4V7H

Structure of the 80S rRNA and proteins and P/E tRNA for eukaryotic ribosome based on cryo-EM map of Thermomyces lanuginosus ribosome at 8.9A resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Comprehensive molecular structure of the eukaryotic ribosome.

Taylor, D.J.Devkota, B.Huang, A.D.Topf, M.Narayanan, E.Sali, A.Harvey, S.C.Frank, J.

(2009) Structure 17: 1591-1604

  • DOI: 10.1016/j.str.2009.09.015
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Despite the emergence of a large number of X-ray crystallographic models of the bacterial 70S ribosome over the past decade, an accurate atomic model of the eukaryotic 80S ribosome is still not available. Eukaryotic ribosomes possess more ribosomal p ...

    Despite the emergence of a large number of X-ray crystallographic models of the bacterial 70S ribosome over the past decade, an accurate atomic model of the eukaryotic 80S ribosome is still not available. Eukaryotic ribosomes possess more ribosomal proteins and ribosomal RNA than do bacterial ribosomes, which are implicated in extraribosomal functions in the eukaryotic cells. By combining cryo-EM with RNA and protein homology modeling, we obtained an atomic model of the yeast 80S ribosome complete with all ribosomal RNA expansion segments and all ribosomal proteins for which a structural homolog can be identified. Mutation or deletion of 80S ribosomal proteins can abrogate maturation of the ribosome, leading to several human diseases. We have localized one such protein unique to eukaryotes, rpS19e, whose mutations are associated with Diamond-Blackfan anemia in humans. Additionally, we characterize crucial interactions between the dynamic stalk base of the ribosome with eukaryotic elongation factor 2.


    Organizational Affiliation

    Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biology and Department of Biological Sciences, Columbia University, New York, NY 10032, USA. Electronic address: jf2192@columbia.edu.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S0(A)AB193Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S3AC188Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S9(A)AD158Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S2AE162Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S22(A)AH125Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S20AJ96Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S14(A)AK125Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S23(A)AL118Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S18AM130Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S13AO84Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S15AS71Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
RACK1 proteinAR313Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
s19e proteinAT141Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L32B0109Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L39B148Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L30eB298Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein LP0B8118Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L2BB243Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L3BC362Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L5BE237Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L7(A)BF213Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L8(A)BG113Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L9(A)BH179Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L11(B)BJ151Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L12BK138Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L15(A)BL192Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L17(A)BN150Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18(A)BO121Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L21(A)BQ116Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L23BR131Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L24(A)BS45Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L25BT80Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L26(A)BU116Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L35BX86Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L37(A)BY52Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L42BZ92Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S29(A)AN50Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S11AQ80Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L43B972Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L1BA213Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L4(B)BD257Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L10BI165Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L16(A)BM178Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L19BP176Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L28BV142Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L31(A)BW79Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S5AG186Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S16(A)AI138Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 19
MoleculeChainsLengthOrganism
P/E tRNAA776Thermomyces lanuginosus

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Entity ID: 51
MoleculeChainsLengthOrganism
5S ribosomal RNAB3113Thermomyces lanuginosus

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Entity ID: 52
MoleculeChainsLengthOrganism
5.8S ribosomal RNAB4157Thermomyces lanuginosus

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Entity ID: 53
MoleculeChainsLengthOrganism
26S ribosomal RNAB53170Thermomyces lanuginosus

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Entity ID: 1
MoleculeChainsLengthOrganism
18S rRNAAA1761Thermomyces lanuginosus
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other
  • Version 1.2: 2015-04-22
    Changes: Other
  • Version 1.3: 2017-11-22
    Changes: Data collection
  • Version 1.4: 2018-07-18
    Changes: Data collection
  • Version 1.5: 2019-12-18
    Changes: Derived calculations, Other