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 1.2 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: https://doi.org/10.1038/ncomms13223
  • Primary Citation of Related Structures:  
    5T2A, 5T2C

  • 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.

    • Organizational Affiliation: 

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


Macromolecules

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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
eL18198Leishmania donovaniMutation(s): 0 
UniProt
Find proteins for A0A3S7XBN1 (Leishmania donovani)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
uL16213Leishmania donovaniMutation(s): 0 
UniProt
Find proteins for A0A3S5H5C4 (Leishmania donovani)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
uL5188Leishmania donovaniMutation(s): 0 
UniProt
Find proteins for A0A3S5H5A8 (Leishmania donovani)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
eL13220Leishmania donovaniMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
uL13222Leishmania donovaniMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
eL14175Leishmania donovaniMutation(s): 0 
UniProt
Find proteins for Q25278 (Leishmania donovani)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
eL15204Leishmania donovaniMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
uL22166Leishmania donovaniMutation(s): 0 
UniProt
Find proteins for A0A3S7WY02 (Leishmania donovani)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
eL20179Leishmania donovaniMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
eL19245Leishmania donovaniMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
eL21159Leishmania donovaniMutation(s): 0 
UniProt
Find proteins for A0A3Q8ICH0 (Leishmania donovani)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
eL22129Leishmania donovaniMutation(s): 0 
UniProt
Find proteins for A0A3Q8IJA8 (Leishmania donovani)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
uL14139Leishmania donovaniMutation(s): 0 
UniProt
Find proteins for A0A3Q8IIA7 (Leishmania donovani)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
uL23145Leishmania donovaniMutation(s): 0 
UniProt
Find proteins for D1M863 (Leishmania donovani)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
eL24124Leishmania donovaniMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
uL24143Leishmania donovaniMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
eL27134Leishmania donovaniMutation(s): 0 
UniProt
Find proteins for E9BP34 (Leishmania donovani)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
uL15145Leishmania donovaniMutation(s): 0 
UniProt
Find proteins for A0A3Q8IGI9 (Leishmania donovani)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
eL28AA [auth a]147Leishmania donovaniMutation(s): 0 
UniProt
Find proteins for A0A3Q8I959 (Leishmania donovani)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
eL29BA [auth b]70Leishmania donovaniMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
uL2CA [auth c]260Leishmania donovaniMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
uL3DA [auth d]419Leishmania donovaniMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
eL30EA [auth e]104Leishmania donovaniMutation(s): 0 
UniProt
Find proteins for A0A3Q8IET6 (Leishmania donovani)
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
eL31FA [auth f]183Leishmania donovaniMutation(s): 0 
UniProt
Find proteins for E9BSK4 (Leishmania donovani)
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
eL32GA [auth g]133Leishmania donovaniMutation(s): 0 
UniProt
Find proteins for A0A3S7X954 (Leishmania donovani)
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
eL34HA [auth h]168Leishmania donovaniMutation(s): 0 
UniProt
Find proteins for A0A3Q8IHK2 (Leishmania donovani)
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
uL29IA [auth i]127Leishmania donovaniMutation(s): 0 
UniProt
Find proteins for E9BIP6 (Leishmania donovani)
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
eL33JA [auth j]144Leishmania donovaniMutation(s): 0 
UniProt
Find proteins for A0A3Q8II82 (Leishmania donovani)
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
eL36KA [auth k]105Leishmania donovaniMutation(s): 0 
UniProt
Find proteins for A0A3S7X961 (Leishmania donovani)
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
eL37LA [auth l]83Leishmania donovaniMutation(s): 0 
UniProt
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
eL43MA [auth m]92Leishmania donovaniMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
eL38NA [auth n]83Leishmania donovaniMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
eL39OA [auth o]51Leishmania donovaniMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
uL4PA [auth p]373Leishmania donovaniMutation(s): 0 
UniProt
Find proteins for A0A3S5H7L0 (Leishmania donovani)
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
eL40QA [auth q]128Leishmania donovaniMutation(s): 0 
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Find proteins for A0A3Q8ISR1 (Leishmania donovani)
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
eL42RA [auth r]106Leishmania donovaniMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
uL18SA [auth s]305Leishmania donovaniMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
eL6TA [auth t]195Leishmania donovaniMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
