› 6sg9

Electron Microscopy
3.1Å resolution

Head domain of the mt-SSU assemblosome from Trypanosoma brucei

Released:
DOI: 10.2210/pdb6sg9/pdb
PDB entry 6sg9 coloured by chain, front view.
PDB entry 6sg9 coloured by chain, side view.
PDB entry 6sg9 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-10175

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 53-mer (preferred)
PDBe Complex ID:
PDB-CPX-104892 (preferred)
Entry contents:
52 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (53 distinct):
uS5m Chain: CE
Molecule details ›
Chain: CE
Length: 435 amino acids
Theoretical weight: 50.15 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
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
Ribosomal protein S24/S35 mitochondrial conserved domain-containing protein Chain: FJ
Molecule details ›
Chain: FJ
Length: 362 amino acids
Theoretical weight: 42.51 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: D0A8R9 (Residues: 1-362; Coverage: 100%)
Gene name: TbgDal_XI11890
mt-SAF28 Chain: FY
Molecule details ›
Chain: FY
Length: 188 amino acids
Theoretical weight: 21.47 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: A0A3L6L5M9 (Residues: 1-188; Coverage: 100%)
Gene name: DPX39_060023800
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
uS3m Chain: CC
Molecule details ›
Chain: CC
Length: 74 amino acids
Theoretical weight: 9.07 KDa
Source organism: Trypanosoma brucei brucei
Ribosomal protein S9 Chain: CI
Molecule details ›
Chain: CI
Length: 443 amino acids
Theoretical weight: 50.2 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q57W62 (Residues: 1-443; Coverage: 100%)
Gene names: Tb08.28F14.630, Tb927.8.3110
Sequence domains: Ribosomal protein S9/S16
uS10m Chain: CJ
Molecule details ›
Chain: CJ
Length: 817 amino acids
Theoretical weight: 94.32 KDa
Source organism: Trypanosoma brucei brucei
uS14m Chain: CN
Molecule details ›
Chain: CN
Length: 166 amino acids
Theoretical weight: 19.9 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q580I0 (Residues: 1-166; Coverage: 100%)
Gene names: Tb08.29O9.64, Tb927.8.1430
uS19m Chain: CS
Molecule details ›
Chain: CS
Length: 244 amino acids
Theoretical weight: 28.36 KDa
Source organism: Trypanosoma brucei brucei
Small ribosomal subunit protein mS29 Chain: Cg
Molecule details ›
Chain: Cg
Length: 498 amino acids
Theoretical weight: 57.05 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q585C2 (Residues: 1-498; Coverage: 100%)
Gene names: Tb06.3A7.780, Tb927.6.1250
Sequence domains: Mitochondrial ribosomal death-associated protein 3
mS33 Chain: Ci
Molecule details ›
Chain: Ci
Length: 181 amino acids
Theoretical weight: 21.24 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q57WW0 (Residues: 1-181; Coverage: 100%)
Gene names: Tb03.27F10.720, Tb927.3.770
Mitochondrial SSU ribosomal protein Chain: Ck
Molecule details ›
Chain: Ck
Length: 874 amino acids
Theoretical weight: 98.38 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q387C7 (Residues: 1-874; Coverage: 100%)
Gene name: Tb11.47.0024
mS49 Chain: DB
Molecule details ›
Chain: DB
Length: 1181 amino acids
Theoretical weight: 137.23 KDa
Source organism: Trypanosoma brucei brucei
mS50 Chain: DC
Molecule details ›
Chain: DC
Length: 1165 amino acids
Theoretical weight: 131.72 KDa
Source organism: Trypanosoma brucei brucei
Mitochondrial SSU ribosomal protein Chain: DE
Molecule details ›
Chain: DE
Length: 747 amino acids
Theoretical weight: 85 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q386Q7 (Residues: 1-747; Coverage: 100%)
Gene name: Tb11.02.0130
mS53 Chain: DF
Molecule details ›
Chain: DF
Length: 666 amino acids
Theoretical weight: 75.31 KDa
Source organism: Trypanosoma brucei brucei
mS54 Chain: DG
Molecule details ›
Chain: DG
Length: 631 amino acids
Theoretical weight: 72.05 KDa
Source organism: Trypanosoma brucei brucei
mS55 (KRIPP8) Chain: DH
Molecule details ›
Chain: DH
Length: 581 amino acids
Theoretical weight: 66.68 KDa
Source organism: Trypanosoma brucei brucei
mS57 Chain: DJ
Molecule details ›
Chain: DJ
Length: 396 amino acids
Theoretical weight: 45.96 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q584U8 (Residues: 1-396; Coverage: 100%)
Gene names: Tb06.4M18.330, Tb927.6.2080
mS58 Chain: DK
Molecule details ›
Chain: DK
Length: 324 amino acids
Theoretical weight: 35.62 KDa
Source organism: Trypanosoma brucei brucei
Rhodanese domain-containing protein Chain: DT
Molecule details ›
Chain: DT
Length: 247 amino acids
Theoretical weight: 30.1 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q586G5 (Residues: 1-247; Coverage: 100%)
Gene names: Tb06.30P15.560, Tb927.6.4930
Sequence domains: Rhodanese-like domain
mS69 Chain: DV
Molecule details ›
Chain: DV
Length: 183 amino acids
Theoretical weight: 21.59 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q57UZ6 (Residues: 1-183; Coverage: 100%)
