5XY3 image
Deposition Date 2017-07-06
Release Date 2017-08-30
Last Version Date 2024-10-16
Entry Detail
PDB ID:
5XY3
Keywords:
Title:
Large subunit of Trichomonas vaginalis ribosome
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
3.20 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:25S ribosomal RNA
Chain IDs:A (auth: 1)
Chain Length:2765
Number of Molecules:1
Biological Source:Trichomonas vaginalis
Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:B (auth: 3)
Chain Length:118
Number of Molecules:1
Biological Source:Trichomonas vaginalis
Polymer Type:polyribonucleotide
Molecule:5.8S ribosomal RNA
Chain IDs:C (auth: 4)
Chain Length:162
Number of Molecules:1
Biological Source:Trichomonas vaginalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L8, putative
Gene (Uniprot):TVAG_005910, TVAG_104490, TVAG_371270, TVAG_484180, TVAG_487750
Chain IDs:D (auth: A)
Chain Length:151
Number of Molecules:1
Biological Source:Trichomonas vaginalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Uncharacterized protein
Gene (Uniprot):TVAG_013060, TVAG_059650, TVAG_124190
Chain IDs:E (auth: B)
Chain Length:58
Number of Molecules:1
Biological Source:Trichomonas vaginalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein, putative
Gene (Uniprot):TVAG_128790, TVAG_189110
Chain IDs:F (auth: C)
Chain Length:370
Number of Molecules:1
Biological Source:Trichomonas vaginalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L5
Gene (Uniprot):TVAG_113720
Chain IDs:G (auth: D)
Chain Length:110
Number of Molecules:1
Biological Source:Trichomonas vaginalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L6, putative
Gene (Uniprot):TVAG_099510
Chain IDs:H (auth: E)
Chain Length:132
Number of Molecules:1
Biological Source:Trichomonas vaginalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L30p/L7e, putative
Gene (Uniprot):TVAG_159370
Chain IDs:I (auth: F)
Chain Length:102
Number of Molecules:1
Biological Source:Trichomonas vaginalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L7Ae, putative
Gene (Uniprot):TVAG_009840
Chain IDs:J (auth: G)
Chain Length:116
Number of Molecules:1
Biological Source:Trichomonas vaginalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L6, putative
Gene (Uniprot):TVAG_054500, TVAG_198960, TVAG_255140, TVAG_297470
Chain IDs:K (auth: H)
Chain Length:124
Number of Molecules:1
Biological Source:Trichomonas vaginalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein, putative
Gene (Uniprot):TVAG_232820
Chain IDs:L (auth: I)
Chain Length:209
Number of Molecules:1
Biological Source:Trichomonas vaginalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L11, putative
Gene (Uniprot):TVAG_044560, TVAG_046840, TVAG_092870, TVAG_194850, TVAG_343970
Chain IDs:M (auth: J)
Chain Length:81
Number of Molecules:1
Biological Source:Trichomonas vaginalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L13e, putative
Gene (Uniprot):TVAG_112230
Chain IDs:N (auth: L)
Chain Length:51
Number of Molecules:1
Biological Source:Trichomonas vaginalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L14, putative
Gene (Uniprot):TVAG_026460
Chain IDs:O (auth: M)
Chain Length:128
Number of Molecules:1
Biological Source:Trichomonas vaginalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L15
Gene (Uniprot):TVAG_148950, TVAG_200220, TVAG_276360
Chain IDs:P (auth: N)
Chain Length:204
Number of Molecules:1
Biological Source:Trichomonas vaginalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L13, putative
Gene (Uniprot):TVAG_026230
Chain IDs:Q (auth: O)
Chain Length:104
Number of Molecules:1
Biological Source:Trichomonas vaginalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L22, putative
Gene (Uniprot):TVAG_083260, TVAG_109440, TVAG_296170, TVAG_473910
Chain IDs:R (auth: P)
Chain Length:92
Number of Molecules:1
Biological Source:Trichomonas vaginalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18, putative
Gene (Uniprot):TVAG_121100, TVAG_395470
Chain IDs:S (auth: Q)
Chain Length:186
Number of Molecules:1
Biological Source:Trichomonas vaginalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L19-3, putative
Gene (Uniprot):TVAG_006170, TVAG_185160, TVAG_185170, TVAG_185180
Chain IDs:T (auth: R)
Chain Length:178
Number of Molecules:1
Biological Source:Trichomonas vaginalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18a
Gene (Uniprot):TVAG_263760
Chain IDs:U (auth: S)
Chain Length:176
Number of Molecules:1
Biological Source:Trichomonas vaginalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L21e, putative
Gene (Uniprot):TVAG_231250
Chain IDs:V (auth: T)
Chain Length:159
Number of Molecules:1
Biological Source:Trichomonas vaginalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L22-1, putative
Gene (Uniprot):TVAG_057020, TVAG_225760
Chain IDs:W (auth: U)
Chain Length:106
Number of Molecules:1
Biological Source:Trichomonas vaginalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L23, putative
Gene (Uniprot):TVAG_015800, TVAG_024110, TVAG_074940, TVAG_345430, TVAG_345440, TVAG_345450
Chain IDs:X (auth: V)
Chain Length:140
Number of Molecules:1
Biological Source:Trichomonas vaginalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L24e, putative
Gene (Uniprot):TVAG_101690, TVAG_190290, TVAG_324900, TVAG_431350
Chain IDs:Y (auth: W)
Chain Length:113
Number of Molecules:1
Biological Source:Trichomonas vaginalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L23, putative
