5XXB image
Entry Detail
PDB ID:
5XXB
EMDB ID:
Keywords:
Title:
Large subunit of Toxoplasma gondii ribosome
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2017-07-03
Release Date:
2017-08-30
Method Details:
Experimental Method:
Resolution:
3.17 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polyribonucleotide
Description:25S RNA
Chain IDs:A (auth: 1)
Chain Length:3477
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Description:5S RNA
Chain IDs:B (auth: 3)
Chain Length:124
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polyribonucleotide
Description:5.8S RNA
Chain IDs:C (auth: 4)
Chain Length:158
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Ribosomal protein uL2
Chain IDs:D (auth: A)
Chain Length:54
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Ribosomal protein uL3
Chain IDs:E (auth: B)
Chain Length:108
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Ribosomal protein uL4
Chain IDs:F (auth: C)
Chain Length:120
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Ribosomal protein uL18
Chain IDs:G (auth: D)
Chain Length:134
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Ribosomal protein eL6
Chain IDs:H (auth: E)
Chain Length:112
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Ribosomal protein uL30
Chain IDs:I (auth: F)
Chain Length:258
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Ribosomal protein eL8
Chain IDs:J (auth: G)
Chain Length:123
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Ribosomal protein uL6
Chain IDs:K (auth: H)
Chain Length:101
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Ribosomal protein uL16
Chain IDs:L (auth: I)
Chain Length:221
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Ribosomal protein uL5
Chain IDs:M (auth: J)
Chain Length:84
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Ribosomal protein eL13
Chain IDs:N (auth: K)
Chain Length:51
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Ribosomal protein eL14
Chain IDs:O (auth: L)
Chain Length:134
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Ribosomal protein eL15
Chain IDs:P (auth: M)
Chain Length:205
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Ribosomal protein uL13
Chain IDs:Q (auth: N)
Chain Length:269
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Ribosomal protein uL22
Chain IDs:R (auth: O)
Chain Length:96
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Ribosomal protein eL18
Chain IDs:S (auth: P)
Chain Length:129
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Ribosomal protein eL19
Chain IDs:T (auth: Q)
Chain Length:187
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Ribosomal protein eL20
Chain IDs:U (auth: R)
Chain Length:183
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Ribosomal protein eL21
Chain IDs:V (auth: S)
Chain Length:157
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Ribosomal protein eL22
Chain IDs:W (auth: T)
Chain Length:133
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Ribosomal protein uL14
Chain IDs:X (auth: U)
Chain Length:139
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Ribosomal protein eL24
Chain IDs:Y (auth: V)
Chain Length:155
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Ribosomal protein uL23
Chain IDs:Z (auth: W)
Chain Length:167
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Ribosomal protein uL24
Chain IDs:AA (auth: X)
Chain Length:141
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Ribosomal protein eL27
Chain IDs:BA (auth: Y)
Chain Length:146
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Ribosomal protein uL15
Chain IDs:CA (auth: Z)
Chain Length:147
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Ribosomal protein eL29
Chain IDs:DA (auth: a)
Chain Length:54
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Ribosomal protein eL30
Chain IDs:EA (auth: b)
Chain Length:108
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Ribosomal protein eL31
Chain IDs:FA (auth: c)
Chain Length:120
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Ribosomal protein eL32
Chain IDs:GA (auth: d)
Chain Length:134
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Ribosomal protein eL33
Chain IDs:HA (auth: e)
Chain Length:112
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Ribosomal protein eL34
Chain IDs:IA (auth: f)
Chain Length:258
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Ribosomal protein uL29
Chain IDs:JA (auth: g)
Chain Length:123
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Ribosomal protein eL36
Chain IDs:KA (auth: h)
Chain Length:101
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Ribosomal protein eL37
Chain IDs:LA (auth: i)
Chain Length:221
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Ribosomal protein eL38
Chain IDs:MA (auth: j)
Chain Length:84
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Ribosomal protein eL39
Chain IDs:NA (auth: k)
Chain Length:51
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Ribosomal protein eL40
Chain IDs:OA (auth: l)
Chain Length:134
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Ribosomal protein eL42
Chain IDs:PA (auth: n)
Chain Length:269
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Ribosomal protein eL43
Chain IDs:QA (auth: o)
Chain Length:96
Number of Molecules:1
Biological Source:Toxoplasma gondii
Polymer Type:polypeptide(L)
Description:Ribosomal protein eL28
Chain IDs:RA (auth: p)
Chain Length:129
Number of Molecules:1
Biological Source:Toxoplasma gondii
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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures