› 5xyi

Electron Microscopy
3.35Å resolution

Small subunit of Trichomonas vaginalis ribosome

Released:
DOI: 10.2210/pdb5xyi/pdb
PDB entry 5xyi coloured by chain, front view.
PDB entry 5xyi coloured by chain, side view.
PDB entry 5xyi coloured by chain, top view.
Source organism: Trichomonas vaginalis
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-6788

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-106824 (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: 256 amino acids
Theoretical weight: 28.58 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2EFE7 (Residues: 1-256; Coverage: 100%)
Gene names: TVAG_240050, TVAG_474410
Sequence domains: Ribosomal protein S2
Structure domains: Glucose-6-phosphate isomerase like protein; domain 1
Ribosomal protein S3Ae, putative Chain: B
Molecule details ›
Chain: B
Length: 247 amino acids
Theoretical weight: 28.09 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2G9Z8 (Residues: 1-247; Coverage: 100%)
Gene name: TVAG_047460
Sequence domains: Ribosomal S3Ae family
S5 DRBM domain-containing protein Chain: C
Molecule details ›
Chain: C
Length: 272 amino acids
Theoretical weight: 30.08 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2EHK3 (Residues: 1-272; Coverage: 100%)
Gene name: TVAG_142440
Sequence domains:
Structure domains:
40S ribosomal protein S3 Chain: D
Molecule details ›
Chain: D
Length: 216 amino acids
Theoretical weight: 24.51 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2DIM3 (Residues: 1-216; Coverage: 100%)
Gene names: TVAG_106800, TVAG_178710, TVAG_263040, TVAG_314710, TVAG_420140, TVAG_462690
Sequence domains:
Structure domains:
40S ribosomal protein S4 Chain: E
Molecule details ›
Chain: E
Length: 255 amino acids
Theoretical weight: 28.59 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2FC75 (Residues: 1-255; Coverage: 100%)
Gene name: TVAG_335480
Sequence domains:
Structure domains:
Small ribosomal subunit protein uS7 domain-containing protein Chain: F
Molecule details ›
Chain: F
Length: 193 amino acids
Theoretical weight: 21.67 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2E4S6 (Residues: 1-193; Coverage: 100%)
Gene name: TVAG_246200
Sequence domains: Ribosomal protein S7p/S5e
Structure domains: Ribosomal protein S7 domain
40S ribosomal protein S6 Chain: G
Molecule details ›
Chain: G
Length: 216 amino acids
Theoretical weight: 24.58 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2DEJ9 (Residues: 1-216; Coverage: 100%)
Gene names: TVAG_033590, TVAG_282960, TVAG_462810, TVAG_486930
Sequence domains: Ribosomal protein S6e
40S ribosomal protein S7 Chain: H
Molecule details ›
Chain: H
Length: 168 amino acids
Theoretical weight: 18.71 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2G5X6 (Residues: 1-168; Coverage: 100%)
Gene names: TVAG_143030, TVAG_375490
Sequence domains: Ribosomal protein S7e
40S ribosomal protein S8 Chain: I
Molecule details ›
Chain: I
Length: 197 amino acids
Theoretical weight: 22.12 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2E1L5 (Residues: 1-197; Coverage: 100%)
Gene names: TVAG_066030, TVAG_164160, TVAG_206300, TVAG_435430
Sequence domains: Ribosomal protein S8e
Small ribosomal subunit protein uS4 N-terminal domain-containing protein Chain: J
Molecule details ›
Chain: J
Length: 185 amino acids
Theoretical weight: 21.81 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2DNY3 (Residues: 1-185; Coverage: 100%)
Gene names: TVAG_010560, TVAG_495360
Sequence domains:
Plectin/eS10 N-terminal domain-containing protein Chain: K
Molecule details ›
Chain: K
Length: 141 amino acids
Theoretical weight: 16.25 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2EBA2 (Residues: 1-141; Coverage: 100%)
Gene name: TVAG_329340
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: 155 amino acids
