5OPT image
Deposition Date 2017-08-10
Release Date 2017-11-15
Last Version Date 2024-11-20
Entry Detail
PDB ID:
5OPT
Keywords:
Title:
Structure of KSRP in context of Trypanosoma cruzi 40S
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
4.00 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:18S rRNA
Chain IDs:IA (auth: E)
Chain Length:2319
Number of Molecules:1
Biological Source:Trypanosoma cruzi
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S4
Gene (Uniprot):Tc00.1047053509683.117, Tc00.1047053511051.39, Tc00.1047053511051.50
Chain IDs:F (auth: L)
Chain Length:273
Number of Molecules:1
Biological Source:Trypanosoma cruzi (strain CL Brener)
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S23, putative
Gene (Uniprot):Tc00.1047053504181.20, Tc00.1047053504181.30, Tc00.1047053509695.180, Tc00.1047053509695.184
Chain IDs:G (auth: M)
Chain Length:143
Number of Molecules:1
Biological Source:Trypanosoma cruzi (strain CL Brener)
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S5, putative
Gene (Uniprot):Tc00.1047053506297.150, Tc00.1047053506297.160
Chain IDs:H (auth: O)
Chain Length:190
Number of Molecules:1
Biological Source:Trypanosoma cruzi (strain CL Brener)
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S6
Gene (Uniprot):Tc00.1047053510769.49
Chain IDs:AA (auth: P)
Chain Length:318
Number of Molecules:1
Biological Source:Trypanosoma cruzi (strain CL Brener)
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S7, putative
Gene (Uniprot):Tc00.1047053506593.30
Chain IDs:I (auth: Q)
Chain Length:211
Number of Molecules:1
Biological Source:Trypanosoma cruzi (strain CL Brener)
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S13, putative
Gene (Uniprot):Tc00.1047053511291.90
Chain IDs:J (auth: R)
Chain Length:151
Number of Molecules:1
Biological Source:Trypanosoma cruzi (strain CL Brener)
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S27, putative
Gene (Uniprot):Tc00.1047053506963.14, Tc00.1047053511233.14, Tc00.1047053511277.175
Chain IDs:K (auth: S)
Chain Length:86
Number of Molecules:1
Biological Source:Trypanosoma cruzi (strain CL Brener)
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S26
Gene (Uniprot):Tc00.1047053503801.20, Tc00.1047053508817.60
Chain IDs:L (auth: T)
Chain Length:112
Number of Molecules:1
Biological Source:Trypanosoma cruzi (strain CL Brener)
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S33, putative
Gene (Uniprot):Tc00.1047053511237.60
Chain IDs:M (auth: U)
Chain Length:112
Number of Molecules:1
Biological Source:Trypanosoma cruzi (strain CL Brener)
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S14, putative
Gene (Uniprot):Tc00.1047053409117.20, Tc00.1047053506945.230, Tc00.1047053508823.50
Chain IDs:N (auth: V)
Chain Length:144
Number of Molecules:1
Biological Source:Trypanosoma cruzi (strain CL Brener)
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S3a-2
Gene (Uniprot):Tc00.1047053511001.9, Tc00.1047053511001.18
Chain IDs:O (auth: W)
Chain Length:261
Number of Molecules:1
Biological Source:Trypanosoma cruzi (strain CL Brener)
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S11, putative
Gene (Uniprot):Tc00.1047053508319.70, Tc00.1047053508405.40
Chain IDs:P (auth: X)
Chain Length:173
Number of Molecules:1
Biological Source:Trypanosoma cruzi (strain CL Brener)
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S24
Gene (Uniprot):Tc00.1047053507681.150, Tc00.1047053507681.160
Chain IDs:Q (auth: Y)
Chain Length:137
Number of Molecules:1
Biological Source:Trypanosoma cruzi (strain CL Brener)
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S8
Gene (Uniprot):Tc00.1047053511903.110
Chain IDs:R (auth: Z)
Chain Length:221
Number of Molecules:1
Biological Source:Trypanosoma cruzi (strain CL Brener)
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S25, putative
Gene (Uniprot):Tc00.1047053504105.94, Tc00.1047053509233.190
Chain IDs:X (auth: a)
Chain Length:110
Number of Molecules:1
Biological Source:Trypanosoma cruzi (strain CL Brener)
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S9, putative
Gene (Uniprot):Tc00.1047053504163.30, Tc00.1047053506401.120
Chain IDs:S (auth: b)
Chain Length:190
Number of Molecules:1
Biological Source:Trypanosoma cruzi (strain CL Brener)
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S30
Gene (Uniprot):Tc00.1047053507019.83, Tc00.1047053507019.86
Chain IDs:GA (auth: c)
Chain Length:66
Number of Molecules:1
Biological Source:Trypanosoma cruzi (strain CL Brener)
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S2, putative
Gene (Uniprot):Tc00.1047053503833.40, Tc00.1047053506213.60, Tc00.1047053511287.120, Tc00.1047053511287.40
Chain IDs:U (auth: d)
Chain Length:263
Number of Molecules:1
Biological Source:Trypanosoma cruzi (strain CL Brener)
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S15a, putative
Gene (Uniprot):Tc00.1047053506297.330
Chain IDs:V (auth: e)
Chain Length:2319
Number of Molecules:1
Biological Source:Trypanosoma cruzi (strain CL Brener)
