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
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein RACK1 (RACK1)A [auth Aa]319Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 2
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40S ribosomal protein rpS0 (S2p)B [auth AA]252Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 3
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40S ribosomal protein rpS3 (S3p)C [auth AB]240Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 4
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40S ribosomal protein rpS4 (S4e)D [auth AD]261Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein rpS9 (S4p)E [auth AC]197Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 6
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40S ribosomal protein rpS2 (S5p)F [auth AE]254Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein rpS7 (S7e)G [auth AG]144Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein rpS5 (S7p)H [auth AF]225Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein rpS22 (S8p)I [auth AH]130Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein rpS16 (S9p)J [auth AI]143Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein rpS20 (S10p)K [auth AJ]121Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein rpS14 (S11p)L [auth AK]137Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein rpS23 (S12p)M [auth AL]145Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein rpS18 (S13p)N [auth AM]146Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein rpS29 (S14p)O [auth AN]56Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein rpS13 (S15p)P [auth AO]151Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein rpS17 (S17e)Q [auth AQ]136Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein rpS11 (S17p)R [auth AP]156Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein rpS15 (S19p)S [auth AR]142Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein rpS19 (S19e)T [auth AS]144Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein rpS21 (S21e)U [auth AT]87Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein rpS25 (S25e)V [auth AV]108Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein rpS26 (S26e)W [auth AW]93Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein rpS27 (S27e)X [auth AX]82Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein rpS28 (S28e)Y [auth AY]67Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein rpS30 (S30e)Z [auth AZ]63Saccharomyces cerevisiaeMutation(s): 0 
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Unknown 40S ribosomal protein XS1AA [auth Ab]37Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 28
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Unknown 40S ribosomal protein XS2BA [auth Ac]26Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 29
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40S ribosomal protein S24CA [auth AU]135Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein rpL1 (L1p)DA [auth BA]217Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein rpL2 (L2p)EA [auth BB]254Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein rpL3 (L3p)FA [auth BC]388Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein rpL4 (L4p)GA [auth BD]362Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein rpL11 (L5p)HA [auth BE]174Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein rpL6 (L6e)IA [auth BG]176Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 36
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60S ribosomal protein rpL9 (L6p)JA [auth BF]191Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein rpL8 (L7ae)KA [auth BH]256Saccharomyces cerevisiaeMutation(s): 0 
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60S acidic ribosomal protein rpP0 (L10P)LA [auth Bs]312Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein rpL12 (L11p)MA [auth BJ]165Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein rpL16 (L13p)NA [auth BK]199Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein rpL14 (L14e)OA [auth BN]138Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein rpL23 (L14p)PA [auth BM]137Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein rpL15 (L15e)QA [auth BP]204Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein rpL28 (L15p)RA [auth BO]149Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein rpL18 (L18e)SA [auth BR]186Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein rpL19 (L19e)TA [auth BT]189Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein rpL21 (L21e)UA [auth BU]160Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein rpL22 (L22e)VA [auth BW]121Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein rpL17 (L22p)WA [auth BV]170Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 50
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60S ribosomal protein rpL25 (L23p)XA [auth BX]142Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 51
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60S ribosomal protein rpL24 (L24e)YA [auth BZ]155Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 52
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60S ribosomal protein rpL26 (L24p)ZA [auth BY]123Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 53
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60S ribosomal protein rpL27 (L27e)AB [auth Ba]136Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 54
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60S ribosomal protein rpL29 (L29e)BB [auth Bd]59Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 55
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60S ribosomal protein rpL35 (L29p)CB [auth Bc]120Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein rpL30 (L30e)DB [auth Bf]105Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 57
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60S ribosomal protein rpL7 (L30p)EB [auth Be]244Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 58
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60S ribosomal protein rpL31 (L31e)FB [auth Bg]113Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 59
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60S ribosomal protein pL32 (L32e)GB [auth Bh]130Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein rpL34 (L34e)HB [auth Bi]118Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein rpL33 (L35ae)IB [auth Bj]107Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 62
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein rpL36 (L36e)JB [auth Bk]100Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 63
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60S ribosomal protein rpL43 (L37ae)KB [auth Bm]92Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 64
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60S ribosomal protein rpL37 (L37e)LB [auth Bl]88Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 65
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60S ribosomal protein rpL38 (L38e)MB [auth Bn]78Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 66
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60S ribosomal protein rpL39 (L39e)NB [auth Bo]51Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 67
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60S ribosomal protein rpL40 (L40e)OB [auth Bp]52Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 68
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60S ribosomal protein rpL41 (L41e)PB [auth Bq]25Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 69
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60S ribosomal protein rpL42 (L44e)QB [auth Br]106Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 70
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown proteinRB [auth Bx],
SB [auth By]
21Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 71
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown proteinTB [auth Bz]15Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetailsImage
60S acidic ribosomal protein rpP11 (P1)UB [auth Bt],
VB [auth Bu]
106Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 73
MoleculeChainsSequence LengthOrganismDetailsImage
60S acidic ribosomal protein (P2)WB [auth Bv],
XB [auth Bw]
106Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 74
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60S ribosomal protein rpL5 (L18p)YB [auth BQ]297Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 75
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60S ribosomal protein rpL13 (L13e)ZB [auth BL]170Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 76
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein rpL20 (L18ae)AC [auth BS]167Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 77
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60S ribosomal protein rpL10 (L10e)BC [auth BI]221Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 78
MoleculeChainsLengthOrganismImage
18S rRNACC [auth CA]1800Saccharomyces cerevisiae
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Entity ID: 79
MoleculeChainsLengthOrganismImage
P-SITE TRNA ASPDC [auth CB]75Saccharomyces 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')EC [auth CC]11Saccharomyces cerevisiae
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Entity ID: 81
MoleculeChainsLengthOrganismImage
25S rRNAFC [auth DA]3396Saccharomyces cerevisiae
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Entity ID: 82
MoleculeChainsLengthOrganismImage
5.8S rRNAGC [auth DB]158Saccharomyces cerevisiae
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Entity ID: 83
MoleculeChainsLengthOrganismImage
5S rRNAHC [auth DC]118Saccharomyces cerevisiae
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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