4V6I

Localization of the small subunit ribosomal proteins into a 6.1 A cryo-EM map of Saccharomyces cerevisiae translating 80S ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.80 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

Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-A resolution.

Armache, J.P.Jarasch, A.Anger, A.M.Villa, E.Becker, T.Bhushan, S.Jossinet, F.Habeck, M.Dindar, G.Franckenberg, S.Marquez, V.Mielke, T.Thomm, M.Berninghausen, O.Beatrix, B.Soding, J.Westhof, E.Wilson, D.N.Beckmann, R.

(2010) Proc Natl Acad Sci U S A 107: 19748-19753

  • DOI: 10.1073/pnas.1009999107
  • Primary Citation of Related Structures:  
    3IZD, 4V6I

  • PubMed Abstract: 
  • Protein biosynthesis, the translation of the genetic code into polypeptides, occurs on ribonucleoprotein particles called ribosomes. Although X-ray structures of bacterial ribosomes are available, high-resolution structures of eukaryotic 80S ribosomes are lacking ...

    Protein biosynthesis, the translation of the genetic code into polypeptides, occurs on ribonucleoprotein particles called ribosomes. Although X-ray structures of bacterial ribosomes are available, high-resolution structures of eukaryotic 80S ribosomes are lacking. Using cryoelectron microscopy and single-particle reconstruction, we have determined the structure of a translating plant (Triticum aestivum) 80S ribosome at 5.5-Å resolution. This map, together with a 6.1-Å map of a Saccharomyces cerevisiae 80S ribosome, has enabled us to model ∼98% of the rRNA. Accurate assignment of the rRNA expansion segments (ES) and variable regions has revealed unique ES-ES and r-protein-ES interactions, providing insight into the structure and evolution of the eukaryotic ribosome.


    Related Citations: 
    • Localization of eukaryote-specific ribosomal proteins in a 5.5-A cryo-EM map of the 80S eukaryotic ribosome.
      Armache, J.P., Jarasch, A., Anger, A.M., Villa, E., Becker, T., Bhushan, S., Jossinet, F., Habeck, M., Dindar, G., Franckenberg, S., Marquez, V., Mielke, T., Thomm, M., Berninghausen, O., Beatrix, B., Soding, J., Westhof, E., Wilson, D.N., Beckmann, R.
      (2010) Proc Natl Acad Sci U S A 107: 19754

    Organizational Affiliation

    Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.



Macromolecules

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Entity ID: 1
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40S ribosomal protein RACK1 (RACK1) Aa319Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein rpS0 (S2p) AA252Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein rpS3 (S3p) AB240Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein rpS4 (S4e) AD261Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein rpS9 (S4p) AC197Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein rpS2 (S5p) AE254Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein rpS7 (S7e) AG144Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 8
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40S ribosomal protein rpS5 (S7p) AF225Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein rpS22 (S8p) AH130Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein rpS16 (S9p) AI143Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein rpS20 (S10p) AJ121Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein rpS14 (S11p) AK137Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein rpS23 (S12p) AL145Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein rpS18 (S13p) AM146Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein rpS29 (S14p) AN56Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein rpS13 (S15p) AO151Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein rpS17 (S17e) AQ136Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein rpS11 (S17p) AP156Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein rpS15 (S19p) AR142Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein rpS19 (S19e) AS144Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein rpS21 (S21e) AT87Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein rpS25 (S25e) AV108Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein rpS26 (S26e) AW93Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein rpS27 (S27e) AX82Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein rpS28 (S28e) AY67Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein rpS30 (S30e) AZ63Saccharomyces cerevisiaeMutation(s): 0 
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Unknown 40S ribosomal protein XS1 Ab37Saccharomyces cerevisiaeMutation(s): 0 
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Unknown 40S ribosomal protein XS2 Ac26Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S24 AU135Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein rpL1 (L1p) BA217Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein rpL2 (L2p) BB254Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein rpL3 (L3p) BC388Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein rpL4 (L4p) BD362Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein rpL11 (L5p) BE174Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein rpL6 (L6e) BG176Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein rpL9 (L6p) BF191Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein rpL8 (L7ae) BH256Saccharomyces cerevisiaeMutation(s): 0 
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60S acidic ribosomal protein rpP0 (L10P) Bs312Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein rpL12 (L11p) BJ165Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein rpL16 (L13p) BK199Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein rpL14 (L14e) BN138Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein rpL23 (L14p) BM137Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein rpL15 (L15e) BP204Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein rpL28 (L15p) BO149Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein rpL18 (L18e) BR186Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein rpL19 (L19e) BT189Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein rpL21 (L21e) BU160Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein rpL22 (L22e) BW121Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein rpL17 (L22p) BV170Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein rpL25 (L23p) BX142Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein rpL24 (L24e) BZ155Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein rpL26 (L24p) BY123Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein rpL27 (L27e) Ba136Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein rpL29 (L29e) Bd59Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein rpL35 (L29p) Bc120Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein rpL30 (L30e) Bf105Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein rpL7 (L30p) Be244Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein rpL31 (L31e) Bg113Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein pL32 (L32e) Bh130Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein rpL34 (L34e) Bi118Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 61
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60S ribosomal protein rpL33 (L35ae) Bj107Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P05744 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 62
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein rpL36 (L36e) Bk100Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 63
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60S ribosomal protein rpL43 (L37ae) Bm92Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0CX25 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 64
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60S ribosomal protein rpL37 (L37e) Bl88Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P49166 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 65
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60S ribosomal protein rpL38 (L38e) Bn78Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 66
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60S ribosomal protein rpL39 (L39e) Bo51Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P04650 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 67
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60S ribosomal protein rpL40 (L40e) Bp52Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0CH08 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 68
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein rpL41 (L41e) Bq25Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0CX87 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 69
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60S ribosomal protein rpL42 (L44e) Br106Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0CX27 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 70
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Unknown protein BxBy21Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 71
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Unknown protein Bz15Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 72
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60S acidic ribosomal protein rpP11 (P1) BtBu106Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P05318 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 73
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60S acidic ribosomal protein (P2) BvBw106Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P05319 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 74
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60S ribosomal protein rpL5 (L18p) BQ297Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 75
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60S ribosomal protein rpL13 (L13e) BL170Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 76
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60S ribosomal protein rpL20 (L18ae) BS167Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q943F3 (Oryza sativa subsp. japonica)
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Entity ID: 77
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60S ribosomal protein rpL10 (L10e) BI221Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P41805 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 78
MoleculeChainsLengthOrganismImage
18S rRNACA1800Saccharomyces cerevisiae
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Entity ID: 79
MoleculeChainsLengthOrganismImage
P-SITE TRNA ASPCB75Saccharomyces cerevisiae
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  • Entity ID: 80
    MoleculeChainsLengthOrganismImage
    MRNA, RNA (5'-R(P*AP*AP*AP*AP*GP*AP*CP*UP*UP*CP*A)-3')CC11Saccharomyces cerevisiae
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    Entity ID: 81
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    25S rRNADA3396Saccharomyces cerevisiae
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    Entity ID: 82
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    5.8S rRNADB158Saccharomyces cerevisiae
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    Entity ID: 83
    MoleculeChainsLengthOrganismImage
    5S rRNADC118Saccharomyces cerevisiae
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 8.80 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: 2014-07-09
      Type: Initial release
    • Version 1.1: 2014-12-10
      Changes: Other
    • Version 1.2: 2015-03-25
      Changes: Other
    • Version 1.3: 2019-12-18
      Changes: Data collection, Database references, Other