3JBO

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.80 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: 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 ...

    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.


    Related Citations: 
    • Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine.
      Wong, W., Bai, X.C., Brown, A., Fernandez, I.S., Hanssen, E., Condron, M., Tan, Y.H., Baum, J., Scheres, S.H.
      (2014) Elife 3: --

    Organizational Affiliation

    Department of Biological Sciences, Columbia University, New York, NY 10027, USA Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA Howard Hughes Medical Institute, Columbia University, New York, NY 10032, USA jf2192@cumc.columbia.edu.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein uS12C [auth Q]144Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0306900
UniProt
Find proteins for O97248 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein uS13D [auth S]128Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1126200
UniProt
Find proteins for Q8IIA2 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein uS14E [auth T]48Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0705700
UniProt
Find proteins for C0H4K8 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein uS9F [auth M]138Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0813900
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Find proteins for Q8IAX5 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein uS15G [auth U]149Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1358800
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Find proteins for Q8IDB0 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 8
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40S ribosomal protein uS17H [auth V]156Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0317600
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Find proteins for O77381 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 9
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40S ribosomal protein uS4I [auth E]185Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0520000
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Entity ID: 10
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40S ribosomal protein uS19J [auth X]103Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1317800
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Find proteins for C0H5C2 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 11
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40S ribosomal protein uS5K [auth G]224Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1447000
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Entity ID: 12
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40S ribosomal protein eS17L [auth W]108Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1242700
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Entity ID: 13
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40S ribosomal protein eS12M [auth R]114Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: RPS12MAL3P2.28PFC0295C
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Entity ID: 14
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40S ribosomal protein uS7N [auth I]189Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0721600
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Entity ID: 15
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40S ribosomal protein eS10O79Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0719700
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Entity ID: 16
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40S ribosomal protein eS19P [auth Y]154Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0422400
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Entity ID: 17
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40S ribosomal protein eS21Q [auth Z]72Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1144000
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Entity ID: 18
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40S ribosomal protein eS24R [auth 1]120Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0519400
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Entity ID: 19
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40S ribosomal protein eS25S [auth 2]68Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1421200
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Entity ID: 20
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40S ribosomal protein uS2T [auth C]195Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF10_0264
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Entity ID: 21
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40S ribosomal protein eS26U [auth 3]95Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0217800
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Find proteins for O96258 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 22
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40S ribosomal protein eS27V [auth 4]76Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1308300
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Entity ID: 23
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40S ribosomal protein eS28W [auth 5]65Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1461300
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Entity ID: 24
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40S ribosomal protein eS30X [auth 6]43Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: RPS30PFB0885w
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Entity ID: 25
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40S ribosomal protein eS1Y [auth B]210Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: MAL3P7.35PFC1020c
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Entity ID: 26
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40S ribosomal protein uS3Z [auth D]209Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1465900
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Entity ID: 27
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40S ribosomal protein eS4AA [auth F]257Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1105400
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Entity ID: 28
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40S ribosomal protein eS6BA [auth H]214Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1342000
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Entity ID: 29
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40S ribosomal protein uS8CA [auth K]129Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0316800
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Find proteins for O77395 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 30
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40S ribosomal protein eS7DA [auth J]188Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1302800
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein uS10EA [auth N]98Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1003500
UniProt
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Entity ID: 32
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40S ribosomal protein uS11FA [auth P]127Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 33
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40S ribosomal protein eS8GA [auth L]214Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1408600
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Entity ID: 37
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60S ribosomal protein eL13KA [auth AL]211Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0814000
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Entity ID: 38
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60S ribosomal protein eL24LA [auth A0]62Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1309100
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Entity ID: 39
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60S ribosomal protein uL15MA [auth AO]147Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0618300
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Entity ID: 40
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60S ribosomal protein eL44NA [auth Ai]95Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: RPL44MAL3P2.9PFC0200W
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Entity ID: 41
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60S ribosomal protein eL28OA [auth A2]118Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1142500
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Entity ID: 42
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60S ribosomal protein eL29PA [auth A4]66Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1460300
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Find proteins for C6S3J6 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 43
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60S ribosomal protein eL30QA [auth A6]98Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1019400
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Entity ID: 44
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60S ribosomal protein eL31RA [auth A7]102Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0503800
