Biological Assembly 1  

 3D View: Structure

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 71-mer - A1BCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 71-mer - A2B1CDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 3469.65 kDa 
• Atom Count: 200172 
• Residue Count: 16210 
• Unique protein chains: 71
• Unique nucleic acid chains: 9

5T2A

CryoEM structure of the Leishmania donovani 80S ribosome at 2.9 Angstrom resolution

• DOI: 10.2210/pdb5T2A/pdb
• EMDataResource: EMD-8343

• Classification: RIBOSOME
• Organism(s): Leishmania donovani
• Mutation(s): No 


• Deposited: 2016-08-23 Released: 2017-01-25 
• Deposition Author(s): Zhang, X., Lai, M., Zhou, Z.H.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structures and stabilization of kinetoplastid-specific split rRNAs revealed by comparing leishmanial and human ribosomes.

Zhang, X., Lai, M., Chang, W., Yu, I., Ding, K., Mrazek, J., Ng, H.L., Yang, O.O., Maslov, D.A., Zhou, Z.H.

(2016) Nat Commun 7: 13223-13223

• PubMed: 27752045 
• DOI: 10.1038/ncomms13223
• Structures With Same Primary Citation


• PubMed Abstract: 
  

The recent success in ribosome structure determination by cryoEM has opened the door to defining structural differences between ribosomes of pathogenic organisms and humans and to understand ribosome-targeting antibiotics. Here, by direct electron-counting cryoEM, we have determined the structures of the Leishmania donovani and human ribosomes at 2.9 Å and 3.6 Å, respectively. Our structure of the leishmanial ribosome elucidates the organization of the six fragments of its large subunit rRNA (as opposed to a single 28S rRNA in most eukaryotes, including humans) and reveals atomic details of a unique 20 amino acid extension of the uL13 protein that pins down the ends of three of the rRNA fragments. The structure also fashions many large rRNA expansion segments. Direct comparison of our human and leishmanial ribosome structures at the decoding A-site sheds light on how the bacterial ribosome-targeting drug paromomycin selectively inhibits the eukaryotic L. donovani, but not human, ribosome.

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Organizational Affiliation: 

Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California 90095, USA.

Macromolecules

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details
eL18	I	198	Leishmania donovani	Mutation(s): 0
Find proteins for E9BUI1 (Leishmania donovani (strain BPK282A1)) Go to UniProtKB:  E9BUI1

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details
uL16	J	213	Leishmania donovani	Mutation(s): 0
Find proteins for E9B840 (Leishmania donovani (strain BPK282A1)) Go to UniProtKB:  E9B840

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details
uL5	K	188	Leishmania donovani	Mutation(s): 0
Find proteins for E9BFL1 (Leishmania donovani (strain BPK282A1)) Go to UniProtKB:  E9BFL1

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details
eL13	L	220	Leishmania donovani	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details
uL13	M	222	Leishmania donovani	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details
eL14	N	175	Leishmania donovani	Mutation(s): 0  Gene Names: RPL14, LPD23
Find proteins for Q25278 (Leishmania donovani) Go to UniProtKB:  Q25278

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details
eL15	O	204	Leishmania donovani	Mutation(s): 0
Find proteins for E9BMB4 (Leishmania donovani (strain BPK282A1)) Go to UniProtKB:  E9BMB4

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details
uL22	P	166	Leishmania donovani	Mutation(s): 0
Find proteins for E9BGL6 (Leishmania donovani (strain BPK282A1)) Go to UniProtKB:  E9BGL6

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details
eL20	Q	179	Leishmania donovani	Mutation(s): 0
Find proteins for E9BRT7 (Leishmania donovani (strain BPK282A1)) Go to UniProtKB:  E9BRT7

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details
eL19	R	245	Leishmania donovani	Mutation(s): 0
Find proteins for E9B8Q2 (Leishmania donovani (strain BPK282A1)) Go to UniProtKB:  E9B8Q2

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details
eL21	S	159	Leishmania donovani	Mutation(s): 0
Find proteins for E9BRE2 (Leishmania donovani (strain BPK282A1)) Go to UniProtKB:  E9BRE2

