› 5xxu

Electron Microscopy
3.35Å resolution

Small subunit of Toxoplasma gondii ribosome

Released:
DOI: 10.2210/pdb5xxu/pdb
PDB entry 5xxu coloured by chain, front view.
PDB entry 5xxu coloured by chain, side view.
PDB entry 5xxu coloured by chain, top view.
Source organism: Toxoplasma gondii
Primary publication:
Cryo-EM structures of the 80S ribosomes from human parasites Trichomonas vaginalis and Toxoplasma gondii.
Li Z, Guo Q, Zheng L, Ji Y, Xie YT, Lai DH, Lun ZR, Suo X, Gao N
Cell Res 27 1275-1288 (2017)
PMID: 28809395
Related structures: EMD-6780

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 34-mer (preferred)
PDBe Complex ID:
PDB-CPX-101316 (preferred)
Entry contents:
33 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (34 distinct):
Small ribosomal subunit protein uS2 Chain: A
Molecule details ›
Chain: A
Length: 287 amino acids
Theoretical weight: 31.55 KDa
Source organism: Toxoplasma gondii
UniProt:
  • Canonical: Q8MPF7 (Residues: 1-287; Coverage: 100%)
Sequence domains: Ribosomal protein S2
Structure domains: Glucose-6-phosphate isomerase like protein; domain 1
Small ribosomal subunit protein eS1 Chain: B
Molecule details ›
Chain: B
Length: 259 amino acids
Theoretical weight: 29.43 KDa
Source organism: Toxoplasma gondii
UniProt:
  • Canonical: B9PGG2 (Residues: 1-259; Coverage: 100%)
Gene names: BN1205_022930, TGVEG_232710
Sequence domains: Ribosomal S3Ae family
S5 DRBM domain-containing protein Chain: C
Molecule details ›
Chain: C
Length: 269 amino acids
Theoretical weight: 29.39 KDa
Source organism: Toxoplasma gondii
UniProt:
  • Canonical: B9PZF2 (Residues: 1-269; Coverage: 100%)
Gene names: BN1205_106930, TGVEG_305520
Sequence domains:
Structure domains:
40S ribosomal protein S3 Chain: D
Molecule details ›
Chain: D
Length: 235 amino acids
Theoretical weight: 26.12 KDa
Source organism: Toxoplasma gondii
UniProt:
  • Canonical: A0A0F7UXI8 (Residues: 1-235; Coverage: 100%)
Gene name: BN1205_023340
Sequence domains:
Structure domains:
40S ribosomal protein S4 Chain: E
Molecule details ›
Chain: E
Length: 263 amino acids
Theoretical weight: 30.2 KDa
Source organism: Toxoplasma gondii
UniProt:
  • Canonical: Q1JSZ0 (Residues: 1-263; Coverage: 100%)
Gene name: TgIb.0120c
Sequence domains:
Structure domains:
Small ribosomal subunit protein uS7 domain-containing protein Chain: F
Molecule details ›
Chain: F
Length: 192 amino acids
Theoretical weight: 21.65 KDa
Source organism: Toxoplasma gondii
UniProt:
  • Canonical: B9PPE8 (Residues: 1-192; Coverage: 100%)
Gene names: BN1205_102420, TGVEG_242330
Sequence domains: Ribosomal protein S7p/S5e
Structure domains: Ribosomal protein S7 domain
40S ribosomal protein S6 Chain: G
Molecule details ›
Chain: G
Length: 256 amino acids
Theoretical weight: 29.03 KDa
Source organism: Toxoplasma gondii
UniProt:
  • Canonical: B9PVR5 (Residues: 1-256; Coverage: 100%)
Gene names: BN1205_008650, TGVEG_210690
Sequence domains: Ribosomal protein S6e
Structure domains: Single alpha-helices involved in coiled-coils or other helix-helix interfaces
