ISDA: 6HIY

Deposition Date 2018-08-31

Release Date 2018-09-26

Last Version Date 2024-11-13

Entry Detail

PDB ID:

6HIY

Keywords:

RIBOSOME

Title:

Cryo-EM structure of the Trypanosoma brucei mitochondrial ribosome - This entry contains the body of the small mitoribosomal subunit in complex with mt-IF-3

Biological Source:

Source Organism:

Trypanosoma brucei brucei (Taxon ID: 5702)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.27 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:9S rRNA
Chain IDs:KA (auth: CA)
Chain Length:621
Number of Molecules:1
Biological Source:Trypanosoma brucei brucei

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mS55m
Gene (Uniprot):Tb10.70.0530
Chain IDs:O (auth: CE)
Chain Length:435
Number of Molecules:1
Biological Source:Trypanosoma brucei brucei

UniProt ID:Q38AX6 Pfam ID:PF03719

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:bS6m
Gene (Uniprot):Tb10.70.4850
Chain IDs:P (auth: CF)
Chain Length:160
Number of Molecules:1
Biological Source:Trypanosoma brucei brucei

UniProt ID:Q38BW5

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uS8m
Gene (Uniprot):Tb10.389.0130
Chain IDs:Q (auth: CH)
Chain Length:282
Number of Molecules:1
Biological Source:Trypanosoma brucei brucei

UniProt ID:Q388R7 Pfam ID:PF00410

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uS9m
Gene (Uniprot):Tb08.28F14.630
Chain IDs:R (auth: CI)
Chain Length:443
Number of Molecules:1
Biological Source:Trypanosoma brucei brucei

UniProt ID:Q57W62 Pfam ID:PF00380

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uS11m
Gene (Uniprot):Tb10.406.0510
Chain IDs:S (auth: CK)
Chain Length:326
Number of Molecules:1
Biological Source:Trypanosoma brucei brucei

UniProt ID:Q389T7

Polymer Type:polypeptide(L)
Molecule:uS12m
Chain IDs:T (auth: CL)
Chain Length:87
Number of Molecules:1
Biological Source:Trypanosoma brucei brucei

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uS15m
Gene (Uniprot):TB927.1.1200
Chain IDs:U (auth: CO)
Chain Length:429
Number of Molecules:1
Biological Source:Trypanosoma brucei brucei

UniProt ID:Q4GZ99

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:bS16m
Gene (Uniprot):Tb11.02.5670
Chain IDs:V (auth: CP)
Chain Length:188
Number of Molecules:1
Biological Source:Trypanosoma brucei brucei

UniProt ID:Q384N9

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uS17m
Gene (Uniprot):Tb09.211.2580
Chain IDs:W (auth: CQ)
Chain Length:263
Number of Molecules:1
Biological Source:Trypanosoma brucei brucei

UniProt ID:Q38DP8 Pfam ID:PF00366

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:bS18m
Gene (Uniprot):Tb10.6k15.3900
Chain IDs:X (auth: CR)
Chain Length:320
Number of Molecules:1
Biological Source:Trypanosoma brucei brucei

UniProt ID:Q38AS2

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uS21m
Gene (Uniprot):Tb03.26J7.200
Chain IDs:Y (auth: CU)
Chain Length:193
Number of Molecules:1
Biological Source:Trypanosoma brucei brucei

UniProt ID:Q580M9

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mt-IF-3
Gene (Uniprot):Tb07.27M11.140
Chain IDs:Z (auth: CZ)
Chain Length:360
Number of Molecules:1
Biological Source:Trypanosoma brucei brucei

UniProt ID:Q57WU2

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mS22
Gene (Uniprot):Tb09.211.2430
Chain IDs:AA (auth: Ca)
Chain Length:621
Number of Molecules:1
Biological Source:Trypanosoma brucei brucei

UniProt ID:Q38DR3

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mS23
Gene (Uniprot):Tb05.30H13.670
Chain IDs:BA (auth: Cb)
Chain Length:324
Number of Molecules:1
Biological Source:Trypanosoma brucei brucei

UniProt ID:Q57VB2

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mS26
Gene (Uniprot):Tb09.211.3000
Chain IDs:CA (auth: Cd)
Chain Length:440
Number of Molecules:1
Biological Source:Trypanosoma brucei brucei

UniProt ID:Q38DK6

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mS34
Gene (Uniprot):Tb08.5H5.370
Chain IDs:DA (auth: Cj)
Chain Length:257
Number of Molecules:1
Biological Source:Trypanosoma brucei brucei

UniProt ID:Q57UK0

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mS37
Gene (Uniprot):Tb10.70.6600
Chain IDs:EA (auth: Cm)
Chain Length:215
Number of Molecules:1
Biological Source:Trypanosoma brucei brucei

UniProt ID:Q38C96

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mS38
Gene (Uniprot):Tb07.29K4.740
Chain IDs:FA (auth: Cn)
Chain Length:250
Number of Molecules:1
Biological Source:Trypanosoma brucei brucei

UniProt ID:Q57VQ9

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mS41
Gene (Uniprot):Tb10.26.0750
Chain IDs:GA (auth: Cp)
Chain Length:188
Number of Molecules:1
Biological Source:Trypanosoma brucei brucei

UniProt ID:Q389L3

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mS42
Gene (Uniprot):Tb06.4F7.290
Chain IDs:HA (auth: Cq)
Chain Length:263
Number of Molecules:1
Biological Source:Trypanosoma brucei brucei

UniProt ID:Q586A1 Pfam ID:PF02777

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mS43
Gene (Uniprot):Tb04.26G5.610
Chain IDs:IA (auth: Cr)
Chain Length:320
Number of Molecules:1
Biological Source:Trypanosoma brucei brucei