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details
eL22	T	129	Leishmania donovani	Mutation(s): 0
Find proteins for E9BU52 (Leishmania donovani (strain BPK282A1)) Go to UniProtKB:  E9BU52

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details
uL14	U	139	Leishmania donovani	Mutation(s): 0
Find proteins for E9BSQ4 (Leishmania donovani (strain BPK282A1)) Go to UniProtKB:  E9BSQ4

Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details
uL23	V	145	Leishmania donovani	Mutation(s): 0
Find proteins for D1M863 (Leishmania donovani) Go to UniProtKB:  D1M863

Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details
eL24	W	124	Leishmania donovani	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details
uL24	X	143	Leishmania donovani	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details
eL27	Y	134	Leishmania donovani	Mutation(s): 0
Find proteins for E9BP34 (Leishmania donovani (strain BPK282A1)) Go to UniProtKB:  E9BP34

Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details
uL15	Z	145	Leishmania donovani	Mutation(s): 0
Find proteins for E9BSQ2 (Leishmania donovani (strain BPK282A1)) Go to UniProtKB:  E9BSQ2

Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details
eL28	a	147	Leishmania donovani	Mutation(s): 0
Find proteins for E9BAU9 (Leishmania donovani (strain BPK282A1)) Go to UniProtKB:  E9BAU9

Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details
eL29	b	70	Leishmania donovani	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details
uL2	c	260	Leishmania donovani	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details
uL3	d	419	Leishmania donovani	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details
eL30	e	104	Leishmania donovani	Mutation(s): 0
Find proteins for E9BRQ6 (Leishmania donovani (strain BPK282A1)) Go to UniProtKB:  E9BRQ6

Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details
eL31	f	183	Leishmania donovani	Mutation(s): 0
Find proteins for E9BSK4 (Leishmania donovani (strain BPK282A1)) Go to UniProtKB:  E9BSK4

Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details
eL32	g	133	Leishmania donovani	Mutation(s): 0
Find proteins for E9BS76 (Leishmania donovani (strain BPK282A1)) Go to UniProtKB:  E9BS76

Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details
eL34	h	168	Leishmania donovani	Mutation(s): 0
Find proteins for E9BUA1 (Leishmania donovani (strain BPK282A1)) Go to UniProtKB:  E9BUA1

Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details
uL29	i	127	Leishmania donovani	Mutation(s): 0
Find proteins for E9BIP6 (Leishmania donovani (strain BPK282A1)) Go to UniProtKB:  E9BIP6

Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details
eL33	j	144	Leishmania donovani	Mutation(s): 0
Find proteins for E9BR22 (Leishmania donovani (strain BPK282A1)) Go to UniProtKB:  E9BR22

Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details
eL36	k	105	Leishmania donovani	Mutation(s): 0
Find proteins for E9BS63 (Leishmania donovani (strain BPK282A1)) Go to UniProtKB:  E9BS63

Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details
eL37	l	83	Leishmania donovani	Mutation(s): 0  Gene Names: RPL37
Find proteins for P62885 (Leishmania donovani) Go to UniProtKB:  P62885

Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details
eL43	m	92	Leishmania donovani	Mutation(s): 0
Find proteins for E9BFK4 (Leishmania donovani (strain BPK282A1)) Go to UniProtKB:  E9BFK4

Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details
eL38	n	83	Leishmania donovani	Mutation(s): 0
Find proteins for E9B7P2 (Leishmania donovani (strain BPK282A1)) Go to UniProtKB:  E9B7P2

Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details
eL39	o	51	Leishmania donovani	Mutation(s): 0
Find proteins for E9BCX6 (Leishmania donovani (strain BPK282A1)) Go to UniProtKB:  E9BCX6

Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details
uL4	p	373	Leishmania donovani	Mutation(s): 0
Find proteins for E9BKR3 (Leishmania donovani (strain BPK282A1)) Go to UniProtKB:  E9BKR3

Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details
eL40	q	128	Leishmania donovani	Mutation(s): 0
Find proteins for E9BMW6 (Leishmania donovani (strain BPK282A1)) Go to UniProtKB:  E9BMW6

Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details
eL42	r	106	Leishmania donovani	Mutation(s): 0
Find proteins for E9BBL5 (Leishmania donovani (strain BPK282A1)) Go to UniProtKB:  E9BBL5

Entity ID: 45
Molecule	Chains	Sequence Length	Organism	Details
uL18	s	305	Leishmania donovani	Mutation(s): 0
Find proteins for E9BS61 (Leishmania donovani (strain BPK282A1)) Go to UniProtKB:  E9BS61

Entity ID: 46
Molecule	Chains	Sequence Length	Organism	Details
eL6	t	195	Leishmania donovani	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 47
Molecule	Chains	Sequence Length	Organism	Details
uL30	u	252	Leishmania donovani	Mutation(s): 0
Find proteins for E9BI29 (Leishmania donovani (strain BPK282A1)) Go to UniProtKB:  E9BI29

Entity ID: 48
Molecule	Chains	Sequence Length	Organism	Details
eL8	v	348	Leishmania donovani	Mutation(s): 0
Find proteins for E9B949 (Leishmania donovani (strain BPK282A1)) Go to UniProtKB:  E9B949

Entity ID: 49
Molecule	Chains	Sequence Length	Organism	Details
uL6	w	190	Leishmania donovani	Mutation(s): 0
Find proteins for E9BFB5 (Leishmania donovani (strain BPK282A1)) Go to UniProtKB:  E9BFB5

Entity ID: 50
Molecule	Chains	Sequence Length	Organism	Details
eS1	0	264	Leishmania donovani	Mutation(s): 0
Find proteins for E9BRS2 (Leishmania donovani (strain BPK282A1)) Go to UniProtKB:  E9BRS2

Entity ID: 51
Molecule	Chains	Sequence Length	Organism	Details
eS4	1	273	Leishmania donovani	Mutation(s): 0
Find proteins for E9BBI6 (Leishmania donovani (strain BPK282A1)) Go to UniProtKB:  E9BBI6

Entity ID: 53
Molecule	Chains	Sequence Length	Organism	Details
eS6	3	249	Leishmania donovani	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 54
Molecule	Chains	Sequence Length	Organism	Details
eS7	4	200	Leishmania donovani	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 55
Molecule	Chains	Sequence Length	Organism	Details
eS8	5	220	Leishmania donovani	Mutation(s): 0
Find proteins for E9BH78 (Leishmania donovani (strain BPK282A1)) Go to UniProtKB:  E9BH78

Entity ID: 56
Molecule	Chains	Sequence Length	Organism	Details
uS4	6	190	Leishmania donovani	Mutation(s): 0
Find proteins for E9BTJ0 (Leishmania donovani (strain BPK282A1)) Go to UniProtKB:  E9BTJ0

Entity ID: 57
Molecule	Chains	Sequence Length	Organism	Details
RACK1	7	312	Leishmania donovani	Mutation(s): 0
Find proteins for Q9BIJ5 (Leishmania donovani) Go to UniProtKB:  Q9BIJ5

Entity ID: 58
Molecule	Chains	Sequence Length	Organism	Details
uS14	8	57	Leishmania donovani	Mutation(s): 0
Find proteins for E9BJV7 (Leishmania donovani (strain BPK282A1)) Go to UniProtKB:  E9BJV7

Entity ID: 59
Molecule	Chains	Sequence Length	Organism	Details
uS2	AC	246	Leishmania donovani	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 60
Molecule	Chains	Sequence Length	Organism	Details
eS10	AD	153	Leishmania donovani	Mutation(s): 0
Find proteins for E9BTG4 (Leishmania donovani (strain BPK282A1)) Go to UniProtKB:  E9BTG4

Entity ID: 61
Molecule	Chains	Sequence Length	Organism	Details
uS17	AE	173	Leishmania donovani	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 62
Molecule	Chains	Sequence Length	Organism	Details
uS15	AG	151	Leishmania donovani	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 63
Molecule	Chains	Sequence Length	Organism	Details
uS11	AH	144	Leishmania donovani	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 64
Molecule	Chains	Sequence Length	Organism	Details
uS19	AI	152	Leishmania donovani	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 65
Molecule	Chains	Sequence Length	Organism	Details
uS8	AJ	130	Leishmania donovani	Mutation(s): 0
Find proteins for E9BAV6 (Leishmania donovani (strain BPK282A1)) Go to UniProtKB:  E9BAV6

