5T5H image
Deposition Date 2016-08-31
Release Date 2016-10-12
Last Version Date 2024-12-25
Entry Detail
PDB ID:
5T5H
Keywords:
RIBOSOME
Title:
Structure and assembly model for the Trypanosoma cruzi 60S ribosomal subunit
Biological Source:
Source Organism:
Trypanosoma cruzi (Taxon ID: 5693)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
2.54 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
5T5H validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:RNA LARGE SUBUNIT ALPHA
Chain IDs:A
Chain Length:132
Number of Molecules:1
Biological Source:Trypanosoma cruzi
Polymer Type:polyribonucleotide
Molecule:RNA LARGE SUBUNIT BETA
Chain IDs:B
Chain Length:941
Number of Molecules:1
Biological Source:Trypanosoma cruzi
Polymer Type:polyribonucleotide
Molecule:5.8S rRNA
Chain IDs:C
Chain Length:125
Number of Molecules:1
Biological Source:Trypanosoma cruzi
Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:D
Chain Length:63
Number of Molecules:1
Biological Source:Trypanosoma cruzi
Polymer Type:polyribonucleotide
Molecule:srRNA1
Chain IDs:E
Chain Length:245
Number of Molecules:1
Biological Source:Trypanosoma cruzi
Polymer Type:polyribonucleotide
Molecule:srRNA3
Chain IDs:F
Chain Length:397
Number of Molecules:1
Biological Source:Trypanosoma cruzi
Polymer Type:polyribonucleotide
Molecule:srRNA2
Chain IDs:G
Chain Length:66
Number of Molecules:1
Biological Source:Trypanosoma cruzi
Polymer Type:polyribonucleotide
Molecule:srRNA4
Chain IDs:H
Chain Length:91
Number of Molecules:1
Biological Source:Trypanosoma cruzi
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18
Gene (Uniprot):RPL18
Chain IDs:I
Chain Length:192
Number of Molecules:1
Biological Source:Trypanosoma cruzi
UniProt ID:Q4DZP2 Pfam ID:PF17135
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L11
Gene (Uniprot):Tc00.1047053508197.10
Chain IDs:J (auth: L)
Chain Length:65
Number of Molecules:1
Biological Source:Trypanosoma cruzi
UniProt ID:Q4CNF4 Pfam ID:PF00673
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13
Gene (Uniprot):Tc00.1047053508153.280, Tc00.1047053508153.290, Tc00.1047053510323.30
Chain IDs:K (auth: N)
Chain Length:81
Number of Molecules:1
Biological Source:Trypanosoma cruzi
UniProt ID:Q4E661 Pfam ID:PF01294
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13a
Gene (Uniprot):TCDM_14423
Chain IDs:L (auth: O)
Chain Length:203
Number of Molecules:1
Biological Source:Trypanosoma cruzi
UniProt ID:V5DCT1 Pfam ID:PF00572
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein L14
Gene (Uniprot):Tc00.1047053511825.200
Chain IDs:M (auth: P)
Chain Length:58
Number of Molecules:1
Biological Source:Trypanosoma cruzi
UniProt ID:Q4DQ35 Pfam ID:PF00467, PF01929
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L15
Gene (Uniprot):Tc00.1047053510767.10
Chain IDs:N (auth: Q)
Chain Length:50
Number of Molecules:1
Biological Source:Trypanosoma cruzi
UniProt ID:Q4CTG9 Pfam ID:PF00827
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L17
Gene (Uniprot):Tc00.1047053506213.80, Tc00.1047053511287.30
Chain IDs:O (auth: R)
Chain Length:337
Number of Molecules:1
Biological Source:Trypanosoma cruzi
UniProt ID:Q4DC23 Pfam ID:PF00237
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18a
Gene (Uniprot):Tc00.1047053511001.120
Chain IDs:P (auth: S)
Chain Length:177
Number of Molecules:1
Biological Source:Trypanosoma cruzi
UniProt ID:Q4DZ31 Pfam ID:PF01775
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L19-like protein
Gene (Uniprot):RpL19
Chain IDs:Q (auth: T)
Chain Length:150
Number of Molecules:1
Biological Source:Trypanosoma cruzi
UniProt ID:Q9BMP1 Pfam ID:PF01280
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L21E (60S)
Gene (Uniprot):Tc00.1047053506405.149
Chain IDs:R (auth: U)
Chain Length:146
Number of Molecules:1
Biological Source:Trypanosoma cruzi
UniProt ID:Q4DED2 Pfam ID:PF01157
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L22
Gene (Uniprot):Tc00.1047053504147.120
Chain IDs:S (auth: V)
Chain Length:99
Number of Molecules:1
Biological Source:Trypanosoma cruzi
