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
  • 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 ...

    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 LengthOrganismDetailsImage
eL18I198Leishmania donovaniMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
uL16J213Leishmania donovaniMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
uL5K188Leishmania donovaniMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
eL13L220Leishmania donovaniMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
uL13M222Leishmania donovaniMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
eL14N175Leishmania donovaniMutation(s): 0 
Gene Names: RPL14LPD23
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
eL15O204Leishmania donovaniMutation(s): 0 
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Entity ID: 16
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uL22P166Leishmania donovaniMutation(s): 0 
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Entity ID: 17
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eL20Q179Leishmania donovaniMutation(s): 0 
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Entity ID: 18
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eL19R245Leishmania donovaniMutation(s): 0 
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Entity ID: 19
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eL21S159Leishmania donovaniMutation(s): 0 
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Entity ID: 20
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eL22T129Leishmania donovaniMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
uL14U139Leishmania donovaniMutation(s): 0 
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Entity ID: 22
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uL23V145Leishmania donovaniMutation(s): 0 
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Entity ID: 23
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eL24W124Leishmania donovaniMutation(s): 0 
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Entity ID: 24
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uL24X143Leishmania donovaniMutation(s): 0 
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Entity ID: 25
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eL27Y134Leishmania donovaniMutation(s): 0 
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Entity ID: 26
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uL15Z145Leishmania donovaniMutation(s): 0 
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Entity ID: 27
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eL28AA [auth a]147Leishmania donovaniMutation(s): 0 
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Entity ID: 28
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eL29BA [auth b]70Leishmania donovaniMutation(s): 0 
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Entity ID: 29
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uL2CA [auth c]260Leishmania donovaniMutation(s): 0 
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Entity ID: 30
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uL3DA [auth d]419Leishmania donovaniMutation(s): 0 
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Entity ID: 31
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eL30EA [auth e]104Leishmania donovaniMutation(s): 0 
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Entity ID: 32
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eL31FA [auth f]183Leishmania donovaniMutation(s): 0 
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Entity ID: 33
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eL32GA [auth g]133Leishmania donovaniMutation(s): 0 
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Entity ID: 34
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eL34HA [auth h]168Leishmania donovaniMutation(s): 0 
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Entity ID: 35
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uL29IA [auth i]127Leishmania donovaniMutation(s): 0 
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Entity ID: 36
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eL33JA [auth j]144Leishmania donovaniMutation(s): 0 
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Entity ID: 37
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eL36KA [auth k]105Leishmania donovaniMutation(s): 0 
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Entity ID: 38
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eL37LA [auth l]83Leishmania donovaniMutation(s): 0 
Gene Names: RPL37
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Entity ID: 39
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eL43MA [auth m]92Leishmania donovaniMutation(s): 0 
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eL38NA [auth n]83Leishmania donovaniMutation(s): 0 
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eL39OA [auth o]51Leishmania donovaniMutation(s): 0 
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Entity ID: 42
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uL4PA [auth p]373Leishmania donovaniMutation(s): 0 
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Entity ID: 43
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eL40QA [auth q]128Leishmania donovaniMutation(s): 0 
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Entity ID: 44
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eL42RA [auth r]106Leishmania donovaniMutation(s): 0 
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uL18SA [auth s]305Leishmania donovaniMutation(s): 0 
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Entity ID: 46
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eL6TA [auth t]195Leishmania donovaniMutation(s): 0 
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uL30UA [auth u]252Leishmania donovaniMutation(s): 0 
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Entity ID: 48
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eL8VA [auth v]348Leishmania donovaniMutation(s): 0 
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uL6WA [auth w]190Leishmania donovaniMutation(s): 0 
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Entity ID: 50
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eS1XA [auth 0]264Leishmania donovaniMutation(s): 0 
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eS4YA [auth 1]273Leishmania donovaniMutation(s): 0 
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eS6AB [auth 3]249Leishmania donovaniMutation(s): 0 
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eS7BB [auth 4]200Leishmania donovaniMutation(s): 0 
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eS8CB [auth 5]220Leishmania donovaniMutation(s): 0 
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uS4DB [auth 6]190Leishmania donovaniMutation(s): 0 
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RACK1EB [auth 7]312Leishmania donovaniMutation(s): 0 
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uS14FB [auth 8]57Leishmania donovaniMutation(s): 0 
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Entity ID: 59
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uS2GB [auth AC]246Leishmania donovaniMutation(s): 0 
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Entity ID: 60
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eS10HB [auth AD]153Leishmania donovaniMutation(s): 0 
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Entity ID: 61
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uS17IB [auth AE]173Leishmania donovaniMutation(s): 0 
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Entity ID: 62
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uS15JB [auth AG]151Leishmania donovaniMutation(s): 0 
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Entity ID: 63
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uS11KB [auth AH]144Leishmania donovaniMutation(s): 0 
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Entity ID: 64
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uS19LB [auth AI]152Leishmania donovaniMutation(s): 0 
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Entity ID: 65
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uS8MB [auth AJ]130Leishmania donovaniMutation(s): 0 
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Entity ID: 66
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uS9NB [auth AK]149Leishmania donovaniMutation(s): 0 
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Entity ID: 67
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eS17OB [auth AL]143Leishmania donovaniMutation(s): 0 
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Entity ID: 68
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uS13PB [auth AM]153Leishmania donovaniMutation(s): 0 
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Entity ID: 69
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uS7QB [auth AN]190Leishmania donovaniMutation(s): 0 
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Entity ID: 70
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eS19RB [auth AO]179Leishmania donovaniMutation(s): 0 
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Entity ID: 71
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uS5SB [auth AP]265Leishmania donovaniMutation(s): 0 
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Entity ID: 72
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uS10TB [auth AQ]116Leishmania donovaniMutation(s): 0 
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Entity ID: 73
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eS21UB [auth AR]164Leishmania donovaniMutation(s): 0 
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Entity ID: 74
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uS12VB [auth AS]143Leishmania donovaniMutation(s): 0 
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Entity ID: 75
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eS24WB [auth AT]137Leishmania donovaniMutation(s): 0 
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Entity ID: 76
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eS26XB [auth AV]112Leishmania donovaniMutation(s): 0 
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Entity ID: 77
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eS27YB [auth AW]86Leishmania donovaniMutation(s): 0 
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Entity ID: 78
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uS3ZB [auth AX]219Leishmania donovaniMutation(s): 0 
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Entity ID: 79
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eS30AC [auth AY]66Leishmania donovaniMutation(s): 0 
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Entity ID: 80
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eS28BC [auth AZ]87Leishmania donovaniMutation(s): 0 
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Entity ID: 1
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LSU-alphaA1,781Leishmania donovani
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Entity ID: 2
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LSU-betaB1,465Leishmania donovani
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Entity ID: 3
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5.8S rRNAC262Leishmania donovani
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Entity ID: 4
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5S rRNAD120Leishmania donovani
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Entity ID: 5
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srRNA1E213Leishmania donovani
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Entity ID: 6
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srRNA3F73Leishmania donovani
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Entity ID: 7
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srRNA2G183Leishmania donovani
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Entity ID: 8
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srRNA4H127Leishmania donovani
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Entity ID: 52
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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 

Structure Validation

View Full Validation Report



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