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein SA
Gene (Uniprot):Tc00.1047053510425.19
Chain IDs:T (auth: f)
Chain Length:245
Number of Molecules:1
Biological Source:Trypanosoma cruzi (strain CL Brener)
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S21, putative
Gene (Uniprot):Tc00.1047053510101.420
Chain IDs:W (auth: g)
Chain Length:236
Number of Molecules:1
Biological Source:Trypanosoma cruzi (strain CL Brener)
Polymer Type:polypeptide(L)
Molecule:RNA-binding protein, putative
Gene (Uniprot):Tc00.1047053511727.270
Chain IDs:HA (auth: h)
Chain Length:257
Number of Molecules:1
Biological Source:Trypanosoma cruzi (strain CL Brener)
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S12
Gene (Uniprot):Tc00.1047053503395.50, Tc00.1047053506181.59
Chain IDs:Y (auth: i)
Chain Length:141
Number of Molecules:1
Biological Source:Trypanosoma cruzi (strain CL Brener)
Polymer Type:polypeptide(L)
Molecule:Ubiquitin/ribosomal protein S27a, putative
Gene (Uniprot):Tc00.1047053510409.39
Chain IDs:Z (auth: j)
Chain Length:150
Number of Molecules:1
Biological Source:Trypanosoma cruzi (strain CL Brener)
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S17, putative
Gene (Uniprot):Tc00.1047053508827.70
Chain IDs:BA (auth: k)
Chain Length:196
Number of Molecules:1
Biological Source:Trypanosoma cruzi (strain CL Brener)
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S20, putative
Gene (Uniprot):Tc00.1047053508475.10, Tc00.1047053508823.120, Tc00.1047053508823.140
Chain IDs:CA (auth: l)
Chain Length:273
Number of Molecules:1
Biological Source:Trypanosoma cruzi (strain CL Brener)
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S3, putative
Gene (Uniprot):Tc00.1047053504021.109, Tc00.1047053507677.39, Tc00.1047053509353.30
Chain IDs:DA (auth: m)
Chain Length:143
Number of Molecules:1
Biological Source:Trypanosoma cruzi (strain CL Brener)
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S10, putative
Gene (Uniprot):Tc00.1047053506679.140, Tc00.1047053506679.150
Chain IDs:EA (auth: n)
Chain Length:161
Number of Molecules:1
Biological Source:Trypanosoma cruzi (strain CL Brener)
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S19, putative
Gene (Uniprot):Tc00.1047053510879.20
Chain IDs:FA (auth: o)
Chain Length:190
Number of Molecules:1
Biological Source:Trypanosoma cruzi (strain CL Brener)
Polymer Type:polypeptide(L)
Molecule:Activated protein kinase C receptor, putative
Gene (Uniprot):Tc00.1047053511211.120, Tc00.1047053511211.130
Chain IDs:A (auth: p)
Chain Length:318
Number of Molecules:1
Biological Source:Trypanosoma cruzi (strain CL Brener)
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S29, putative
Gene (Uniprot):Tc00.1047053506025.14, Tc00.1047053511209.54, Tc00.1047053511805.15
Chain IDs:B (auth: q)
Chain Length:211
Number of Molecules:1
Biological Source:Trypanosoma cruzi (strain CL Brener)
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S16, putative
Gene (Uniprot):Tc00.1047053503899.20, Tc00.1047053503899.30
Chain IDs:C (auth: r)
Chain Length:151
Number of Molecules:1
Biological Source:Trypanosoma cruzi (strain CL Brener)
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S15, putative
Gene (Uniprot):Tc00.1047053511809.130, Tc00.1047053511809.99, Tc00.1047053511811.10
Chain IDs:D (auth: t)
Chain Length:112
Number of Molecules:1
Biological Source:Trypanosoma cruzi (strain CL Brener)
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S18, putative
Gene (Uniprot):Tc00.1047053506679.100, Tc00.1047053506679.94
Chain IDs:E (auth: u)
Chain Length:112
Number of Molecules:1
Biological Source:Trypanosoma cruzi (strain CL Brener)
Ligand Molecules
Primary Citation
The cryo-EM Structure of a Novel 40S Kinetoplastid-Specific Ribosomal Protein.
Structure 25 1785 1794.e3 (2017)
PMID: 29107485 DOI: 10.1016/j.str.2017.09.014

Abstact

Kinetoplastids are potentially lethal protozoan pathogens affecting more than 20 million people worldwide. There is a critical need for more specific targets for the development of safer anti-kinetoplastid therapeutic molecules that can replace the scarce and highly cytotoxic current drugs. The kinetoplastid ribosome represents a potential therapeutic target due to its relative structural divergence when compared with its human counterpart. However, several kinetoplastid-specific ribosomal features remain uncharacterized. Here, we present the near-atomic cryoelectron microscopy structure of a novel bona fide kinetoplastid-specific ribosomal (r-) protein (KSRP) bound to the ribosome. KSRP is an essential protein located at the solvent face of the 40S subunit, where it binds and stabilizes kinetoplastid-specific domains of rRNA, suggesting its role in ribosome integrity. KSRP also interacts with the r-protein eS6 at a region that is only conserved in kinetoplastids. The kinetoplastid-specific ribosomal environment of KSRP provides a promising target for the design of safer anti-kinetoplastidian drugs.

Legend

Protein

Chemical

Disease

Primary Citation of related structures