› 5xy3

Electron Microscopy
3.2Å resolution

Large subunit of Trichomonas vaginalis ribosome

Released:
DOI: 10.2210/pdb5xy3/pdb
PDB entry 5xy3 coloured by chain, front view.
PDB entry 5xy3 coloured by chain, side view.
PDB entry 5xy3 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-6784

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 43-mer (preferred)
PDBe Complex ID:
PDB-CPX-106823 (preferred)
Entry contents:
40 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (43 distinct):
Large ribosomal subunit protein uL2 C-terminal domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 251 amino acids
Theoretical weight: 26.95 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2E6Z8 (Residues: 1-251; Coverage: 100%)
Gene names: TVAG_005910, TVAG_104490, TVAG_371270, TVAG_484180, TVAG_487750
Sequence domains:
60S ribosomal protein L3 Chain: B
Molecule details ›
Chain: B
Length: 415 amino acids
Theoretical weight: 46.9 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2DD62 (Residues: 1-415; Coverage: 100%)
Gene names: TVAG_013060, TVAG_059650, TVAG_124190
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 C-terminal domain-containing protein Chain: C
Molecule details ›
Chain: C
Length: 370 amino acids
Theoretical weight: 40.32 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2E4D0 (Residues: 1-370; Coverage: 100%)
Gene names: TVAG_128790, TVAG_189110
Sequence domains:
Large ribosomal subunit protein uL18 C-terminal eukaryotes domain-containing protein Chain: D
Molecule details ›
Chain: D
Length: 308 amino acids
Theoretical weight: 34.93 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2DNM5 (Residues: 1-308; Coverage: 100%)
Gene name: TVAG_113720
Sequence domains:
60S ribosomal protein L6, putative Chain: E
Molecule details ›
Chain: E
Length: 151 amino acids
Theoretical weight: 16.05 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2FXW1 (Residues: 1-151; Coverage: 100%)
Gene name: TVAG_099510
Ribosomal protein L30p/L7e, putative Chain: F
Molecule details ›
Chain: F
Length: 239 amino acids
Theoretical weight: 26.84 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2F592 (Residues: 1-239; Coverage: 100%)
Gene name: TVAG_159370
Sequence domains:
60S ribosomal protein L7a Chain: G
Molecule details ›
Chain: G
Length: 244 amino acids
Theoretical weight: 27.6 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2ET60 (Residues: 1-244; Coverage: 100%)
Gene name: TVAG_009840
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Ribosomal protein L6, putative Chain: H
Molecule details ›
Chain: H
Length: 197 amino acids
Theoretical weight: 22.93 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2DDT1 (Residues: 1-197; Coverage: 100%)
Gene names: TVAG_054500, TVAG_198960, TVAG_255140, TVAG_297470
Ribosomal protein, putative Chain: I
Molecule details ›
Chain: I
Length: 209 amino acids
Theoretical weight: 23.8 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2FVZ6 (Residues: 1-209; Coverage: 100%)
Gene name: TVAG_232820
Sequence domains: Ribosomal protein L16p/L10e
60S ribosomal protein L11, putative Chain: J
Molecule details ›
Chain: J
Length: 169 amino acids
Theoretical weight: 19.37 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2E7L8 (Residues: 1-169; Coverage: 100%)
Gene names: TVAG_044560, TVAG_046840, TVAG_092870, TVAG_194850, TVAG_343970
Sequence domains:
Ribosomal protein L13e, putative Chain: L
Molecule details ›
Chain: L
Length: 189 amino acids
Theoretical weight: 21.87 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2G4E1 (Residues: 1-189; Coverage: 100%)
Gene name: TVAG_112230
Sequence domains: Ribosomal protein L13e
Large ribosomal subunit protein eL14 domain-containing protein Chain: M
Molecule details ›
Chain: M
Length: 128 amino acids
Theoretical weight: 14.73 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2DZ49 (Residues: 1-128; Coverage: 100%)
Gene name: TVAG_026460
Sequence domains: Ribosomal protein L14
Ribosomal protein L15 Chain: N
Molecule details ›
Chain: N
Length: 204 amino acids
Theoretical weight: 24.32 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2ECR7 (Residues: 1-204; Coverage: 100%)
Gene names: TVAG_148950, TVAG_200220, TVAG_276360
Sequence domains: Ribosomal L15
Ribosomal protein L13, putative Chain: O
Molecule details ›
Chain: O
Length: 200 amino acids
Theoretical weight: 22.57 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2DZ26 (Residues: 1-200; Coverage: 100%)
