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: 8.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.4 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
  • Primary Citation of Related Structures:  

  • 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

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S0(A)
AB
193N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S3
AC
188N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S9(A)
AD
158N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S2
AE
162N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S5
AG
186N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S22(A)
AH
125N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S16(A)
AI
138N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S20
AJ
96N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S14(A)
AK
125N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S23(A)
AL
118N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S18
AM
130N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S29(A)
AN
50N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S13
AO
84N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S11
AQ
80N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S15
AS
71N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
RACK1 protein
AR
313N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
s19e protein
AT
141N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L32
B0
109N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L39
B1
48N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L30e
B2
98N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein LP0
B8
118N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L43
B9
72N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L1
BA
213N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L2
BB
243N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L3
BC
362N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L4(B)
BD
257N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L5
BE
237N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L7(A)
BF
213N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L8(A)
BG
113N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L9(A)
BH
179N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L10
BI
165N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L11(B)
BJ
151N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L12
BK
138N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L15(A)
BL
192N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L16(A)
BM
178N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L17(A)
BN
150N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18(A)
BO
121N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L19
BP
176N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L21(A)
BQ
116N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L23
BR
131N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L24(A)
BS
45N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L25
BT
80N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L26(A)
BU
116N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L28
BV
142N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L31(A)
BW
79N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L35
BX
86N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L37(A)
BY
52N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L42
BZ
92N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 1
MoleculeChainsLengthOrganism
18S rRNAAA1761Thermomyces lanuginosus
Entity ID: 19
MoleculeChainsLengthOrganism
P/E tRNAA776Thermomyces lanuginosus
Entity ID: 51
MoleculeChainsLengthOrganism
5S ribosomal RNAB3113Thermomyces lanuginosus
Entity ID: 52
MoleculeChainsLengthOrganism
5.8S ribosomal RNAB4157Thermomyces lanuginosus
Entity ID: 53
MoleculeChainsLengthOrganism
26S ribosomal RNAB53170Thermomyces lanuginosus
Small Molecules
Modified Residues  11 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
A7
RNA LINKINGC9 H13 N2 O9 PU
5MC
Query on 5MC
A7
RNA LINKINGC10 H16 N3 O8 PC
M2G
Query on M2G
A7
RNA LINKINGC12 H18 N5 O8 PG
1MA
Query on 1MA
A7
RNA LINKINGC11 H16 N5 O7 PA
OMC
Query on OMC
A7
RNA LINKINGC10 H16 N3 O8 PC
YYG
Query on YYG
A7
RNA LINKINGC21 H29 N6 O12 PG
2MG
Query on 2MG
A7
RNA LINKINGC11 H16 N5 O8 PG
OMG
Query on OMG
A7
RNA LINKINGC11 H16 N5 O8 PG
7MG
Query on 7MG
A7
RNA LINKINGC11 H18 N5 O8 PG
5MU
Query on 5MU
A7
RNA LINKINGC10 H15 N2 O9 PU
H2U
Query on H2U
A7
RNA LINKINGC9 H15 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
OTHERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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