4V7H | pdb_00004v7h

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

Validation slider image for 4V7H

This is version 1.6 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: https://doi.org/10.1016/j.str.2009.09.015
  • Primary Citation Related Structures: 
    4V7H

  • 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 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
    • Wadsworth Center, Empire State Plaza, Albany, NY 12201-0509, USA.

Macromolecule Content 

  • Total Structure Weight: 2,462.33 kDa 
  • Atom Count: 165,754 
  • Modeled Residue Count: 12,073 
  • Deposited Residue Count: 12,107 
  • Unique protein chains: 48
  • Unique nucleic acid chains: 5

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S0(A)B [auth AB]193Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S3C [auth AC]188Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S9(A)D [auth AD]158Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S2E [auth AE]162Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S5F [auth AG]186Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S22(A)G [auth AH]125Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S16(A)H [auth AI]138Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S20I [auth AJ]96Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S14(A)J [auth AK]125Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S23(A)K [auth AL]118Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S18L [auth AM]130Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S29(A)M [auth AN]50Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S13N [auth AO]84Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S11O [auth AQ]80Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
40S ribosomal protein S15P [auth AS]71Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
RACK1 proteinQ [auth AR]313Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
s19e proteinR [auth AT]141Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L32T [auth B0]109Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L39U [auth B1]48Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L30eV [auth B2]98Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein LP0W [auth B8]118Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L43X [auth B9]72Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L1Y [auth BA]213Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L2Z [auth BB]243Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L3AA [auth BC]362Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L4(B)BA [auth BD]257Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 29
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L5CA [auth BE]237Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 30
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L7(A)DA [auth BF]213Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 31
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L8(A)EA [auth BG]113Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 32
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L9(A)FA [auth BH]179Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 33
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L10GA [auth BI]165Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 34
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L11(B)HA [auth BJ]151Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 35
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L12IA [auth BK]138Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 36
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L15(A)JA [auth BL]192Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 37
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L16(A)KA [auth BM]178Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 38
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L17(A)LA [auth BN]150Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 39
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L18(A)MA [auth BO]121Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 40
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L19NA [auth BP]176Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 41
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L21(A)OA [auth BQ]116Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 42
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L23PA [auth BR]131Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 43
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L24(A)QA [auth BS]45Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 44
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L25RA [auth BT]80Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 45
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L26(A)SA [auth BU]116Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 46
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L28TA [auth BV]142Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 47
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L31(A)UA [auth BW]79Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 48
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L35VA [auth BX]86Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 49
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L37(A)WA [auth BY]52Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 50
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L42XA [auth BZ]92Thermomyces lanuginosusMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
18S rRNAA [auth AA]1,761Thermomyces lanuginosus
Sequence Annotations
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Reference Sequence
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Entity ID: 19
MoleculeChains LengthOrganismImage
P/E tRNAS [auth A7]76Thermomyces lanuginosus
Sequence Annotations
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Reference Sequence
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Entity ID: 51
MoleculeChains LengthOrganismImage
5S ribosomal RNAYA [auth B3]113Thermomyces lanuginosus
Sequence Annotations
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Reference Sequence
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Entity ID: 52
MoleculeChains LengthOrganismImage
5.8S ribosomal RNAZA [auth B4]157Thermomyces lanuginosus
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Reference Sequence
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Entity ID: 53
MoleculeChains LengthOrganismImage
26S ribosomal RNAAB [auth B5]3,170Thermomyces lanuginosus
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONSPIDER

Structure Validation

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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: 2015-04-22
    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
  • Version 1.6: 2024-02-28
    Changes: Data collection, Database references