5T2A

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

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

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

  • DOI: 10.1038/ncomms13223
  • Primary Citation of Related Structures:  
  • Also Cited By: 5OSG

  • 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-co ...

    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.

    Organizational Affiliation: 

    Center of Cryo Electron Microscopy, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
eL18
I
198Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BUI1 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BUI1
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
uL16
J
213Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9B840 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9B840
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
uL5
K
188Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BFL1 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BFL1
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
eL13
L
220N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
uL13
M
222N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
eL14
N
175Leishmania donovaniMutation(s): 0 
Gene Names: RPL14 (LPD23)
Find proteins for Q25278 (Leishmania donovani)
Go to Gene View: RPL14
Go to UniProtKB:  Q25278
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
eL15
O
204Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BMB4 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BMB4
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
uL22
P
166Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BGL6 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BGL6
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
eL20
Q
179Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BRT7 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BRT7
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
eL19
R
245Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9B8Q2 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9B8Q2
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
eL21
S
159Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BRE2 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BRE2
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
eL22
T
129Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BU52 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BU52
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
uL14
U
139Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BSQ4 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BSQ4
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
uL23
V
145Leishmania donovaniMutation(s): 0 
Find proteins for D1M863 (Leishmania donovani)
Go to UniProtKB:  D1M863
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
eL24
W
124N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
uL24
X
143N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
eL27
Y
134Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BP34 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BP34
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
uL15
Z
145Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BSQ2 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BSQ2
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
eL28
a
147Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BAU9 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BAU9
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
eL29
b
70N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
uL2
c
260N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
uL3
d
419N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
eL30
e
104Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BRQ6 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BRQ6
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
eL31
f
183Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BSK4 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BSK4
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
eL32
g
133Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BS76 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BS76
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
eL34
h
168Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BUA1 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BUA1
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
uL29
i
127Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BIP6 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BIP6
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
eL33
j
144Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BR22 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BR22
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
eL36
k
105Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BS63 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BS63
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
eL37
l
83Leishmania donovaniMutation(s): 0 
Gene Names: RPL37
Find proteins for P62885 (Leishmania donovani)
Go to Gene View: RPL37
Go to UniProtKB:  P62885
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
eL43
m
92Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BFK4 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BFK4
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
eL38
n
83Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9B7P2 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9B7P2
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
eL39
o
51Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BCX6 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BCX6
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
uL4
p
373Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BKR3 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BKR3
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
eL40
q
128Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BMW6 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BMW6
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
eL42
r
106Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BBL5 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BBL5
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
uL18
s
305Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BS61 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BS61
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
eL6
t
195N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
uL30
u
252Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BI29 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BI29
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
eL8
v
348Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9B949 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9B949
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
uL6
w
190Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BFB5 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BFB5
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
eS1
0
264Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BRS2 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BRS2
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
eS4
1
273Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BBI6 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BBI6
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
eS6
3
249N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
eS7
4
200N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
eS8
5
220Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BH78 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BH78
Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
uS4
6
190Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BTJ0 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BTJ0
Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
RACK1
7
312Leishmania donovaniMutation(s): 0 
Find proteins for Q9BIJ5 (Leishmania donovani)
Go to UniProtKB:  Q9BIJ5
Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
uS14
8
57Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BJV7 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BJV7
Entity ID: 59
MoleculeChainsSequence LengthOrganismDetails
uS2
AC
246N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 60
MoleculeChainsSequence LengthOrganismDetails
eS10
AD
153Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BTG4 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BTG4
Entity ID: 61
MoleculeChainsSequence LengthOrganismDetails
uS17
AE
173N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 62
MoleculeChainsSequence LengthOrganismDetails
uS15
AG
151N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 63
MoleculeChainsSequence LengthOrganismDetails
uS11
AH
144N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 64
MoleculeChainsSequence LengthOrganismDetails
uS19
AI
152N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 65
MoleculeChainsSequence LengthOrganismDetails
uS8
AJ
130Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BAV6 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BAV6
Entity ID: 66
MoleculeChainsSequence LengthOrganismDetails
uS9
AK
149Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BI96 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BI96
Entity ID: 67
MoleculeChainsSequence LengthOrganismDetails
eS17
AL
143N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 68
MoleculeChainsSequence LengthOrganismDetails
uS13
AM
153Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BTF9 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BTF9
Entity ID: 69
MoleculeChainsSequence LengthOrganismDetails
uS7
AN
190Leishmania majorMutation(s): 0 
Find proteins for Q868B1 (Leishmania major)
Go to UniProtKB:  Q868B1
Entity ID: 70
MoleculeChainsSequence LengthOrganismDetails
eS19
AO
179Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BR60 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BR60
Entity ID: 71
MoleculeChainsSequence LengthOrganismDetails
uS5
AP
265N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 72
MoleculeChainsSequence LengthOrganismDetails
uS10
AQ
116Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BJI2 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BJI2
Entity ID: 73
MoleculeChainsSequence LengthOrganismDetails
eS21
AR
164N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 74
MoleculeChainsSequence LengthOrganismDetails
uS12
AS
143N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 75
MoleculeChainsSequence LengthOrganismDetails
eS24
AT
137N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 76
MoleculeChainsSequence LengthOrganismDetails
eS26
AV
112N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 77
MoleculeChainsSequence LengthOrganismDetails
eS27
AW
86N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 78
MoleculeChainsSequence LengthOrganismDetails
uS3
AX
219N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 79
MoleculeChainsSequence LengthOrganismDetails
eS30
AY
66Leishmania donovani (strain BPK282A1)Mutation(s): 0 
Find proteins for E9BLG3 (Leishmania donovani (strain BPK282A1))
Go to UniProtKB:  E9BLG3
Entity ID: 80
MoleculeChainsSequence LengthOrganismDetails
eS28
AZ
87N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 1
MoleculeChainsLengthOrganism
LSU-alphaA1781Leishmania donovani
Entity ID: 2
MoleculeChainsLengthOrganism
LSU-betaB1465Leishmania donovani
Entity ID: 3
MoleculeChainsLengthOrganism
5.8S rRNAC262Leishmania donovani
Entity ID: 4
MoleculeChainsLengthOrganism
5S rRNAD120Leishmania donovani
Entity ID: 5
MoleculeChainsLengthOrganism
srRNA1E213Leishmania donovani
Entity ID: 6
MoleculeChainsLengthOrganism
srRNA3F73Leishmania donovani
Entity ID: 7
MoleculeChainsLengthOrganism
srRNA2G183Leishmania donovani
Entity ID: 8
MoleculeChainsLengthOrganism
srRNA4H127Leishmania donovani
Entity ID: 52
MoleculeChainsLengthOrganism
18S rRNA22205Leishmania donovani
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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