Gene names: Tb08.4A8.150, Tb927.8.4550
mS70 Chain: DW
Molecule details ›
Chain: DW
Length: 179 amino acids
Theoretical weight: 21.25 KDa
Source organism: Trypanosoma brucei brucei
mS71 Chain: DX
Molecule details ›
Chain: DX
Length: 169 amino acids
Theoretical weight: 20.09 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q383G5 (Residues: 1-169; Coverage: 100%)
Gene name: Tb11.01.2920
mS72 Chain: DY
Molecule details ›
Chain: DY
Length: 163 amino acids
Theoretical weight: 19.34 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q57YD4 (Residues: 1-163; Coverage: 100%)
Gene names: Tb07.13M20.50, Tb927.7.3240
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
mt-SAF4 Chain: F4
Molecule details ›
Chain: F4
Length: 811 amino acids
Theoretical weight: 91.55 KDa
Source organism: Trypanosoma brucei brucei
mt-SAF12 (KRIPP18) Chain: FD
Molecule details ›
Chain: FD
Length: 579 amino acids
Theoretical weight: 65.05 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q583U2 (Residues: 1-579; Coverage: 100%)
Gene names: Tb06.3D8.320, Tb927.6.610
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
mt-SAF15 Chain: FG
Molecule details ›
Chain: FG
Length: 463 amino acids
Theoretical weight: 53.27 KDa
Source organism: Trypanosoma brucei brucei
mt-SAF16 Chain: FH
Molecule details ›
Chain: FH
Length: 457 amino acids
Theoretical weight: 50.91 KDa
Source organism: Trypanosoma brucei brucei
mt-SAF17 Chain: FI
Molecule details ›
Chain: FI
Length: 445 amino acids
Theoretical weight: 50.15 KDa
Source organism: Trypanosoma brucei brucei
Mitochondrial glycoprotein-like protein Chain: FK
Molecule details ›
Chain: FK
Length: 372 amino acids
Theoretical weight: 41.24 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q57XS8 (Residues: 1-372; Coverage: 100%)
Gene names: Tb07.21H15.310, Tb927.7.7080
Sequence domains: Mitochondrial glycoprotein
mt-SAF20 Chain: FL
Molecule details ›
Chain: FL
Length: 353 amino acids
Theoretical weight: 40.29 KDa
Source organism: Trypanosoma brucei brucei
mt-SAF25 Chain: FV
Molecule details ›
Chain: FV
Length: 264 amino acids
Theoretical weight: 29.47 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q38C60 (Residues: 37-300; Coverage: 88%)
Gene name: Tb10.70.6030
mt-SAF34 Chain: Fe
Molecule details ›
Chain: Fe
Length: 123 amino acids
Theoretical weight: 14.86 KDa
Source organism: Trypanosoma brucei brucei
UniProt:
  • Canonical: Q387L0 (Residues: 1-123; Coverage: 100%)
Gene name: Tb11.03.0725
UNK-a Chain: Ua
Molecule details ›
Chain: Ua
Length: 70 amino acids
Theoretical weight: 5.98 KDa
Source organism: Trypanosoma brucei brucei
UNK-b Chain: Ub
Molecule details ›
Chain: Ub
Length: 42 amino acids
Theoretical weight: 3.59 KDa
Source organism: Trypanosoma brucei brucei
UNK-c Chain: Uc
Molecule details ›
Chain: Uc
Length: 12 amino acids
Theoretical weight: 1.04 KDa
Source organism: Trypanosoma brucei brucei
UNK-d Chain: Ud
Molecule details ›
Chain: Ud
Length: 59 amino acids
Theoretical weight: 5.04 KDa
Source organism: Trypanosoma brucei brucei
UNK-e Chain: Ue
Molecule details ›
Chain: Ue
Length: 29 amino acids
Theoretical weight: 2.49 KDa
Source organism: Trypanosoma brucei brucei
UNK-f Chain: Uf
Molecule details ›
Chain: Uf
Length: 9 amino acids
Theoretical weight: 784 Da
Source organism: Trypanosoma brucei brucei
UNK-g Chain: Ug
Molecule details ›
Chain: Ug
Length: 167 amino acids
Theoretical weight: 14.23 KDa
Source organism: Trypanosoma brucei brucei
UNK-h Chain: Uh
Molecule details ›
Chain: Uh
Length: 255 amino acids
Theoretical weight: 21.72 KDa
Source organism: Trypanosoma brucei brucei
UNK-i Chain: Ui
Molecule details ›
Chain: Ui
Length: 32 amino acids
Theoretical weight: 2.74 KDa
Source organism: Trypanosoma brucei brucei
UNK-j Chain: Uj
Molecule details ›
Chain: Uj
Length: 19 amino acids
Theoretical weight: 1.64 KDa
Source organism: Trypanosoma brucei brucei
UNK-k Chain: Uk
Molecule details ›
Chain: Uk
Length: 27 amino acids
Theoretical weight: 2.32 KDa
Source organism: Trypanosoma brucei brucei
UNK-l Chain: Ul
Molecule details ›
Chain: Ul
Length: 14 amino acids
Theoretical weight: 1.21 KDa
Source organism: Trypanosoma brucei brucei
UNK-m Chain: Um
Molecule details ›
Chain: Um
Length: 11 amino acids
Theoretical weight: 954 Da
Source organism: Trypanosoma brucei brucei
UNK-x Chain: Ux
Molecule details ›
Chain: Ux
Length: 108 amino acids
Theoretical weight: 9.21 KDa
Source organism: Trypanosoma brucei brucei
9S rRNA Chain: CA
Molecule details ›
Chain: CA
Length: 802 nucleotides
Theoretical weight: 256.38 KDa
Sequence domains: Trypanosomatid mitochondrial small subunit ribosomal RNA

Ligands and Environments

4 bound ligands:
Ligand GTP 1 x GTP
Ligand MG 1 x MG
Ligand ZN 5 x ZN
Ligand SAH 2 x SAH
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.1Å
Relevant EMDB volumes: EMD-10175

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)