Gene name: TVAG_026230
Sequence domains: Ribosomal protein L13
Ribosomal protein L22, putative Chain: P
Molecule details ›
Chain: P
Length: 164 amino acids
Theoretical weight: 18.53 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2DM53 (Residues: 1-164; Coverage: 100%)
Gene names: TVAG_083260, TVAG_109440, TVAG_296170, TVAG_473910
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein uL15/eL18 domain-containing protein Chain: Q
Molecule details ›
Chain: Q
Length: 186 amino acids
Theoretical weight: 21.12 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2D7Q5 (Residues: 1-186; Coverage: 100%)
Gene names: TVAG_121100, TVAG_395470
Sequence domains: Ribosomal protein 60S L18 and 50S L18e
Large ribosomal subunit protein eL19 domain-containing protein Chain: R
Molecule details ›
Chain: R
Length: 178 amino acids
Theoretical weight: 21.06 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2D8G1 (Residues: 1-178; Coverage: 100%)
Gene names: TVAG_006170, TVAG_185160, TVAG_185170, TVAG_185180
Sequence domains: Ribosomal protein L19e
60S ribosomal protein L18a Chain: S
Molecule details ›
Chain: S
Length: 176 amino acids
Theoretical weight: 19.85 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2EP03 (Residues: 1-176; Coverage: 100%)
Gene name: TVAG_263760
Sequence domains: Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A
Ribosomal protein L21e, putative Chain: T
Molecule details ›
Chain: T
Length: 159 amino acids
Theoretical weight: 17.91 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2F2S5 (Residues: 1-159; Coverage: 100%)
Gene name: TVAG_231250
Sequence domains: Ribosomal protein L21e
Large ribosomal subunit protein eL22 Chain: U
Molecule details ›
Chain: U
Length: 106 amino acids
Theoretical weight: 12.24 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2DNV5 (Residues: 1-106; Coverage: 100%)
Gene names: TVAG_057020, TVAG_225760
Sequence domains: Ribosomal L22e protein family
60S ribosomal protein L23, putative Chain: V
Molecule details ›
Chain: V
Length: 140 amino acids
Theoretical weight: 14.84 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2DP51 (Residues: 1-140; Coverage: 100%)
Gene names: TVAG_015800, TVAG_024110, TVAG_074940, TVAG_345430, TVAG_345440, TVAG_345450
Sequence domains: Ribosomal protein L14p/L23e
Ribosomal protein L24e, putative Chain: W
Molecule details ›
Chain: W
Length: 113 amino acids
Theoretical weight: 13.28 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2DJQ1 (Residues: 1-113; Coverage: 100%)
Gene names: TVAG_101690, TVAG_190290, TVAG_324900, TVAG_431350
Sequence domains: Ribosomal protein L24e
Ribosomal protein L23, putative Chain: X
Molecule details ›
Chain: X
Length: 140 amino acids
Theoretical weight: 15.58 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2DUV8 (Residues: 1-140; Coverage: 100%)
Gene name: TVAG_160160
Sequence domains: Ribosomal protein L23
Ribosomal protein L24, putative Chain: Y
Molecule details ›
Chain: Y
Length: 138 amino acids
Theoretical weight: 15.78 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2DKF2 (Residues: 1-138; Coverage: 100%)
Gene name: TVAG_190230
Sequence domains: Ribosomal proteins L26 eukaryotic, L24P archaeal
Ribosomal protein L27e, putative Chain: Z
Molecule details ›
Chain: Z
Length: 139 amino acids
Theoretical weight: 15.95 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2DNC1 (Residues: 1-139; Coverage: 100%)
Gene names: TVAG_140290, TVAG_215980, TVAG_302830, TVAG_306310, TVAG_337950
Sequence domains: Ribosomal L27e protein family
Large ribosomal subunit protein uL15/eL18 domain-containing protein Chain: a
Molecule details ›
Chain: a
Length: 151 amino acids
Theoretical weight: 17.01 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2DHU7 (Residues: 1-151; Coverage: 100%)
Gene names: TVAG_121550, TVAG_300490, TVAG_346410, TVAG_401890
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
60S ribosomal protein L29 Chain: b
Molecule details ›
Chain: b
Length: 58 amino acids
Theoretical weight: 6.82 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2DM33 (Residues: 1-58; Coverage: 100%)
Gene names: TVAG_083040, TVAG_158840, TVAG_451230
Sequence domains: Ribosomal L29e protein family
Ribosomal protein eL8/eL30/eS12/Gadd45 domain-containing protein Chain: c
Molecule details ›
Chain: c
Length: 112 amino acids
Theoretical weight: 12.32 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2E6Z9 (Residues: 1-112; Coverage: 100%)