UniProt ID:Q585I1 Pfam ID:PF02777

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mS47
Gene (Uniprot):Tb11.01.1910
Chain IDs:JA (auth: Cv)
Chain Length:1211
Number of Molecules:1
Biological Source:Trypanosoma brucei brucei

UniProt ID:Q383R4 Pfam ID:PF16113

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mS48
Gene (Uniprot):Tb08.5H5.480
Chain IDs:A (auth: DA)
Chain Length:64
Number of Molecules:1
Biological Source:Trypanosoma brucei brucei

UniProt ID:Q57UJ2

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mS51
Gene (Uniprot):Tb11.02.3180
Chain IDs:B (auth: DD)
Chain Length:812
Number of Molecules:1
Biological Source:Trypanosoma brucei brucei

UniProt ID:Q385L8

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mS56
Gene (Uniprot):Tb06.26G9.580
Chain IDs:C (auth: DI)
Chain Length:407
Number of Molecules:1
Biological Source:Trypanosoma brucei brucei

UniProt ID:Q587C2

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mS59
Gene (Uniprot):Tb10.70.4220
Chain IDs:D (auth: DL)
Chain Length:307
Number of Molecules:1
Biological Source:Trypanosoma brucei brucei

UniProt ID:Q38BS2

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mS60
Gene (Uniprot):Tb07.22O10.790
Chain IDs:E (auth: DM)
Chain Length:294
Number of Molecules:1
Biological Source:Trypanosoma brucei brucei

UniProt ID:Q57XL2

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mS61
Gene (Uniprot):Tb09.211.4510
Chain IDs:F (auth: DN)
Chain Length:293
Number of Molecules:1
Biological Source:Trypanosoma brucei brucei

UniProt ID:Q38D60

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mS62
Gene (Uniprot):Tb11.01.3300
Chain IDs:G (auth: DO)
Chain Length:282
Number of Molecules:1
Biological Source:Trypanosoma brucei brucei

UniProt ID:Q383D1

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mS63
Gene (Uniprot):Tb09.160.3800
Chain IDs:H (auth: DP)
Chain Length:274
Number of Molecules:1
Biological Source:Trypanosoma brucei brucei

UniProt ID:Q38F25

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mS64
Gene (Uniprot):Tb11.01.5460
Chain IDs:I (auth: DQ)
Chain Length:268
Number of Molecules:1
Biological Source:Trypanosoma brucei brucei

UniProt ID:Q382E8 Pfam ID:PF10469

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mS65
Gene (Uniprot):Tb05.6E7.450
Chain IDs:J (auth: DR)
Chain Length:270
Number of Molecules:1
Biological Source:Trypanosoma brucei brucei

UniProt ID:Q57UA2

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mS66
Gene (Uniprot):Tb10.61.3110
Chain IDs:K (auth: DS)
Chain Length:261
Number of Molecules:1
Biological Source:Trypanosoma brucei brucei

UniProt ID:Q388L7 Pfam ID:PF14311

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mS68
Gene (Uniprot):Tb03.48O8.680
Chain IDs:L (auth: DU)
Chain Length:228
Number of Molecules:1
Biological Source:Trypanosoma brucei brucei

UniProt ID:Q582T9 Pfam ID:PF00240

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:mS73
Gene (Uniprot):Tb06.26G9.560
Chain IDs:M (auth: DZ)
Chain Length:94
Number of Molecules:1
Biological Source:Trypanosoma brucei brucei

UniProt ID:Q587C4

Polymer Type:polypeptide(L)
Molecule:mS74
Chain IDs:N (auth: Da)
Chain Length:64
Number of Molecules:1
Biological Source:Trypanosoma brucei brucei

Polymer Type:polypeptide(L)
Molecule:Unknown protein
Chain IDs:LA (auth: UQ)
Chain Length:32
Number of Molecules:1
Biological Source:Trypanosoma brucei brucei

Polymer Type:polypeptide(L)
Molecule:Unknown protein
Chain IDs:MA (auth: UR)
Chain Length:8
Number of Molecules:1
Biological Source:Trypanosoma brucei brucei

Polymer Type:polypeptide(L)
Molecule:Unknown protein
Chain IDs:NA (auth: US)
Chain Length:54
Number of Molecules:1
Biological Source:Trypanosoma brucei brucei

Polymer Type:polypeptide(L)
Molecule:Unknown protein
Chain IDs:OA (auth: UT)
Chain Length:44
Number of Molecules:1
Biological Source:Trypanosoma brucei brucei

Ligand Molecules

SPD

SPM

Primary Citation

Evolutionary shift toward protein-based architecture in trypanosomal mitochondrial ribosomes.

Ramrath, D.J.F, Niemann, M, Leibundgut, M, Bieri, P, Prange, C, Horn, E.K, Leitner, A, Boehringer, D, Schneider, A, Ban, N.Show

Science 362 ? ? (2018)

PMID: 30213880 DOI: 10.1126/science.aau7735

Abstact

Ribosomal RNA (rRNA) plays key functional and architectural roles in ribosomes. Using electron microscopy, we determined the atomic structure of a highly divergent ribosome found in mitochondria of Trypanosoma brucei, a unicellular parasite that causes sleeping sickness in humans. The trypanosomal mitoribosome features the smallest rRNAs and contains more proteins than all known ribosomes. The structure shows how the proteins have taken over the role of architectural scaffold from the rRNA: They form an autonomous outer shell that surrounds the entire particle and stabilizes and positions the functionally important regions of the rRNA. Our results also reveal the "minimal" set of conserved rRNA and protein components shared by all ribosomes that help us define the most essential functional elements.

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Protein

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Disease

Primary Citation of related structures