5T2A

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 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
  • 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-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

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



Macromolecules

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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
eL18
I
198Leishmania donovaniMutation(s): 0 
Find proteins for E9BUI1 (Leishmania donovani (strain BPK282A1))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
uL16
J
213Leishmania donovaniMutation(s): 0 
Find proteins for E9B840 (Leishmania donovani (strain BPK282A1))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
uL5
K
188Leishmania donovaniMutation(s): 0 
Find proteins for E9BFL1 (Leishmania donovani (strain BPK282A1))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
eL13
L
220Leishmania donovaniMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
uL13
M
222Leishmania donovaniMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
eL14
N
175Leishmania donovaniMutation(s): 0 
Gene Names: RPL14LPD23
Find proteins for Q25278 (Leishmania donovani)
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
eL15
O
204Leishmania donovaniMutation(s): 0 
Find proteins for E9BMB4 (Leishmania donovani (strain BPK282A1))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
uL22
P
166Leishmania donovaniMutation(s): 0 
Find proteins for E9BGL6 (Leishmania donovani (strain BPK282A1))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
eL20
Q
179Leishmania donovaniMutation(s): 0 
Find proteins for E9BRT7 (Leishmania donovani (strain BPK282A1))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
eL19
R
245Leishmania donovaniMutation(s): 0 
Find proteins for E9B8Q2 (Leishmania donovani (strain BPK282A1))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
eL21
S
159Leishmania donovaniMutation(s): 0 
Find proteins for E9BRE2 (Leishmania donovani (strain BPK282A1))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
eL22
T
129Leishmania donovaniMutation(s): 0 
Find proteins for E9BU52 (Leishmania donovani (strain BPK282A1))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
uL14
U
139Leishmania donovaniMutation(s): 0 
Find proteins for E9BSQ4 (Leishmania donovani (strain BPK282A1))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
uL23
V
145Leishmania donovaniMutation(s): 0 
Find proteins for D1M863 (Leishmania donovani)
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
eL24
W
124Leishmania donovaniMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
uL24
X
143Leishmania donovaniMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
eL27
Y
134Leishmania donovaniMutation(s): 0 
Find proteins for E9BP34 (Leishmania donovani (strain BPK282A1))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
uL15
Z
145Leishmania donovaniMutation(s): 0 
Find proteins for E9BSQ2 (Leishmania donovani (strain BPK282A1))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
eL28
a
147Leishmania donovaniMutation(s): 0 
Find proteins for E9BAU9 (Leishmania donovani (strain BPK282A1))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
eL29
b
70Leishmania donovaniMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
uL2
c
260Leishmania donovaniMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
uL3
d
419Leishmania donovaniMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
eL30
e
104Leishmania donovaniMutation(s): 0 
Find proteins for E9BRQ6 (Leishmania donovani (strain BPK282A1))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
eL31
f
183Leishmania donovaniMutation(s): 0 
Find proteins for E9BSK4 (Leishmania donovani (strain BPK282A1))
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
eL32
g
133Leishmania donovaniMutation(s): 0 
Find proteins for E9BS76 (Leishmania donovani (strain BPK282A1))
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
eL34
h
168Leishmania donovaniMutation(s): 0 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
uL29
i
127Leishmania donovaniMutation(s): 0 
Find proteins for E9BIP6 (Leishmania donovani (strain BPK282A1))
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
eL33
j
144Leishmania donovaniMutation(s): 0 
Find proteins for E9BR22 (Leishmania donovani (strain BPK282A1))
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
eL36
k
105Leishmania donovaniMutation(s): 0 
Find proteins for E9BS63 (Leishmania donovani (strain BPK282A1))
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
eL37
l
83Leishmania donovaniMutation(s): 0 
Gene Names: RPL37
Find proteins for P62885 (Leishmania donovani)
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
eL43
m
92Leishmania donovaniMutation(s): 0 
Find proteins for E9BFK4 (Leishmania donovani (strain BPK282A1))
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
eL38
n
83Leishmania donovaniMutation(s): 0 
Find proteins for E9B7P2 (Leishmania donovani (strain BPK282A1))
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
eL39
o
51Leishmania donovaniMutation(s): 0 
Find proteins for E9BCX6 (Leishmania donovani (strain BPK282A1))
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
uL4
p
373Leishmania donovaniMutation(s): 0 
Find proteins for E9BKR3 (Leishmania donovani (strain BPK282A1))
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
eL40
q
128Leishmania donovaniMutation(s): 0 
Find proteins for E9BMW6 (Leishmania donovani (strain BPK282A1))
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
eL42
r
106Leishmania donovaniMutation(s): 0 
Find proteins for E9BBL5 (Leishmania donovani (strain BPK282A1))
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
uL18
s
305Leishmania donovaniMutation(s): 0 
Find proteins for E9BS61 (Leishmania donovani (strain BPK282A1))
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
eL6
t
195Leishmania donovaniMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
uL30
u
252Leishmania donovaniMutation(s): 0 
Find proteins for E9BI29 (Leishmania donovani (strain BPK282A1))
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
eL8
v