Entity ID: 66
Molecule	Chains	Sequence Length	Organism	Details
uS9	AK	149	Leishmania donovani	Mutation(s): 0
Find proteins for E9BI96 (Leishmania donovani (strain BPK282A1)) Go to UniProtKB:  E9BI96

Entity ID: 67
Molecule	Chains	Sequence Length	Organism	Details
eS17	AL	143	Leishmania donovani	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 68
Molecule	Chains	Sequence Length	Organism	Details
uS13	AM	153	Leishmania donovani	Mutation(s): 0
Find proteins for E9BTF9 (Leishmania donovani (strain BPK282A1)) Go to UniProtKB:  E9BTF9

Entity ID: 69
Molecule	Chains	Sequence Length	Organism	Details
uS7	AN	190	Leishmania donovani	Mutation(s): 0
Find proteins for Q868B1 (Leishmania major) Go to UniProtKB:  Q868B1

Entity ID: 70
Molecule	Chains	Sequence Length	Organism	Details
eS19	AO	179	Leishmania donovani	Mutation(s): 0
Find proteins for E9BR60 (Leishmania donovani (strain BPK282A1)) Go to UniProtKB:  E9BR60

Entity ID: 71
Molecule	Chains	Sequence Length	Organism	Details
uS5	AP	265	Leishmania donovani	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 72
Molecule	Chains	Sequence Length	Organism	Details
uS10	AQ	116	Leishmania donovani	Mutation(s): 0
Find proteins for E9BJI2 (Leishmania donovani (strain BPK282A1)) Go to UniProtKB:  E9BJI2

Entity ID: 73
Molecule	Chains	Sequence Length	Organism	Details
eS21	AR	164	Leishmania donovani	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 74
Molecule	Chains	Sequence Length	Organism	Details
uS12	AS	143	Leishmania donovani	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 75
Molecule	Chains	Sequence Length	Organism	Details
eS24	AT	137	Leishmania donovani	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 76
Molecule	Chains	Sequence Length	Organism	Details
eS26	AV	112	Leishmania donovani	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 77
Molecule	Chains	Sequence Length	Organism	Details
eS27	AW	86	Leishmania donovani	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 78
Molecule	Chains	Sequence Length	Organism	Details
uS3	AX	219	Leishmania donovani	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 79
Molecule	Chains	Sequence Length	Organism	Details
eS30	AY	66	Leishmania donovani	Mutation(s): 0
Find proteins for E9BLG3 (Leishmania donovani (strain BPK282A1)) Go to UniProtKB:  E9BLG3

Entity ID: 80
Molecule	Chains	Sequence Length	Organism	Details
eS28	AZ	87	Leishmania donovani	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 1
Molecule	Chains	Length	Organism
LSU-alpha	A	1781	Leishmania donovani

Entity ID: 2
Molecule	Chains	Length	Organism
LSU-beta	B	1465	Leishmania donovani

Entity ID: 3
Molecule	Chains	Length	Organism
5.8S rRNA	C	262	Leishmania donovani

Entity ID: 4
Molecule	Chains	Length	Organism
5S rRNA	D	120	Leishmania donovani

Entity ID: 5
Molecule	Chains	Length	Organism
srRNA1	E	213	Leishmania donovani

Entity ID: 6
Molecule	Chains	Length	Organism
srRNA3	F	73	Leishmania donovani

Entity ID: 7
Molecule	Chains	Length	Organism
srRNA2	G	183	Leishmania donovani

Entity ID: 8
Molecule	Chains	Length	Organism
srRNA4	H	127	Leishmania donovani

Entity ID: 52
Molecule	Chains	Length	Organism
18S rRNA	2	2205	Leishmania donovani

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-08-23 
• Released Date: 2017-01-25 
Deposition Author(s): Zhang, X., Lai, M., Zhou, Z.H.

Revision History 

• Version 1.0: 2017-01-25
  Type: Initial release
  
• Version 1.1: 2018-07-18
  Changes: Data collection