40S ribosomal protein S7 Chain: H
Molecule details ›
Chain: H
Length: 196 amino acids
Theoretical weight: 22.63 KDa
Source organism: Toxoplasma gondii
UniProt:
  • Canonical: B9PNL1 (Residues: 1-196; Coverage: 100%)
Gene names: BN1205_092410, TGVEG_239100
Sequence domains: Ribosomal protein S7e
40S ribosomal protein S8 Chain: I
Molecule details ›
Chain: I
Length: 205 amino acids
Theoretical weight: 23.62 KDa
Source organism: Toxoplasma gondii
UniProt:
  • Canonical: B6KGK3 (Residues: 1-205; Coverage: 100%)
Gene names: BN1205_006420, TGVEG_245460
Sequence domains: Ribosomal protein S8e
Structure domains: Ribosomal protein S8e, subdomain
40S ribosomal protein S9, putative Chain: J
Molecule details ›
Chain: J
Length: 188 amino acids
Theoretical weight: 21.73 KDa
Source organism: Toxoplasma gondii
UniProt:
  • Canonical: B9PQU8 (Residues: 1-188; Coverage: 100%)
Gene names: BN1205_003310, TGVEG_248480
Sequence domains:
Plectin/eS10 N-terminal domain-containing protein Chain: K
Molecule details ›
Chain: K
Length: 152 amino acids
Theoretical weight: 17.43 KDa
Source organism: Toxoplasma gondii
UniProt:
  • Canonical: B9PX63 (Residues: 1-152; Coverage: 100%)
Gene names: BN1205_055450, TGVEG_275810
Sequence domains: Plectin/S10 domain
Structure domains: Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
Small ribosomal subunit protein uS17 N-terminal domain-containing protein Chain: L
Molecule details ›
Chain: L
Length: 161 amino acids
Theoretical weight: 18.72 KDa
Source organism: Toxoplasma gondii
UniProt:
  • Canonical: B9PMU7 (Residues: 1-161; Coverage: 100%)
Gene names: BN1205_067990, TGVEG_226970
Sequence domains:
Structure domains: OB fold (Dihydrolipoamide Acetyltransferase, E2P)
40S ribosomal protein S12 Chain: M
Molecule details ›
Chain: M
Length: 142 amino acids
Theoretical weight: 15.42 KDa
Source organism: Toxoplasma gondii
UniProt:
  • Canonical: B9Q056 (Residues: 1-142; Coverage: 100%)
Gene names: BN1205_044050, TGVEG_205340
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Structure domains: 60s Ribosomal Protein L30; Chain: A;
Small ribosomal subunit protein uS15 N-terminal domain-containing protein Chain: N
Molecule details ›
Chain: N
Length: 151 amino acids
Theoretical weight: 17.21 KDa
Source organism: Toxoplasma gondii
UniProt:
  • Canonical: A0A125YSG6 (Residues: 1-151; Coverage: 100%)
Gene names: BN1205_017665, TGVEG_270380
Sequence domains:
Structure domains: S15/NS1, RNA-binding
Ribosomal protein RPS14 Chain: O
Molecule details ›
Chain: O
Length: 156 amino acids
Theoretical weight: 16.33 KDa
Source organism: Toxoplasma gondii
UniProt:
  • Canonical: A0A125YXW4 (Residues: 1-156; Coverage: 100%)
Gene names: BN1205_049265, TGVEG_263700
Sequence domains: Ribosomal protein S11
Structure domains: Ribosomal protein S11
Ribosomal protein RPS15 Chain: P
Molecule details ›
Chain: P
Length: 150 amino acids
Theoretical weight: 17.19 KDa
Source organism: Toxoplasma gondii
UniProt:
  • Canonical: B9PSN8 (Residues: 1-150; Coverage: 100%)
Gene names: BN1205_034990, TGVEG_213350