Theoretical weight: 18.02 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2DHU8 (Residues: 1-155; Coverage: 100%)
Gene names: TVAG_113950, TVAG_131850, TVAG_313300, TVAG_401900, TVAG_419520
Sequence domains:
Structure domains: OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Ribosomal protein eL8/eL30/eS12/Gadd45 domain-containing protein Chain: M
Molecule details ›
Chain: M
Length: 124 amino acids
Theoretical weight: 13.71 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2FA40 (Residues: 1-124; Coverage: 100%)
Gene name: TVAG_010250
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Small ribosomal subunit protein uS15 N-terminal domain-containing protein Chain: N
Molecule details ›
Chain: N
Length: 151 amino acids
Theoretical weight: 17.07 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2D9L2 (Residues: 1-151; Coverage: 100%)
Gene names: TVAG_066760, TVAG_076150, TVAG_151780, TVAG_459150
Sequence domains:
Structure domains: S15/NS1, RNA-binding
Ribosomal protein S14 Chain: O
Molecule details ›
Chain: O
Length: 159 amino acids
Theoretical weight: 16.69 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: Q76KS8 (Residues: 1-159; Coverage: 100%)
Sequence domains: Ribosomal protein S11
Structure domains: Ribosomal protein S11
Ribosomal protein S19, putative Chain: P
Molecule details ›
Chain: P
Length: 144 amino acids
Theoretical weight: 16.29 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2DVD8 (Residues: 1-144; Coverage: 100%)
Gene names: TVAG_055940, TVAG_074310, TVAG_126060, TVAG_208960
Sequence domains: Ribosomal protein S19
40S ribosomal protein S16, putative Chain: Q
Molecule details ›
Chain: Q
Length: 140 amino acids
Theoretical weight: 15.63 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2D919 (Residues: 1-140; Coverage: 100%)
Gene names: TVAG_020040, TVAG_036220, TVAG_036300, TVAG_094760, TVAG_156650, TVAG_182810
Sequence domains: Ribosomal protein S9/S16
Structure domains: Ribosomal Protein S5; domain 2
40S ribosomal protein S17-B, putative Chain: R
Molecule details ›
Chain: R
Length: 129 amino acids
Theoretical weight: 14.96 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2DPS3 (Residues: 1-129; Coverage: 100%)
Gene names: TVAG_040820, TVAG_258150, TVAG_453470, TVAG_474010
Sequence domains: Ribosomal S17
Structure domains: Ribosomal protein S17e-like
Ribosomal protein S13p/S18e, putative Chain: S
Molecule details ›
Chain: S
Length: 155 amino acids
Theoretical weight: 17.56 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2DTR8 (Residues: 1-155; Coverage: 100%)
Gene names: TVAG_020480, TVAG_065040, TVAG_184530, TVAG_341090, TVAG_419040, TVAG_487360, TVAG_487930
Sequence domains: Ribosomal protein S13/S18
Structure domains: Helicase, Ruva Protein; domain 3
Ribosomal protein S19e, putative Chain: T
Molecule details ›
Chain: T
Length: 148 amino acids
Theoretical weight: 16.58 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2EG54 (Residues: 1-148; Coverage: 100%)
Gene names: TVAG_352520, TVAG_352560, TVAG_352580, TVAG_352600
Sequence domains: Ribosomal protein S19e
Small ribosomal subunit protein uS10 domain-containing protein Chain: U
Molecule details ›
Chain: U
Length: 123 amino acids
Theoretical weight: 13.93 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2FDE0 (Residues: 1-123; Coverage: 100%)
Gene name: TVAG_086300
Sequence domains: Ribosomal protein S10p/S20e
Structure domains: Ribosomal protein S10 domain
40S ribosomal protein S21 Chain: V
Molecule details ›
Chain: V
Length: 89 amino acids
Theoretical weight: 9.85 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2FFS8 (Residues: 1-89; Coverage: 100%)
Gene name: TVAG_022100
Sequence domains: Ribosomal protein S21e
Structure domains: Hypothetical Cytosolic Protein; Chain: A;
Ribosomal protein S15a Chain: W
Molecule details ›
Chain: W
Length: 130 amino acids
