5T5H | pdb_00005t5h

Structure and assembly model for the Trypanosoma cruzi 60S ribosomal subunit

PDB DOI: https://doi.org/10.2210/pdb5T5H/pdb
NAKB: 5T5H
EM Map EMD-8361: EMDB EMDataResource

Classification: RIBOSOME
Organism(s): Trypanosoma cruzi
Mutation(s): No

Deposited: 2016-08-31 Released: 2016-10-12
Deposition Author(s): Liu, Z., Gutierrez-Vargas, C., Wei, J., Grassucci, R.A., Ramesh, M., Espina, N., Sun, M., Tutuncuoglu, B., Madison-Antenucci, S., Woolford Jr., J.L., Tong, L., Frank, J.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States), Howard Hughes Medical Institute (HHMI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.54 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

Structure and assembly model for the Trypanosoma cruzi 60S ribosomal subunit.

Liu, Z., Gutierrez-Vargas, C., Wei, J., Grassucci, R.A., Ramesh, M., Espina, N., Sun, M., Tutuncuoglu, B., Madison-Antenucci, S., Woolford, J.L., Tong, L., Frank, J.

(2016) Proc Natl Acad Sci U S A 113: 12174-12179

PubMed: 27791004 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.1614594113
Primary Citation Related Structures:
5T5H

PubMed Abstract:
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.

Organizational Affiliation

Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032.

Macromolecule Content

Total Structure Weight: 1,591.69 kDa
Atom Count: 105,112
Modeled Residue Count: 8,253
Deposited Residue Count: 8,546
Unique protein chains: 38
Unique nucleic acid chains: 8

Macromolecules

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L18	I	192	Trypanosoma cruzi	Mutation(s): 0
UniProt
Find proteins for Q4DZP2 (Trypanosoma cruzi (strain CL Brener)) Explore Q4DZP2 Go to UniProtKB: Q4DZP2
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UniProt Group	Q4DZP2
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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L11	J [auth L]	65	Trypanosoma cruzi	Mutation(s): 0
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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L13	K [auth N]	205	Trypanosoma cruzi	Mutation(s): 0
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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L13a	L [auth O]	203	Trypanosoma cruzi	Mutation(s): 0
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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein L14	M [auth P]	149	Trypanosoma cruzi	Mutation(s): 0
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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein L15	N [auth Q]	203	Trypanosoma cruzi	Mutation(s): 0
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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L17	O [auth R]	152	Trypanosoma cruzi	Mutation(s): 0
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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L18a	P [auth S]	177	Trypanosoma cruzi	Mutation(s): 0
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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein L19-like protein	Q [auth T]	150	Trypanosoma cruzi	Mutation(s): 0
UniProt
Find proteins for Q9BMP1 (Trypanosoma cruzi) Explore Q9BMP1 Go to UniProtKB: Q9BMP1
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9BMP1
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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein L21E (60S)	R [auth U]	146	Trypanosoma cruzi	Mutation(s): 0
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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L22	S [auth V]	99	Trypanosoma cruzi	Mutation(s): 0
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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L23	T [auth W]	127	Trypanosoma cruzi	Mutation(s): 0
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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L23a	U [auth X]	116	Trypanosoma cruzi	Mutation(s): 0
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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein L24	V [auth Y]	61	Trypanosoma cruzi	Mutation(s): 0
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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L26	W [auth Z]	113	Trypanosoma cruzi	Mutation(s): 0
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Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein L27	X [auth a]	132	Trypanosoma cruzi	Mutation(s): 0
UniProt
Find proteins for Q9U4H7 (Trypanosoma cruzi) Explore Q9U4H7 Go to UniProtKB: Q9U4H7
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9U4H7
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Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L27A/L29	Y [auth b]	144	Trypanosoma cruzi	Mutation(s): 0
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Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L28	Z [auth c]	125	Trypanosoma cruzi	Mutation(s): 0
UniProt
Find proteins for O00822 (Trypanosoma cruzi) Explore O00822 Go to UniProtKB: O00822
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O00822
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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein L29	AA [auth d]	63	Trypanosoma cruzi	Mutation(s): 0
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Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L2	BA [auth e]	245	Trypanosoma cruzi	Mutation(s): 0
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Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein L13	CA [auth f]	397	Trypanosoma cruzi	Mutation(s): 0
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Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L30	DA [auth g]	66	Trypanosoma cruzi	Mutation(s): 0
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Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal subunit protein L31	EA [auth h]	169	Trypanosoma cruzi	Mutation(s): 0
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Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L32	FA [auth i]	113	Trypanosoma cruzi	Mutation(s): 0
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Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L34	GA [auth j]	104	Trypanosoma cruzi	Mutation(s): 0
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Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L35	HA [auth k]	120	Trypanosoma cruzi	Mutation(s): 0
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Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein L35A	IA [auth l]	136	Trypanosoma cruzi	Mutation(s): 0
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Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein L36	JA [auth m]	95	Trypanosoma cruzi	Mutation(s): 0
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Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein L37	KA [auth n]	81	Trypanosoma cruzi	Mutation(s): 0
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Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L37a	LA [auth o]	85	Trypanosoma cruzi	Mutation(s): 0
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Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein L38	MA [auth p]	58	Trypanosoma cruzi	Mutation(s): 0
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Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein L39	NA [auth q]	50	Trypanosoma cruzi	Mutation(s): 0
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Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L4	OA [auth r]	337	Trypanosoma cruzi	Mutation(s): 0
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Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L44	PA [auth t]	93	Trypanosoma cruzi	Mutation(s): 0
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Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L5	QA [auth u]	254	Trypanosoma cruzi	Mutation(s): 0
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Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L6	RA [auth v]	171	Trypanosoma cruzi	Mutation(s): 0
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Entity ID: 45
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L7	SA [auth w]	215	Trypanosoma cruzi	Mutation(s): 0
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Entity ID: 46
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein L7a-like protein	TA [auth x]	223	Trypanosoma cruzi	Mutation(s): 0
UniProt
Find proteins for Q9BMP0 (Trypanosoma cruzi) Explore Q9BMP0 Go to UniProtKB: Q9BMP0
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9BMP0
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