3JBP

Cryo-electron microscopy reconstruction of the Plasmodium falciparum 80S ribosome bound to E-tRNA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Dynamical features of the Plasmodium falciparum ribosome during translation.

Sun, M.Li, W.Blomqvist, K.Das, S.Hashem, Y.Dvorin, J.D.Frank, J.

(2015) Nucleic Acids Res 43: 10515-10524

  • DOI: https://doi.org/10.1093/nar/gkv991
  • Primary Citation of Related Structures:  
    3JBN, 3JBO, 3JBP

  • PubMed Abstract: 

    Plasmodium falciparum, the mosquito-transmitted Apicomplexan parasite, causes the most severe form of human malaria. In the asexual blood-stage, the parasite resides within erythrocytes where it proliferates, multiplies and finally spreads to new erythrocytes. Development of drugs targeting the ribosome, the site of protein synthesis, requires specific knowledge of its structure and work cycle, and, critically, the ways they differ from those in the human host. Here, we present five cryo-electron microscopy (cryo-EM) reconstructions of ribosomes purified from P. falciparum blood-stage schizonts at sub-nanometer resolution. Atomic models were built from these density maps by flexible fitting. Significantly, our study has taken advantage of new capabilities of cryo-EM, in visualizing several structures co-existing in the sample at once, at a resolution sufficient for building atomic models. We have discovered structural and dynamic features that differentiate the ribosomes of P. falciparum from those of mammalian system. Prompted by the absence of RACK1 on the ribosome in our and an earlier study we confirmed that RACK1 does not specifically co-purify with the 80S fraction in schizonts. More extensive studies, using cryo-EM methodology, of translation in the parasite will provide structural knowledge that may lead to development of novel anti-malarials.


  • Organizational Affiliation

    Department of Biological Sciences, Columbia University, New York, NY 10027, USA.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein uS3C [auth D]209Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein uS4D [auth E]185Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein uS5E [auth G]224Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein uS7F [auth I]189Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein uS8G [auth K]129Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein uS9H [auth M]138Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein eS17I [auth W]108Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein eS12J [auth R]114Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein eS10K [auth O]79Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein eS19L [auth Y]154Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein eS21M [auth Z]72Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein eS24N [auth 1]120Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein eS25O [auth 2]68Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein eS26P [auth 3]95Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein eS27Q [auth 4]76Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein eS28R [auth 5]65Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein eS30S [auth 6]43Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
Find proteins for O96269 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein eS1T [auth B]210Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
Find proteins for O97313 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein eS4U [auth F]257Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein eS6V [auth H]214Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein eS7W [auth J]188Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein eS8X [auth L]214Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein uS10Y [auth N]98Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein uS11Z [auth P]127Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein uS12AA [auth Q]144Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein uS13BA [auth S]128Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein uS14CA [auth T]48Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein uS15DA [auth U]149Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein uS17EA [auth V]156Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein uS19FA [auth X]103Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein uS2GA [auth C]195Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL13KA [auth AL]211Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL27LA [auth A1]145Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL28MA [auth A2]118Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL29NA [auth A4]66Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL30OA [auth A6]98Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL31PA [auth A7]102Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL14QA [auth AN]146Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL32RA [auth A8]125Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL33SA [auth A9]103Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL34TA [auth Aa]106Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL36UA [auth Ab]105Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL38VA [auth Ad]76Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL39WA [auth Ae]50Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL40XA [auth Af]51Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL15YA [auth AP]204Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL43ZA [auth Ah]85Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL44AB [auth Ai]95Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL6BB [auth AI]213Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL8CB [auth AJ]244Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL37DB [auth Ac]89Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein uL13EB [auth AK]201Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein uL14FB [auth AM]132Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL18GB [auth AS]186Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein uL15HB [auth AO]147Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein uL16IB [auth AQ]205Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein uL18JB [auth AR]289Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein uL22KB [auth AW]170Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein uL23LB [auth AY]101Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
Find proteins for Q8IE82 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL19MB [auth AT]181Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
Find proteins for C6KSY6 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein uL24NB [auth AZ]121Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
Find proteins for O77364 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein uL29OB [auth A3]119Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
Find proteins for Q8IIB4 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein uL30PB [auth A5]223Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
Find proteins for O97250 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein uL2QB [auth AD]247Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
Find proteins for Q8I3T9 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein uL3RB [auth AE]380Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
Find proteins for Q8IJC6 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein uL4SB [auth AF]390Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
Find proteins for Q8I431 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein uL5TB [auth AG]159Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
Find proteins for Q8IBQ6 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL20UB [auth AU]180Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
Find proteins for Q8IDS6 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein uL6VB [auth AH]185Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
Find proteins for Q8IE85 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL21WB [auth AV]155Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
Find proteins for Q8ILK3 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL41XB [auth Ag]37Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
Find proteins for C6S3G4 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL22YB [auth AX]97Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
Find proteins for Q8IB51 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein eL24ZB [auth A0]62Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
Find proteins for Q8IEM3 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 1
MoleculeChains LengthOrganismImage
18S ribosomal RNA1,608Plasmodium falciparum 3D7
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Entity ID: 2
MoleculeChains LengthOrganismImage
E-tRNAB [auth 7]74Plasmodium falciparum 3D7
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Entity ID: 34
MoleculeChains LengthOrganismImage
28S ribosomal RNAHA [auth AA]3,193Plasmodium falciparum 3D7
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Entity ID: 35
MoleculeChains LengthOrganismImage
5.8S ribosomal RNAIA [auth AC]151Plasmodium falciparum 3D7
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Entity ID: 36
MoleculeChains LengthOrganismImage
5S ribosomal RNAJA [auth AB]118Plasmodium falciparum 3D7
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-14
    Type: Initial release
  • Version 1.1: 2015-12-16
    Changes: Database references
  • Version 1.2: 2018-07-18
    Changes: Data collection
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Refinement description