UniProt ID:Q4DZN3 Pfam ID:PF01776
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L23
Gene (Uniprot):Tc00.1047053508461.490
Chain IDs:T (auth: W)
Chain Length:127
Number of Molecules:1
Biological Source:Trypanosoma cruzi
UniProt ID:Q4E4R0 Pfam ID:PF00238
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L23a
Gene (Uniprot):Tc00.1047053508175.146
Chain IDs:U (auth: X)
Chain Length:116
Number of Molecules:1
Biological Source:Trypanosoma cruzi
UniProt ID:Q4E2Y1 Pfam ID:PF00276
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L24
Gene (Uniprot):Tc00.1047053503611.20, Tc00.1047053503611.40, Tc00.1047053506679.230, Tc00.1047053506679.250
Chain IDs:V (auth: Y)
Chain Length:61
Number of Molecules:1
Biological Source:Trypanosoma cruzi
UniProt ID:Q4E078 Pfam ID:PF01246
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L26
Gene (Uniprot):Tc00.1047053510761.14, Tc00.1047053511067.20, Tc00.1047053511903.130
Chain IDs:W (auth: Z)
Chain Length:113
Number of Molecules:1
Biological Source:Trypanosoma cruzi
UniProt ID:Q4DG45 Pfam ID:PF16906, PF00467
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L27
Gene (Uniprot):C3747_12g1558c, C3747_12g1559c, C4B63_9g2155c, C4B63_9g2158c
Chain IDs:X (auth: a)
Chain Length:132
Number of Molecules:1
Biological Source:Trypanosoma cruzi
UniProt ID:Q9U4H7 Pfam ID:PF00467, PF01777
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L27A/L29
Gene (Uniprot):Tc00.1047053508461.500, Tc00.1047053508461.510
Chain IDs:Y (auth: b)
Chain Length:941
Number of Molecules:1
Biological Source:Trypanosoma cruzi
UniProt ID:Q4E4Q8 Pfam ID:PF00828
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L28
Chain IDs:Z (auth: c)
Chain Length:125
Number of Molecules:1
Biological Source:Trypanosoma cruzi
UniProt ID:O00822 Pfam ID:PF01778
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L29
Gene (Uniprot):Tc00.1047053509749.33, Tc00.1047053509749.36
Chain IDs:AA (auth: d)
Chain Length:63
Number of Molecules:1
Biological Source:Trypanosoma cruzi
UniProt ID:Q4CPD8 Pfam ID:PF01779
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L2
Gene (Uniprot):Tc00.1047053511181.100
Chain IDs:BA (auth: e)
Chain Length:245
Number of Molecules:1
Biological Source:Trypanosoma cruzi
UniProt ID:Q4DPQ8 Pfam ID:PF00181, PF03947
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L13
Gene (Uniprot):TCDM_02783
Chain IDs:CA (auth: f)
Chain Length:397
Number of Molecules:1
Biological Source:Trypanosoma cruzi
UniProt ID:V5B599 Pfam ID:PF00297
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L30
Gene (Uniprot):Tc00.1047053506959.120
Chain IDs:DA (auth: g)
Chain Length:66
Number of Molecules:1
Biological Source:Trypanosoma cruzi
UniProt ID:Q4DIC9 Pfam ID:PF01248
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal subunit protein L31
Gene (Uniprot):TCDM_14322
Chain IDs:EA (auth: h)
Chain Length:91
Number of Molecules:1
Biological Source:Trypanosoma cruzi
UniProt ID:V5C333 Pfam ID:PF01198
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L32
Gene (Uniprot):Tc00.1047053504069.30, Tc00.1047053511145.20
Chain IDs:FA (auth: i)
Chain Length:192
Number of Molecules:1
Biological Source:Trypanosoma cruzi
UniProt ID:Q4D1H8 Pfam ID:PF01655
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L34
Gene (Uniprot):Tc00.1047053506963.20, Tc00.1047053507831.90
Chain IDs:GA (auth: j)
Chain Length:104
Number of Molecules:1
Biological Source:Trypanosoma cruzi
UniProt ID:Q4DB26 Pfam ID:PF01199
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L35
Gene (Uniprot):Tc00.1047053509979.90, Tc00.1047053509979.95, Tc00.1047053510039.90
Chain IDs:HA (auth: k)
Chain Length:120
Number of Molecules:1
Biological Source:Trypanosoma cruzi
UniProt ID:Q4E2E0 Pfam ID:PF00831
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L35A
Gene (Uniprot):Tc00.1047053506559.470
Chain IDs:IA (auth: l)
Chain Length:65
Number of Molecules:1
Biological Source:Trypanosoma cruzi
UniProt ID:Q4E581 Pfam ID:PF01247
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L36