348Leishmania donovaniMutation(s): 0 
Find proteins for E9B949 (Leishmania donovani (strain BPK282A1))
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
uL6
w
190Leishmania donovaniMutation(s): 0 
Find proteins for E9BFB5 (Leishmania donovani (strain BPK282A1))
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
eS1
0
264Leishmania donovaniMutation(s): 0 
Find proteins for E9BRS2 (Leishmania donovani (strain BPK282A1))
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
eS4
1
273Leishmania donovaniMutation(s): 0 
Find proteins for E9BBI6 (Leishmania donovani (strain BPK282A1))
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
eS6
3
249Leishmania donovaniMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
eS7
4
200Leishmania donovaniMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
eS8
5
220Leishmania donovaniMutation(s): 0 
Find proteins for E9BH78 (Leishmania donovani (strain BPK282A1))
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
uS4
6
190Leishmania donovaniMutation(s): 0 
Find proteins for E9BTJ0 (Leishmania donovani (strain BPK282A1))
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
RACK1
7
312Leishmania donovaniMutation(s): 0 
Find proteins for Q9BIJ5 (Leishmania donovani)
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
uS14
8
57Leishmania donovaniMutation(s): 0 
Find proteins for E9BJV7 (Leishmania donovani (strain BPK282A1))
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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetails
uS2
AC
246Leishmania donovaniMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetails
eS10
AD
153Leishmania donovaniMutation(s): 0 
Find proteins for E9BTG4 (Leishmania donovani (strain BPK282A1))
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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetails
uS17
AE
173Leishmania donovaniMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 62
MoleculeChainsSequence LengthOrganismDetails
uS15
AG
151Leishmania donovaniMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 63
MoleculeChainsSequence LengthOrganismDetails
uS11
AH
144Leishmania donovaniMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetails
uS19
AI
152Leishmania donovaniMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 65
MoleculeChainsSequence LengthOrganismDetails
uS8
AJ
130Leishmania donovaniMutation(s): 0 
Find proteins for E9BAV6 (Leishmania donovani (strain BPK282A1))
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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetails
uS9
AK
149Leishmania donovaniMutation(s): 0 
Find proteins for E9BI96 (Leishmania donovani (strain BPK282A1))
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Entity ID: 67
MoleculeChainsSequence LengthOrganismDetails
eS17
AL
143Leishmania donovaniMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 68
MoleculeChainsSequence LengthOrganismDetails
uS13
AM
153Leishmania donovaniMutation(s): 0 
Find proteins for E9BTF9 (Leishmania donovani (strain BPK282A1))
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Entity ID: 69
MoleculeChainsSequence LengthOrganismDetails
uS7
AN
190Leishmania donovaniMutation(s): 0 
Find proteins for Q868B1 (Leishmania major)
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Entity ID: 70
MoleculeChainsSequence LengthOrganismDetails
eS19
AO
179Leishmania donovaniMutation(s): 0 
Find proteins for E9BR60 (Leishmania donovani (strain BPK282A1))
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Entity ID: 71
MoleculeChainsSequence LengthOrganismDetails
uS5
AP
265Leishmania donovaniMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetails
uS10
AQ
116Leishmania donovaniMutation(s): 0 
Find proteins for E9BJI2 (Leishmania donovani (strain BPK282A1))
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Entity ID: 73
MoleculeChainsSequence LengthOrganismDetails
eS21
AR
164Leishmania donovaniMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 74
MoleculeChainsSequence LengthOrganismDetails
uS12
AS
143Leishmania donovaniMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 75
MoleculeChainsSequence LengthOrganismDetails
eS24
AT
137Leishmania donovaniMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 76
MoleculeChainsSequence LengthOrganismDetails
eS26
AV
112Leishmania donovaniMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetails
eS27
AW
86Leishmania donovaniMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 78
MoleculeChainsSequence LengthOrganismDetails
uS3
AX
219Leishmania donovaniMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 79
MoleculeChainsSequence LengthOrganismDetails
eS30
AY
66Leishmania donovaniMutation(s): 0 
Find proteins for E9BLG3 (Leishmania donovani (strain BPK282A1))
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Entity ID: 80
MoleculeChainsSequence LengthOrganismDetails
eS28
AZ
87Leishmania donovaniMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 1
MoleculeChainsLengthOrganism
LSU-alphaA1781Leishmania donovani

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Entity ID: 2
MoleculeChainsLengthOrganism
LSU-betaB1465Leishmania donovani

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Entity ID: 3
MoleculeChainsLengthOrganism
5.8S rRNAC262Leishmania donovani

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Entity ID: 4
MoleculeChainsLengthOrganism
5S rRNAD120Leishmania donovani

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Entity ID: 5
MoleculeChainsLengthOrganism
srRNA1E213Leishmania donovani

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Entity ID: 6
MoleculeChainsLengthOrganism
srRNA3F73Leishmania donovani

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Entity ID: 7
MoleculeChainsLengthOrganism
srRNA2G183Leishmania donovani

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Entity ID: 8
MoleculeChainsLengthOrganism
srRNA4H127Leishmania donovani

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Entity ID: 52
MoleculeChainsLengthOrganism
18S rRNA22205Leishmania donovani
Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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