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 ery ...

    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 uS12Q144Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0306900
Find proteins for O97248 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein uS14T48Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0705700
Find proteins for C0H4K8 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein uS9M138Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0813900
Find proteins for Q8IAX5 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein uS15U149Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1358800
Find proteins for Q8IDB0 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein uS17V156Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0317600
Find proteins for O77381 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein uS4E185Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0520000
Find proteins for Q8I3R0 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein uS19X103Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1317800
Find proteins for C0H5C2 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein uS5G224Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1447000
Find proteins for Q8IL02 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein eS17W108Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1242700
Find proteins for Q8I502 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein eS12R114Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: RPS12MAL3P2.28PFC0295C
Find proteins for O97249 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 14
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40S ribosomal protein uS7I189Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0721600
Find proteins for Q8IBN5 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein eS10O79Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0719700
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein eS19Y154Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0422400
Find proteins for Q8IFP2 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein eS21Z72Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1144000
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Entity ID: 18
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40S ribosomal protein eS241120Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0519400
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Entity ID: 19
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40S ribosomal protein eS25268Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1421200
Find proteins for Q8ILN8 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein uS2C195Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF10_0264
Find proteins for Q8IJD4 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein eS26395Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0217800
Find proteins for O96258 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein eS27476Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1308300
Find proteins for Q8IEN2 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein eS28565Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1461300
Find proteins for Q8IKL9 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein eS30643Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: RPS30PFB0885w
Find proteins for O96269 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein eS1B210Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: MAL3P7.35PFC1020c
Find proteins for O97313 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 26
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40S ribosomal protein uS3D209Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1465900
Find proteins for Q8IKH8 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein eS4F257Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1105400
Find proteins for Q8IIU8 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein eS6H214Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1342000
Find proteins for Q8IDR9 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein uS8K129Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0316800
Find proteins for O77395 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein eS7J188Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1302800
Find proteins for Q8IET7 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein uS10N98Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1003500
Find proteins for Q8IK02 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein uS11P127Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein eL13AL211Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0814000
Find proteins for Q8IAX6 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 38
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60S ribosomal protein eL24A062Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1309100
Find proteins for Q8IEM3 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 39
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60S ribosomal protein uL15AO147Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0618300
Find proteins for C6KT23 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 40
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60S ribosomal protein eL44Ai95Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: RPL44MAL3P2.9PFC0200W
Find proteins for O97231 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 41
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60S ribosomal protein eL28A2118Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1142500
Find proteins for Q8IHU0 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein eL29A466Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1460300
Find proteins for C6S3J6 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein eL31A7102Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0503800
Find proteins for Q8I463 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 45
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60S ribosomal protein eL27A1145Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1460700
Find proteins for Q8IKM5 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 47
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60S ribosomal protein eL32A8125Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0903900
Find proteins for Q8I3B0 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 48
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60S ribosomal protein eL33A9103Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1142600
Find proteins for Q8IHT9 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 49
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60S ribosomal protein eL34Aa106Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0710600
Find proteins for Q8IBY4 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 50
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60S ribosomal protein eL36Ab105Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1109900
Find proteins for Q8I713 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 51
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60S ribosomal protein eL38Ad76Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1130100
Find proteins for Q8II62 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 52
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60S ribosomal protein eL39Ae50Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0611700
Find proteins for C0H4H3 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 53
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60S ribosomal protein eL40Af51Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1365900
Find proteins for Q8ID50 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 54
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60S ribosomal protein eL15AP204Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0415900
Find proteins for C0H4A6 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 55
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60S ribosomal protein eL43Ah85Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: RPL37APFB0455w
Find proteins for O96184 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 56
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60S ribosomal protein eL6AI213Plasmodium falciparum 3D7Mutation(s): 0 
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Entity ID: 57
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60S ribosomal protein eL37Ac89Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0706400
Find proteins for C0H4L5 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 58
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60S ribosomal protein uL13AK201Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1004000
Find proteins for Q8IJZ7 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 59
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60S ribosomal protein uL14AM132Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1331800
Find proteins for Q8IE09 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein eL18AS186Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1341300
Find proteins for C0H5G3 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein uL16AQ205Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1414300
Find proteins for Q8ILV2 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 62
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein uL18AR289Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1424100
Find proteins for Q8ILL3 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 63
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein uL22AW170Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1351400
Find proteins for Q8IDI5 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein uL23AY101Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1323400
Find proteins for Q8IE82 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 65
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein eL19AT181Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0614500
Find proteins for C6KSY6 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein uL24AZ121Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0312800
Find proteins for O77364 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 67
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60S ribosomal protein uL29A3119Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1124900
Find proteins for Q8IIB4 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 68
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60S ribosomal protein uL30A5223Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0307200
Find proteins for O97250 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 70
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein uL3AE380Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1027800
Find proteins for Q8IJC6 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 71
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein uL4AF390Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0507100
Find proteins for Q8I431 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein uL5AG159Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0719600
Find proteins for Q8IBQ6 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 73
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein eL20AU180Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1341200
Find proteins for Q8IDS6 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 75
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60S ribosomal protein eL21AV155Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1426000
Find proteins for Q8ILK3 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 76
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein eL41Ag37Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1144300
Find proteins for C6S3G4 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein eL22AX97Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0821700
Find proteins for Q8IB51 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein eS8L214Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1408600
Find proteins for Q8IM10 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein uS13S128Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1126200
Find proteins for Q8IIA2 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein eL30A698Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1019400
Find proteins for Q8IJK8 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein eL14AN146Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1431700
Find proteins for Q8ILE8 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 69
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60S ribosomal protein uL2AD247Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0516900
Find proteins for Q8I3T9 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 74
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein uL6AH185Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1323100
Find proteins for Q8IE85 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 78
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein eL8AJ244Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1424400
Find proteins for Q8ILL2 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 1
MoleculeChainsLengthOrganismImage
18S ribosomal RNAA1608Plasmodium falciparum 3D7
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Entity ID: 2
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P/E-tRNA775Escherichia coli
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Entity ID: 34
MoleculeChainsLengthOrganismImage
28S ribosomal RNAAA3192Plasmodium falciparum 3D7
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Entity ID: 35
MoleculeChainsLengthOrganismImage
5.8S ribosomal RNAAC151Plasmodium falciparum 3D7
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Entity ID: 36
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5S ribosomal RNAAB118Plasmodium falciparum 3D7
Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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