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Entity ID: 45
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60S ribosomal protein eL27SA [auth A1]145Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1460700
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Entity ID: 46
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60S ribosomal protein eL14TA [auth AN]146Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1431700
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Entity ID: 47
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60S ribosomal protein eL32UA [auth A8]125Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0903900
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Entity ID: 48
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60S ribosomal protein eL33VA [auth A9]103Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1142600
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Entity ID: 49
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60S ribosomal protein eL34WA [auth Aa]106Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0710600
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Entity ID: 50
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60S ribosomal protein eL36XA [auth Ab]105Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1109900
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Find proteins for Q8I713 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 51
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60S ribosomal protein eL38YA [auth Ad]76Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1130100
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Entity ID: 52
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60S ribosomal protein eL39ZA [auth Ae]50Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0611700
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Find proteins for C0H4H3 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 53
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60S ribosomal protein eL40AB [auth Af]51Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1365900
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Entity ID: 54
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60S ribosomal protein eL15BB [auth AP]204Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0415900
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Find proteins for C0H4A6 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 55
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60S ribosomal protein eL43CB [auth Ah]85Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: RPL37APFB0455w
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Find proteins for O96184 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 56
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60S ribosomal protein eL6DB [auth AI]213Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 57
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60S ribosomal protein eL37EB [auth Ac]89Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0706400
UniProt
Find proteins for C0H4L5 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein uL13FB [auth AK]201Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1004000
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Entity ID: 59
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60S ribosomal protein uL14GB [auth AM]132Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1331800
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Entity ID: 60
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60S ribosomal protein eL18HB [auth AS]186Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1341300
UniProt
Find proteins for C0H5G3 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 61
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60S ribosomal protein uL16IB [auth AQ]205Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1414300
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Entity ID: 62
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60S ribosomal protein uL18JB [auth AR]289Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1424100
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Entity ID: 63
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60S ribosomal protein uL22KB [auth AW]170Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1351400
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Entity ID: 64
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60S ribosomal protein uL23LB [auth AY]101Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1323400
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Find proteins for Q8IE82 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 65
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60S ribosomal protein eL19MB [auth AT]181Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0614500
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Find proteins for C6KSY6 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 66
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60S ribosomal protein uL24NB [auth AZ]121Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0312800
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Find proteins for O77364 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 67
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60S ribosomal protein uL29OB [auth A3]119Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1124900
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Entity ID: 68
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60S ribosomal protein uL30PB [auth A5]223Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0307200
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Find proteins for O97250 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 69
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60S ribosomal protein uL2QB [auth AD]247Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0516900
UniProt
Find proteins for Q8I3T9 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 70
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60S ribosomal protein uL3RB [auth AE]380Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1027800
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Find proteins for Q8IJC6 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 71
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60S ribosomal protein uL4SB [auth AF]390Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0507100
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Find proteins for Q8I431 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 72
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60S ribosomal protein uL5TB [auth AG]159Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0719600
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Entity ID: 73
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60S ribosomal protein eL20UB [auth AU]180Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1341200
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Entity ID: 74
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60S ribosomal protein uL6VB [auth AH]185Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1323100
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Find proteins for Q8IE85 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 75
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60S ribosomal protein eL21WB [auth AV]155Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1426000
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Entity ID: 76
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60S ribosomal protein eL41XB [auth Ag]37Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1144300
UniProt
Find proteins for C6S3G4 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 77
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60S ribosomal protein eL22YB [auth AX]97Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0821700
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Find proteins for Q8IB51 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 78
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60S ribosomal protein eL8ZB [auth AJ]244Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1424400
UniProt
Find proteins for Q8ILL2 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 1
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18S ribosomal RNAA1608Plasmodium falciparum 3D7
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Entity ID: 2
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P/E-tRNAB [auth 7]75Escherichia coli
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Entity ID: 34
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28S ribosomal RNAHA [auth AA]3192Plasmodium falciparum 3D7
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Entity ID: 35
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5.8S ribosomal RNAIA [auth AC]151Plasmodium falciparum 3D7
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Entity ID: 36
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5S ribosomal RNAJA [auth AB]118Plasmodium falciparum 3D7
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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: 2016-06-08
    Changes: Atomic model
  • Version 1.3: 2018-07-18
    Changes: Data collection