uL30UA [auth u]252Leishmania donovaniMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
eL8VA [auth v]348Leishmania donovaniMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
uL6WA [auth w]190Leishmania donovaniMutation(s): 0 
UniProt
Find proteins for A0A3S7WWL2 (Leishmania donovani)
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
eS1XA [auth 0]264Leishmania donovaniMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
eS4YA [auth 1]273Leishmania donovaniMutation(s): 0 
UniProt
Find proteins for A0A3Q8I8K3 (Leishmania donovani)
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
eS6AB [auth 3]249Leishmania donovaniMutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
eS7BB [auth 4]200Leishmania donovaniMutation(s): 0 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
eS8CB [auth 5]220Leishmania donovaniMutation(s): 0 
UniProt
Find proteins for A0A3Q8ID68 (Leishmania donovani)
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
uS4DB [auth 6]190Leishmania donovaniMutation(s): 0 
UniProt
Find proteins for A0A3S5H5Z2 (Leishmania donovani)
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
RACK1EB [auth 7]312Leishmania donovaniMutation(s): 0 
UniProt
Find proteins for Q9BIJ5 (Leishmania donovani)
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
uS14FB [auth 8]57Leishmania donovaniMutation(s): 0 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
uS2GB [auth AC]246Leishmania donovaniMutation(s): 0 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
eS10HB [auth AD]153Leishmania donovaniMutation(s): 0 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
uS17IB [auth AE]173Leishmania donovaniMutation(s): 0 
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
uS15JB [auth AG]151Leishmania donovaniMutation(s): 0 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
uS11KB [auth AH]144Leishmania donovaniMutation(s): 0 
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
uS19LB [auth AI]152Leishmania donovaniMutation(s): 0 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
uS8MB [auth AJ]130Leishmania donovaniMutation(s): 0 
UniProt
Find proteins for E9BAV6 (Leishmania donovani)
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
uS9NB [auth AK]149Leishmania donovaniMutation(s): 0 
UniProt
Find proteins for E9BI96 (Leishmania donovani)
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
eS17OB [auth AL]143Leishmania donovaniMutation(s): 0 
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
uS13PB [auth AM]153Leishmania donovaniMutation(s): 0 
UniProt
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
uS7QB [auth AN]190Leishmania donovaniMutation(s): 0 
UniProt
Find proteins for Q868B1 (Leishmania major)
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
eS19RB [auth AO]179Leishmania donovaniMutation(s): 0 
UniProt
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
uS5SB [auth AP]265Leishmania donovaniMutation(s): 0 
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
uS10TB [auth AQ]116Leishmania donovaniMutation(s): 0 
UniProt
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
eS21UB [auth AR]164Leishmania donovaniMutation(s): 0 
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
uS12VB [auth AS]143Leishmania donovaniMutation(s): 0 
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
eS24WB [auth AT]137Leishmania donovaniMutation(s): 0 
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
eS26XB [auth AV]112Leishmania donovaniMutation(s): 0 
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
eS27YB [auth AW]86Leishmania donovaniMutation(s): 0 
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
uS3ZB [auth AX]219Leishmania donovaniMutation(s): 0 
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
eS30AC [auth AY]66Leishmania donovaniMutation(s): 0 
UniProt
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Entity ID: 80
MoleculeChains Sequence LengthOrganismDetailsImage
eS28BC [auth AZ]87Leishmania donovaniMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
LSU-alpha1,781Leishmania donovani
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Entity ID: 2
MoleculeChains LengthOrganismImage
LSU-beta1,465Leishmania donovani
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Entity ID: 3
MoleculeChains LengthOrganismImage
5.8S rRNA262Leishmania donovani
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Entity ID: 4
MoleculeChains LengthOrganismImage
5S rRNA120Leishmania donovani
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Entity ID: 5
MoleculeChains LengthOrganismImage
srRNA1213Leishmania donovani
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Entity ID: 6
MoleculeChains LengthOrganismImage
srRNA373Leishmania donovani
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Entity ID: 7
MoleculeChains LengthOrganismImage
srRNA2183Leishmania donovani
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Entity ID: 8
MoleculeChains LengthOrganismImage
srRNA4127Leishmania donovani
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Entity ID: 52
MoleculeChains LengthOrganismImage
18S rRNAZA [auth 2]2,205Leishmania donovani
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-25
    Type: Initial release
  • Version 1.1: 2018-07-18
    Changes: Data collection
  • Version 1.2: 2024-11-13
    Changes: Data collection, Database references, Structure summary