Gene names: TVAG_005920, TVAG_213810
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Ribosomal protein L31e, putative Chain: d
Molecule details ›
Chain: d
Length: 110 amino acids
Theoretical weight: 12.45 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2D9N8 (Residues: 1-110; Coverage: 100%)
Gene names: TVAG_076410, TVAG_262240
Sequence domains: Ribosomal protein L31e
Ribosomal protein L32, putative Chain: e
Molecule details ›
Chain: e
Length: 132 amino acids
Theoretical weight: 15.25 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2F2J0 (Residues: 1-132; Coverage: 100%)
Gene names: TVAG_265930, TVAG_265950
Sequence domains: Ribosomal protein L32
Ribosomal protein L35Ae, putative Chain: f
Molecule details ›
Chain: f
Length: 102 amino acids
Theoretical weight: 11.67 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2DSF3 (Residues: 1-102; Coverage: 100%)
Gene name: TVAG_067370
Sequence domains: Ribosomal protein L35Ae
Large ribosomal subunit protein eL34 Chain: g
Molecule details ›
Chain: g
Length: 116 amino acids
Theoretical weight: 13.35 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2FWA1 (Residues: 1-116; Coverage: 100%)
Gene names: TVAG_094720, TVAG_094730
Sequence domains: Ribosomal protein L34e
Ribosomal protein L29, putative Chain: h
Molecule details ›
Chain: h
Length: 124 amino acids
Theoretical weight: 14.3 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2E6R2 (Residues: 1-124; Coverage: 100%)
Gene name: TVAG_158830
Sequence domains: Ribosomal L29 protein
Ribosomal protein L36e, putative Chain: i
Molecule details ›
Chain: i
Length: 91 amino acids
Theoretical weight: 10.94 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2EXW7 (Residues: 1-91; Coverage: 100%)
Gene names: TVAG_020530, TVAG_027320, TVAG_207430
Sequence domains: Ribosomal protein L36e
Ribosomal protein L37 Chain: j
Molecule details ›
Chain: j
Length: 81 amino acids
Theoretical weight: 9.36 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2F8Y8 (Residues: 1-81; Coverage: 100%)
Gene names: TVAG_005760, TVAG_339320
Sequence domains: Ribosomal protein L37e
Ribosomal protein L38e, putative Chain: k
Molecule details ›
Chain: k
Length: 74 amino acids
Theoretical weight: 8.47 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2FFH9 (Residues: 1-74; Coverage: 100%)
Gene name: TVAG_066460
Sequence domains: Ribosomal L38e protein family
60S ribosomal protein L39, putative Chain: l
Molecule details ›
Chain: l
Length: 51 amino acids
Theoretical weight: 6.3 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2D9N4 (Residues: 1-51; Coverage: 100%)
Gene names: TVAG_050420, TVAG_076370, TVAG_174110, TVAG_224370, TVAG_246600
Sequence domains: Ribosomal L39 protein
Ubiquitin-like domain-containing protein Chain: m
Molecule details ›
Chain: m
Length: 132 amino acids
Theoretical weight: 15.1 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2DGL5 (Residues: 35-166; Coverage: 80%)
Gene name: TVAG_110140
Sequence domains:
60S ribosomal protein L44, putative Chain: o
Molecule details ›
Chain: o
Length: 104 amino acids
Theoretical weight: 12.47 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2DAI6 (Residues: 1-104; Coverage: 100%)
Gene names: TVAG_034660, TVAG_035120, TVAG_083470, TVAG_126180, TVAG_136040, TVAG_276010, TVAG_470540, TVAG_485680
Sequence domains: Ribosomal protein L44
60S ribosomal protein L37a Chain: p
Molecule details ›
Chain: p
Length: 92 amino acids
Theoretical weight: 10.05 KDa
Source organism: Trichomonas vaginalis
UniProt:
  • Canonical: A2DEM7 (Residues: 1-92; Coverage: 100%)
Gene names: TVAG_083700, TVAG_083720, TVAG_099020, TVAG_124410, TVAG_212620, TVAG_283240
Sequence domains: Ribosomal L37ae protein family
25S ribosomal RNA Chain: 1
Molecule details ›
Chain: 1
Length: 2765 nucleotides
Theoretical weight: 892.22 KDa
Sequence domains: Eukaryotic large subunit ribosomal RNA
5S ribosomal RNA Chain: 3
Molecule details ›
Chain: 3
Length: 118 nucleotides
Theoretical weight: 37.96 KDa
Sequence domains: 5S ribosomal RNA
5.8S ribosomal RNA Chain: 4
Molecule details ›
Chain: 4
Length: 162 nucleotides
Theoretical weight: 52.17 KDa
Sequence domains: 5.8S ribosomal RNA

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.2Å
Relevant EMDB volumes: EMD-6784

Quick links

Citations

2 review citations

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

4 mentions without citation

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