Gene (Uniprot):TCDM_14524
Chain IDs:JA (auth: m)
Chain Length:95
Number of Molecules:1
Biological Source:Trypanosoma cruzi
UniProt ID:V5BDJ2 Pfam ID:PF01158
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L37
Gene (Uniprot):Tc00.1047053506885.14, Tc00.1047053507773.34, Tc00.1047053510431.274
Chain IDs:KA (auth: n)
Chain Length:81
Number of Molecules:1
Biological Source:Trypanosoma cruzi
UniProt ID:Q4DXW6 Pfam ID:PF01907
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L37a
Gene (Uniprot):Tc00.1047053504069.56, Tc00.1047053507641.233, Tc00.1047053511145.46
Chain IDs:LA (auth: o)
Chain Length:203
Number of Molecules:1
Biological Source:Trypanosoma cruzi
UniProt ID:Q4DAV9 Pfam ID:PF01780
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L38
Gene (Uniprot):Tc00.1047053508119.144
Chain IDs:MA (auth: p)
Chain Length:58
Number of Molecules:1
Biological Source:Trypanosoma cruzi
UniProt ID:Q4DQ60 Pfam ID:PF01781
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L39
Gene (Uniprot):Tc00.1047053506573.81, Tc00.1047053511217.145
Chain IDs:NA (auth: q)
Chain Length:50
Number of Molecules:1
Biological Source:Trypanosoma cruzi
UniProt ID:Q4DVC6 Pfam ID:PF00832
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L4
Gene (Uniprot):Tc00.1047053504121.30
Chain IDs:OA (auth: r)
Chain Length:337
Number of Molecules:1
Biological Source:Trypanosoma cruzi
UniProt ID:Q4CQW2 Pfam ID:PF00573, PF14374
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L44
Gene (Uniprot):Tc00.1047053506815.60, Tc00.1047053507105.40
Chain IDs:PA (auth: t)
Chain Length:150
Number of Molecules:1
Biological Source:Trypanosoma cruzi
UniProt ID:Q4CV79 Pfam ID:PF00935
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L5
Gene (Uniprot):Tc00.1047053509671.80, Tc00.1047053510765.60
Chain IDs:QA (auth: u)
Chain Length:146
Number of Molecules:1
Biological Source:Trypanosoma cruzi
UniProt ID:Q4CU61 Pfam ID:PF17144
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L6
Gene (Uniprot):Tc00.1047053507709.50
Chain IDs:RA (auth: v)
Chain Length:99
Number of Molecules:1
Biological Source:Trypanosoma cruzi
UniProt ID:Q4DIV9 Pfam ID:PF01159
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L7
Gene (Uniprot):Tc00.1047053507519.110
Chain IDs:SA (auth: w)
Chain Length:127
Number of Molecules:1
Biological Source:Trypanosoma cruzi
UniProt ID:Q4DNZ7 Pfam ID:PF08079, PF00327
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L7a-like protein
Gene (Uniprot):RpL7a
Chain IDs:TA (auth: x)
Chain Length:116
Number of Molecules:1
Biological Source:Trypanosoma cruzi
UniProt ID:Q9BMP0 Pfam ID:PF01248
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
5MC B ? modified residue
7MG B ? modified residue
A2M B A modified residue
OMC B C modified residue
OMG B G modified residue
OMU B U modified residue
Ligand Molecules
MG
ZN
Primary Citation
Structure and assembly model for the Trypanosoma cruzi 60S ribosomal subunit.
Proc.Natl.Acad.Sci.USA 113 12174 12179 (2016)
PMID: 27791004 DOI: 10.1073/pnas.1614594113

Abstact

Ribosomes of trypanosomatids, a family of protozoan parasites causing debilitating human diseases, possess multiply fragmented rRNAs that together are analogous to 28S rRNA, unusually large rRNA expansion segments, and r-protein variations compared with other eukaryotic ribosomes. To investigate the architecture of the trypanosomatid ribosomes, we determined the 2.5-Å structure of the Trypanosoma cruzi ribosome large subunit by single-particle cryo-EM. Examination of this structure and comparative analysis of the yeast ribosomal assembly pathway allowed us to develop a stepwise assembly model for the eight pieces of the large subunit rRNAs and a number of ancillary "glue" proteins. This model can be applied to the characterization of Trypanosoma brucei and Leishmania spp. ribosomes as well. Together with other details, our atomic-level structure may provide a foundation for structure-based design of antitrypanosome drugs.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
5T5H