Chain: Fd
Molecule details ›
Chain: Fd
Length: 143 amino acids
Theoretical weight: 16.29 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q581T4 (Residues: 1-143; Coverage: 100%)
Gene names: Tb04.2L9.680, Tb927.4.1470
Sequence domains: Probable Zinc-ribbon domain
UNK-A Chain: UA
Molecule details ›
Chain: UA
Length: 21 amino acids
Theoretical weight: 1.81 KDa
Source organism: Trypanosoma brucei brucei
UNK-B Chain: UB
Molecule details ›
Chain: UB
Length: 27 amino acids
Theoretical weight: 2.32 KDa
Source organism: Trypanosoma brucei brucei
UNK-C Chain: UC
Molecule details ›
Chain: UC
Length: 10 amino acids
Theoretical weight: 869 Da
Source organism: Trypanosoma brucei brucei
UNK-D, UNK-M, UNK-Q Chains: UD, UM, UQ
Molecule details ›
Chains: UD, UM, UQ
Length: 9 amino acids
Theoretical weight: 784 Da
Source organism: Trypanosoma brucei brucei
UNK-E, UNK-P Chains: UE, UP
Molecule details ›
Chains: UE, UP
Length: 45 amino acids
Theoretical weight: 3.85 KDa
Source organism: Trypanosoma brucei brucei
UNK-F Chain: UF
Molecule details ›
Chain: UF
Length: 11 amino acids
Theoretical weight: 954 Da
Source organism: Trypanosoma brucei brucei
UNK-G Chain: UG
Molecule details ›
Chain: UG
Length: 17 amino acids
Theoretical weight: 1.46 KDa
Source organism: Trypanosoma brucei brucei
UNK-H Chain: UH
Molecule details ›
Chain: UH
Length: 5 amino acids
Theoretical weight: 444 Da
Source organism: Trypanosoma brucei brucei
UNK-I, UNK-M Chains: UI, UN
Molecule details ›
Chains: UI, UN
Length: 8 amino acids
Theoretical weight: 699 Da
Source organism: Trypanosoma brucei brucei
UNK-J Chain: UJ
Molecule details ›
Chain: UJ
Length: 16 amino acids
Theoretical weight: 1.38 KDa
Source organism: Trypanosoma brucei brucei
UNK-L Chain: UL
Molecule details ›
Chain: UL
Length: 22 amino acids
Theoretical weight: 1.89 KDa
Source organism: Trypanosoma brucei brucei
UNK-O Chain: UO
Molecule details ›
Chain: UO
Length: 30 amino acids
Theoretical weight: 2.57 KDa
Source organism: Trypanosoma brucei brucei
UNK-U Chain: UU
Molecule details ›
Chain: UU
Length: 24 amino acids
Theoretical weight: 2.06 KDa
Source organism: Trypanosoma brucei brucei
UNK-I Chain: UY
Molecule details ›
Chain: UY
Length: 468 amino acids
Theoretical weight: 39.85 KDa
Source organism: Trypanosoma brucei brucei
Methyltransferase Chain: F1
Molecule details ›
Chain: F1
Length: 1041 amino acids
Theoretical weight: 119.8 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q385R2 (Residues: 1-1041; Coverage: 100%)
Gene name: Tb11.02.2710
Sequence domains: Mitochondrial small ribosomal subunit Rsm22
S-adenosyl-methyltransferase mraW-like protein, putative Chain: FF
Molecule details ›
Chain: FF
Length: 474 amino acids
Theoretical weight: 53.32 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q57W60 (Residues: 1-474; Coverage: 100%)
Gene names: Tb08.28F14.650, Tb927.8.3130
Sequence domains: MraW methylase family
9S rRNA Chain: CA
Molecule details ›
Chain: CA
Length: 474 nucleotides
Theoretical weight: 151.51 KDa
Sequence domains: Trypanosomatid mitochondrial small subunit ribosomal RNA

Ligands and Environments

4 bound ligands:
Ligand MG 4 x MG
Ligand PO4 1 x PO4
Ligand PM8 1 x PM8
Ligand ZN 1 x ZN
1 modified residue:
Ligand UBD 1 x UBD

Experiments and Validation Details

Entry percentile scores
Resolution: 3.1Å
Relevant EMDB volumes: EMD-10177

Quick links

Citations

10 review citations

Ribosome Biogenesis and Cancer: Overview on Ribosomal Proteins.
Pecoraro et al. (2021)
9 more

1 mention without citation

Expression and analysis of the SAM-dependent RNA methyltransferase Rsm22 from Saccharomyces cerevisiae.
Alam et al. (2021)