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

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S0(A)
AB
193Thermomyces lanuginosusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S3
AC
188Thermomyces lanuginosusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S9(A)
AD
158Thermomyces lanuginosusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S2
AE
162Thermomyces lanuginosusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S5
AG
186Thermomyces lanuginosusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S22(A)
AH
125Thermomyces lanuginosusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S16(A)
AI
138Thermomyces lanuginosusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S20
AJ
96Thermomyces lanuginosusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S14(A)
AK
125Thermomyces lanuginosusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S23(A)
AL
118Thermomyces lanuginosusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S18
AM
130Thermomyces lanuginosusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S29(A)
AN
50Thermomyces lanuginosusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S13
AO
84Thermomyces lanuginosusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S11
AQ
80Thermomyces lanuginosusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S15
AS
71Thermomyces lanuginosusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
RACK1 protein
AR
313Thermomyces lanuginosusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
s19e protein
AT
141Thermomyces lanuginosusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L32
B0
109Thermomyces lanuginosusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L39
B1
48Thermomyces lanuginosusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L30e
B2
98Thermomyces lanuginosusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein LP0
B8
118Thermomyces lanuginosusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L43
B9
72Thermomyces lanuginosusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L1
BA
213Thermomyces lanuginosusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L2
BB
243Thermomyces lanuginosusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L3
BC
362Thermomyces lanuginosusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L4(B)
BD
257Thermomyces lanuginosusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L5
BE
237Thermomyces lanuginosusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L7(A)
BF
213Thermomyces lanuginosusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L8(A)
BG
113Thermomyces lanuginosusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L9(A)
BH
179Thermomyces lanuginosusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L10
BI
165Thermomyces lanuginosusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L11(B)
BJ
151Thermomyces lanuginosusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L12
BK
138Thermomyces lanuginosusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L15(A)
BL
192Thermomyces lanuginosusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L16(A)
BM
178Thermomyces lanuginosusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L17(A)
BN
150Thermomyces lanuginosusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18(A)
BO
121Thermomyces lanuginosusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L19
BP
176Thermomyces lanuginosusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L21(A)
BQ
116Thermomyces lanuginosusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L23
BR
131Thermomyces lanuginosusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L24(A)
BS
45Thermomyces lanuginosusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L25
BT
80Thermomyces lanuginosusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L26(A)
BU
116Thermomyces lanuginosusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L28
BV
142Thermomyces lanuginosusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L31(A)
BW
79Thermomyces lanuginosusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L37(A)
BY
52Thermomyces lanuginosusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L42
BZ
92Thermomyces lanuginosusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L35
BX
86Thermomyces lanuginosusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar nucleic acids by: Sequence   |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
18S rRNAAA1761Thermomyces lanuginosus

Find similar nucleic acids by: Sequence   |  Structure

Entity ID: 19
MoleculeChainsLengthOrganism
P/E tRNAA776Thermomyces lanuginosus

Find similar nucleic acids by: Sequence   |  Structure

Entity ID: 51
MoleculeChainsLengthOrganism
5S ribosomal RNAB3113Thermomyces lanuginosus

Find similar nucleic acids by: Sequence   |  Structure

Entity ID: 52
MoleculeChainsLengthOrganism
5.8S ribosomal RNAB4157Thermomyces lanuginosus

Find similar nucleic acids by: Sequence   |  Structure

Entity ID: 53
MoleculeChainsLengthOrganism
26S ribosomal RNAB53170Thermomyces 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