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:  
    5T2C, 5T2A

  • 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
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uL16J213Leishmania donovaniMutation(s): 0 
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Entity ID: 11
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uL5K188Leishmania donovaniMutation(s): 0 
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Entity ID: 12
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eL13L220Leishmania donovaniMutation(s): 0 
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Entity ID: 13
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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
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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
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uL14U139Leishmania donovaniMutation(s): 0 
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Entity ID: 22
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uL23V145Leishmania donovaniMutation(s): 0 
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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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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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eL34HA [auth h]168Leishmania donovaniMutation(s): 0 
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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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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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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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Entity ID: 45
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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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Entity ID: 47
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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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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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uS2GB [auth AC]246Leishmania donovaniMutation(s): 0 
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eS10HB [auth AD]153Leishmania donovaniMutation(s): 0 
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uS17IB [auth AE]173Leishmania donovaniMutation(s): 0 
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uS15JB [auth AG]151Leishmania donovaniMutation(s): 0 
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uS11KB [auth AH]144Leishmania donovaniMutation(s): 0 
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uS19LB [auth AI]152Leishmania donovaniMutation(s): 0 
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uS8MB [auth AJ]130Leishmania donovaniMutation(s): 0 
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uS9NB [auth AK]149Leishmania donovaniMutation(s): 0 
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eS17OB [auth AL]143Leishmania donovaniMutation(s): 0 
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uS13PB [auth AM]153Leishmania donovaniMutation(s): 0 
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uS7QB [auth AN]190Leishmania donovaniMutation(s): 0 
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eS19RB [auth AO]179Leishmania donovaniMutation(s): 0 
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uS5SB [auth AP]265Leishmania donovaniMutation(s): 0 
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uS10TB [auth AQ]116Leishmania donovaniMutation(s): 0 
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eS21UB [auth AR]164Leishmania donovaniMutation(s): 0 
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uS12VB [auth AS]143Leishmania donovaniMutation(s): 0 
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eS24WB [auth AT]137Leishmania donovaniMutation(s): 0 
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eS26XB [auth AV]112Leishmania donovaniMutation(s): 0 
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eS27YB [auth AW]86Leishmania donovaniMutation(s): 0 
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uS3ZB [auth AX]219Leishmania donovaniMutation(s): 0 
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eS30AC [auth AY]66Leishmania donovaniMutation(s): 0 
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eS28BC [auth AZ]87Leishmania donovaniMutation(s): 0 
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LSU-alphaA1781Leishmania donovani
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Entity ID: 2
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LSU-betaB1465Leishmania 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
MoleculeChainsLengthOrganismImage
18S rRNAZA [auth 2]2205Leishmania 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