Sequence domains: Ribosomal protein S19
Ribosomal protein RPS16 Chain: Q
Molecule details ›
Chain: Q
Length: 148 amino acids
Theoretical weight: 16.59 KDa
Source organism: Toxoplasma gondii
UniProt:
  • Canonical: B6KC70 (Residues: 64-211; Coverage: 70%)
Gene name: TGVEG_263040
Sequence domains: Ribosomal protein S9/S16
Structure domains: Ribosomal Protein S5; domain 2
Ribosomal protein RPS17 Chain: R
Molecule details ›
Chain: R
Length: 132 amino acids
Theoretical weight: 15.26 KDa
Source organism: Toxoplasma gondii
UniProt:
  • Canonical: B9PXH2 (Residues: 1-132; Coverage: 100%)
Gene name: TGRH88_022800
Sequence domains: Ribosomal S17
Structure domains: Ribosomal protein S17e-like
40S ribosomal protein S18, putative Chain: S
Molecule details ›
Chain: S
Length: 156 amino acids
Theoretical weight: 17.76 KDa
Source organism: Toxoplasma gondii
UniProt:
  • Canonical: B9PMB3 (Residues: 1-156; Coverage: 100%)
Gene names: BN1205_065930, TGVEG_225080
Sequence domains: Ribosomal protein S13/S18
Structure domains: Helicase, Ruva Protein; domain 3
Ribosomal protein RPS19 Chain: T
Molecule details ›
Chain: T
Length: 160 amino acids
Theoretical weight: 18.41 KDa
Source organism: Toxoplasma gondii
UniProt:
  • Canonical: A0A125YMR9 (Residues: 154-313; Coverage: 51%)
Gene name: TGVEG_212290
Sequence domains: Ribosomal protein S19e
Small ribosomal subunit protein uS10 domain-containing protein Chain: U
Molecule details ›
Chain: U
Length: 233 amino acids
Theoretical weight: 25.94 KDa
Source organism: Toxoplasma gondii
UniProt:
  • Canonical: B6KQG9 (Residues: 1-233; Coverage: 100%)
Gene names: BN1205_053570, TGVEG_223050
Sequence domains: Ribosomal protein S10p/S20e
Structure domains: Ribosomal protein S10 domain
40S ribosomal protein S21 Chain: V
Molecule details ›
Chain: V
Length: 82 amino acids
Theoretical weight: 9.05 KDa
Source organism: Toxoplasma gondii
UniProt:
  • Canonical: A0A125YS47 (Residues: 1-82; Coverage: 100%)
Gene names: BN1205_075000, TGVEG_259240
Sequence domains: Ribosomal protein S21e
Structure domains: Hypothetical Cytosolic Protein; Chain: A;
Ribosomal protein RPS15A Chain: W
Molecule details ›
Chain: W
Length: 130 amino acids
Theoretical weight: 14.97 KDa
Source organism: Toxoplasma gondii
UniProt:
  • Canonical: A0A125YJX3 (Residues: 102-231; Coverage: 56%)
Gene name: TGVEG_234450
Sequence domains: Ribosomal protein S8
Structure domains:
Ribosomal protein RPS23 Chain: X
Molecule details ›
Chain: X
Length: 143 amino acids
Theoretical weight: 15.84 KDa
Source organism: Toxoplasma gondii
UniProt:
  • Canonical: B9PHL8 (Residues: 1-143; Coverage: 100%)
Gene names: BN1205_025830, TGVEG_229670
Sequence domains: Ribosomal protein S12/S23
40S ribosomal protein S24 Chain: Y
Molecule details ›
Chain: Y
Length: 135 amino acids
Theoretical weight: 15.23 KDa
Source organism: Toxoplasma gondii
UniProt:
  • Canonical: A0A125YKH1 (Residues: 133-267; Coverage: 51%)
Gene name: TGVEG_215460
Sequence domains: Ribosomal protein S24e
Structure domains: Alpha-Beta Plaits
40S ribosomal protein S25 Chain: Z
Molecule details ›