Theoretical weight: 14.58 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2DLW4 (Residues: 1-130; Coverage: 100%)
Gene names: TVAG_006250, TVAG_462530
Sequence domains: Ribosomal protein S8
Structure domains:
40S ribosomal protein S23, putative Chain: X
Molecule details ›
Chain: X
Length: 144 amino acids
Theoretical weight: 15.59 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2D895 (Residues: 1-144; Coverage: 100%)
Gene names: TVAG_071920, TVAG_109530, TVAG_109730, TVAG_159830, TVAG_198620, TVAG_249090, TVAG_305300, TVAG_430260
Sequence domains: Ribosomal protein S12/S23
Ribosomal protein S24e, putative Chain: Y
Molecule details ›
Chain: Y
Length: 140 amino acids
Theoretical weight: 16.07 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2F0H5 (Residues: 1-140; Coverage: 100%)
Gene names: TVAG_272960, TVAG_272970, TVAG_272980, TVAG_386300
Sequence domains: Ribosomal protein S24e
Structure domains: Alpha-Beta Plaits
40S ribosomal protein S25 Chain: Z
Molecule details ›
Chain: Z
Length: 115 amino acids
Theoretical weight: 12.65 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2ER97 (Residues: 1-115; Coverage: 100%)
Gene name: TVAG_226630
Sequence domains: S25 ribosomal protein
40S ribosomal protein S26 Chain: a
Molecule details ›
Chain: a
Length: 118 amino acids
Theoretical weight: 13.89 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2DST7 (Residues: 1-118; Coverage: 100%)
Gene names: TVAG_040120, TVAG_061920, TVAG_164600, TVAG_242190, TVAG_277940, TVAG_302160, TVAG_333200, TVAG_335820, TVAG_347960
Sequence domains: Ribosomal protein S26e
Structure domains: Ribosomal protein S26e
40S ribosomal protein S27 Chain: b
Molecule details ›
Chain: b
Length: 86 amino acids
Theoretical weight: 9.47 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2FBZ2 (Residues: 1-86; Coverage: 100%)
Gene name: TVAG_064320
Sequence domains: Ribosomal protein S27
Structure domains: Zn-binding ribosomal proteins
40S ribosomal protein S28 Chain: c
Molecule details ›
Chain: c
Length: 68 amino acids
Theoretical weight: 7.65 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2DQN8 (Residues: 1-68; Coverage: 100%)
Gene names: TVAG_050990, TVAG_057380, TVAG_266850, TVAG_272940, TVAG_272950, TVAG_327180
Sequence domains: Ribosomal protein S28e
Structure domains: Nucleic acid-binding proteins
40S ribosomal protein S29, putative Chain: d
Molecule details ›
Chain: d
Length: 57 amino acids
Theoretical weight: 6.84 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2DYA8 (Residues: 1-57; Coverage: 100%)
Gene names: TVAG_107660, TVAG_131520, TVAG_357220, TVAG_366620, TVAG_393120, TVAG_490210
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: 62 amino acids
Theoretical weight: 6.92 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2FHY5 (Residues: 1-62; Coverage: 100%)
Gene name: TVAG_222910
Sequence domains: Ribosomal protein S30
Guanine nucleotide-binding protein beta subunit, putative Chain: g
Molecule details ›
Chain: g
Length: 335 amino acids
Theoretical weight: 37.15 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2ELV7 (Residues: 1-335; Coverage: 100%)
Gene name: TVAG_151920
Sequence domains: WD domain, G-beta repeat
Structure domains: YVTN repeat-like/Quinoprotein amine dehydrogenase
Small ribosomal subunit protein eS32A Chain: n
Molecule details ›
Chain: n
Length: 25 amino acids
Theoretical weight: 3.35 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: P0CX86 (Residues: 1-25; Coverage: 100%)
Gene names: D1290, RPL41A, RPL47A, YDL184C, YL41A
Sequence domains: Ribosomal protein L41
18S Chain: 2
Molecule details ›
Chain: 2
Length: 1577 nucleotides
Theoretical weight: 508.66 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-6788

Quick links

Citations

2 review citations

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

3 mentions without citation

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