Gene (Uniprot):TVAG_160160
Chain IDs:Z (auth: X)
Chain Length:140
Number of Molecules:1
Biological Source:Trichomonas vaginalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L24, putative
Gene (Uniprot):TVAG_190230
Chain IDs:AA (auth: Y)
Chain Length:138
Number of Molecules:1
Biological Source:Trichomonas vaginalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L27e, putative
Gene (Uniprot):TVAG_140290, TVAG_215980, TVAG_302830, TVAG_306310, TVAG_337950
Chain IDs:BA (auth: Z)
Chain Length:139
Number of Molecules:1
Biological Source:Trichomonas vaginalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Uncharacterized protein
Gene (Uniprot):TVAG_121550, TVAG_300490, TVAG_346410, TVAG_401890
Chain IDs:CA (auth: a)
Chain Length:151
Number of Molecules:1
Biological Source:Trichomonas vaginalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L29
Gene (Uniprot):TVAG_083040, TVAG_158840, TVAG_451230
Chain IDs:DA (auth: b)
Chain Length:58
Number of Molecules:1
Biological Source:Trichomonas vaginalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L30, putative
Gene (Uniprot):TVAG_005920, TVAG_213810
Chain IDs:EA (auth: c)
Chain Length:370
Number of Molecules:1
Biological Source:Trichomonas vaginalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L31e, putative
Gene (Uniprot):TVAG_076410, TVAG_262240
Chain IDs:FA (auth: d)
Chain Length:110
Number of Molecules:1
Biological Source:Trichomonas vaginalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L32, putative
Gene (Uniprot):TVAG_265930, TVAG_265950
Chain IDs:GA (auth: e)
Chain Length:132
Number of Molecules:1
Biological Source:Trichomonas vaginalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L35Ae, putative
Gene (Uniprot):TVAG_067370
Chain IDs:HA (auth: f)
Chain Length:102
Number of Molecules:1
Biological Source:Trichomonas vaginalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L34e, putative
Gene (Uniprot):TVAG_094720, TVAG_094730
Chain IDs:IA (auth: g)
Chain Length:116
Number of Molecules:1
Biological Source:Trichomonas vaginalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L29, putative
Gene (Uniprot):TVAG_158830
Chain IDs:JA (auth: h)
Chain Length:124
Number of Molecules:1
Biological Source:Trichomonas vaginalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L36e, putative
Gene (Uniprot):TVAG_020530, TVAG_027320, TVAG_207430
Chain IDs:KA (auth: i)
Chain Length:209
Number of Molecules:1
Biological Source:Trichomonas vaginalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L37
Gene (Uniprot):TVAG_005760, TVAG_339320
Chain IDs:LA (auth: j)
Chain Length:81
Number of Molecules:1
Biological Source:Trichomonas vaginalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L38e, putative
Gene (Uniprot):TVAG_066460
Chain IDs:MA (auth: k)
Chain Length:74
Number of Molecules:1
Biological Source:Trichomonas vaginalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L39, putative
Gene (Uniprot):TVAG_050420, TVAG_076370, TVAG_174110, TVAG_224370, TVAG_246600
Chain IDs:NA (auth: l)
Chain Length:51
Number of Molecules:1
Biological Source:Trichomonas vaginalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ubiquitin, putative
Gene (Uniprot):TVAG_110140
Chain IDs:OA (auth: m)
Chain Length:128
Number of Molecules:1
Biological Source:Trichomonas vaginalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L44, putative
Gene (Uniprot):TVAG_034660, TVAG_035120, TVAG_083470, TVAG_126180, TVAG_136040, TVAG_276010, TVAG_470540, TVAG_485680
Chain IDs:PA (auth: o)
Chain Length:104
Number of Molecules:1
Biological Source:Trichomonas vaginalis
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Uncharacterized protein
Gene (Uniprot):TVAG_083700, TVAG_083720, TVAG_099020, TVAG_124410, TVAG_212620, TVAG_283240
Chain IDs:QA (auth: p)
Chain Length:92
Number of Molecules:1
Biological Source:Trichomonas vaginalis
Ligand Molecules
Primary Citation
Cryo-EM structures of the 80S ribosomes from human parasites Trichomonas vaginalis and Toxoplasma gondii
Cell Res. 27 1275 1288 (2017)
PMID: 28809395 DOI: 10.1038/cr.2017.104

Abstact

As an indispensable molecular machine universal in all living organisms, the ribosome has been selected by evolution to be the natural target of many antibiotics and small-molecule inhibitors. High-resolution structures of pathogen ribosomes are crucial for understanding the general and unique aspects of translation control in disease-causing microbes. With cryo-electron microscopy technique, we have determined structures of the cytosolic ribosomes from two human parasites, Trichomonas vaginalis and Toxoplasma gondii, at resolution of 3.2-3.4 Å. Although the ribosomal proteins from both pathogens are typical members of eukaryotic families, with a co-evolution pattern between certain species-specific insertions/extensions and neighboring ribosomal RNA (rRNA) expansion segments, the sizes of their rRNAs are sharply different. Very interestingly, rRNAs of T. vaginalis are in size comparable to prokaryotic counterparts, with nearly all the eukaryote-specific rRNA expansion segments missing. These structures facilitate the dissection of evolution path for ribosomal proteins and RNAs, and may aid in design of novel translation inhibitors.

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Disease

Primary Citation of related structures