Chain: Z
Length: 161 amino acids
Theoretical weight: 18.71 KDa
Source organism: Toxoplasma gondii
UniProt:
  • Canonical: S7V273 (Residues: 1-161; Coverage: 100%)
Gene name: TGGT1_231140
Sequence domains: S25 ribosomal protein
40S ribosomal protein S26 Chain: a
Molecule details ›
Chain: a
Length: 112 amino acids
Theoretical weight: 12.75 KDa
Source organism: Toxoplasma gondii
UniProt:
  • Canonical: B9PP49 (Residues: 1-112; Coverage: 100%)
Gene names: BN1205_103450, TGVEG_243570
Sequence domains: Ribosomal protein S26e
Structure domains: Ribosomal protein S26e
Ribosomal protein RPS27 Chain: b
Molecule details ›
Chain: b
Length: 82 amino acids
Theoretical weight: 9.11 KDa
Source organism: Toxoplasma gondii
UniProt:
  • Canonical: A0A125YVX8 (Residues: 70-151; Coverage: 54%)
Gene name: TGVEG_217570
Sequence domains: Ribosomal protein S27
Structure domains: Zn-binding ribosomal proteins
Ribosomal protein RPS28 Chain: c
Molecule details ›
Chain: c
Length: 68 amino acids
Theoretical weight: 7.6 KDa
Source organism: Toxoplasma gondii
UniProt:
  • Canonical: A0A125YJ29 (Residues: 51-118; Coverage: 58%)
Gene name: TGVEG_209290
Sequence domains: Ribosomal protein S28e
Structure domains: Nucleic acid-binding proteins
40S ribosomal protein S29, putative Chain: d
Molecule details ›
Chain: d
Length: 54 amino acids
Theoretical weight: 6.53 KDa
Source organism: Toxoplasma gondii
UniProt:
  • Canonical: A0A0F7UYM7 (Residues: 1-54; Coverage: 100%)
Gene name: BN1205_102430
Sequence domains: Ribosomal protein S14p/S29e
Structure domains: 30s Ribosomal Protein S14; Chain N
40S ribosomal protein S30 Chain: e
Molecule details ›
Chain: e
Length: 59 amino acids
Theoretical weight: 6.62 KDa
Source organism: Toxoplasma gondii
UniProt:
  • Canonical: B9PTA0 (Residues: 1-59; Coverage: 100%)
Gene names: BN1205_084880, TGVEG_291850
Sequence domains: Ribosomal protein S30
Ubiquitin-like domain-containing protein Chain: f
Molecule details ›
Chain: f
Length: 154 amino acids
Theoretical weight: 17.35 KDa
Source organism: Toxoplasma gondii
UniProt:
  • Canonical: B9PQ37 (Residues: 1-154; Coverage: 100%)
Gene names: BN1205_006260, TGVEG_245620
Sequence domains:
60S ribosomal protein L41 Chain: m
Molecule details ›
Chain: m
Length: 39 amino acids
Theoretical weight: 5.12 KDa
Source organism: Toxoplasma gondii
UniProt:
  • Canonical: F0JB24 (Residues: 1-39; Coverage: 100%)
Gene names: BN1204_069470, NCLIV_069470
Sequence domains: Ribosomal protein L41
18S Ribosomal RNA Chain: 2
Molecule details ›
Chain: 2
Length: 1791 nucleotides
Theoretical weight: 576.63 KDa
Sequence domains: Eukaryotic small subunit ribosomal RNA

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.35Å
Relevant EMDB volumes: EMD-6780

Quick links

Citations

2 review citations

Structural Heterogeneities of the Ribosome: New Frontiers and Opportunities for Cryo-EM.
Poitevin et al. (2020)
1 more

5 mentions without citation

Cryo-EM structures of the 80S ribosomes from human parasites Trichomonas vaginalis and Toxoplasma gondii.
Li et al. (2017)
4 more