4V5Z

Structure of a mammalian 80S ribosome obtained by docking homology models of the RNA and proteins into an 8.7 A cryo-EM map


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the Mammalian 80S Ribosome at 8.7 A Resolution

Chandramouli, P.Topf, M.Menetret, J.F.Eswar, N.Cannone, J.J.Gutell, R.R.Sali, A.Akey, C.W.

(2008) Structure 16: 535-548

  • DOI: 10.1016/j.str.2008.01.007
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In this paper, we present a structure of the mammalian ribosome determined at approximately 8.7 A resolution by electron cryomicroscopy and single-particle methods. A model of the ribosome was created by docking homology models of subunit rRNAs and c ...

    In this paper, we present a structure of the mammalian ribosome determined at approximately 8.7 A resolution by electron cryomicroscopy and single-particle methods. A model of the ribosome was created by docking homology models of subunit rRNAs and conserved proteins into the density map. We then modeled expansion segments in the subunit rRNAs and found unclaimed density for approximately 20 proteins. In general, many conserved proteins and novel proteins interact with expansion segments to form an integrated framework that may stabilize the mature ribosome. Our structure provides a snapshot of the mammalian ribosome at the beginning of translation and lends support to current models in which large movements of the small subunit and L1 stalk occur during tRNA translocation. Finally, details are presented for intersubunit bridges that are specific to the eukaryotic ribosome. We suggest that these bridges may help reset the conformation of the ribosome to prepare for the next cycle of chain elongation.


    Organizational Affiliation

    Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, MA 02118, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
40S Ribosomal protein RACK1
Aa
317N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
40S Ribosomal protein SA
Ab
295N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
40S Ribosomal protein S3e
Ac
243N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
40S Ribosomal protein S9e
Ad
209N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
40S Ribosomal protein S2e
Ae
179N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
40S Ribosomal protein S5e
Ag
204N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
40S Ribosomal protein S15ae
Ah
130N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
40S Ribosomal protein S16e
Ai
146N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
40S Ribosomal protein S20e
Aj
119N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
40S Ribosomal protein S14e
Ak
151N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
40S Ribosomal protein S23e
Al
143N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
40S Ribosomal protein S18e
Am
152N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
40S Ribosomal protein S29e
An
56N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
40S Ribosomal protein S13e
Ao
89N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
40S Ribosomal protein S11e
Aq
158N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
40S Ribosomal protein S15e
As
145N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
60S Ribosomal protein L8
Ba
257N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
60S Ribosomal protein L3
Bb
403N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
60S Ribosomal protein L4
Bc
421N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
60S Ribosomal protein L11
Bd
178N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
60S Ribosomal protein L9
Be
192N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
60S Ribosomal protein L7a
Bf
266N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 59
MoleculeChainsSequence LengthOrganismDetails
60S acidic ribosomal protein P0
Bg
317N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 60
MoleculeChainsSequence LengthOrganismDetails
60S Ribosomal protein L10
Bh
214N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 61
MoleculeChainsSequence LengthOrganismDetails
60S Ribosomal protein L12
Bi
165N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 62
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L13a
Bj
203N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 63
MoleculeChainsSequence LengthOrganismDetails
60S Ribosomal protein L23
Bk
140N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 64
MoleculeChainsSequence LengthOrganismDetails
60S Ribosomal protein L27a
Bl
148N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 65
MoleculeChainsSequence LengthOrganismDetails
60S Ribosomal protein L15e
Bm
204N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 66
MoleculeChainsSequence LengthOrganismDetails
60S Ribosomal protein L5
Bn
297N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 67
MoleculeChainsSequence LengthOrganismDetails
60S Ribosomal protein L18
Bo
188N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 68
MoleculeChainsSequence LengthOrganismDetails
60S Ribosomal protein L19
Bp
196N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 69
MoleculeChainsSequence LengthOrganismDetails
60S Ribosomal protein L19
B7
13N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 70
MoleculeChainsSequence LengthOrganismDetails
60S Ribosomal protein L21
Bq
160N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 71
MoleculeChainsSequence LengthOrganismDetails
60S Ribosomal protein L17
Br
184N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 72
MoleculeChainsSequence LengthOrganismDetails
60S Ribosomal protein L23a
Bs
156N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 73
MoleculeChainsSequence LengthOrganismDetails
60S Ribosomal protein L26
Bt
145N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 74
MoleculeChainsSequence LengthOrganismDetails
60S Ribosomal protein L24
Bu
157N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 75
MoleculeChainsSequence LengthOrganismDetails
60S Ribosomal protein L35
Bv
123N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 76
MoleculeChainsSequence LengthOrganismDetails
60S Ribosomal protein L35
B8
10N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 77
MoleculeChainsSequence LengthOrganismDetails
60S Ribosomal protein L7
Bw
270N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 78
MoleculeChainsSequence LengthOrganismDetails
60S Ribosomal protein L31
Bx
125N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 79
MoleculeChainsSequence LengthOrganismDetails
60S Ribosomal protein L32
By
135N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 80
MoleculeChainsSequence LengthOrganismDetails
60S Ribosomal protein L32
B9
58N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 81
MoleculeChainsSequence LengthOrganismDetails
60S Ribosomal protein L37a
Bz
92N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 82
MoleculeChainsSequence LengthOrganismDetails
60S Ribosomal protein L37e
B2
97N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 83
MoleculeChainsSequence LengthOrganismDetails
60S Ribosomal protein L39e
B3
51N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 84
MoleculeChainsSequence LengthOrganismDetails
60S Ribosomal protein L44e
B4
106N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 85
MoleculeChainsSequence LengthOrganismDetails
60S Ribosomal protein L10a
B5
212N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 86
MoleculeChainsSequence LengthOrganismDetails
60S Ribosomal protein L30e
B6
115N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 1
MoleculeChainsLengthOrganism
18S Ribosomal RNAAA1563Canis lupus familiaris
Entity ID: 2
MoleculeChainsLengthOrganism
RNA Expansion segment ES3AB35Canis lupus familiaris
Entity ID: 3
MoleculeChainsLengthOrganism
RNA Expansion segment ES4AC32Canis lupus familiaris
Entity ID: 4
MoleculeChainsLengthOrganism
RNA Expansion segment ES6 part IAD42Canis lupus familiaris
Entity ID: 5
MoleculeChainsLengthOrganism
RNA Expansion segment ES6 part IIAE32Canis lupus familiaris
Entity ID: 6
MoleculeChainsLengthOrganism
RNA Expansion segment ES9AF31Canis lupus familiaris
Entity ID: 7
MoleculeChainsLengthOrganism
RNA helixAG14Canis lupus familiaris
Entity ID: 8
MoleculeChainsLengthOrganism
RNA helixAH41Canis lupus familiaris
Entity ID: 25
MoleculeChainsLengthOrganism
5.8S Ribosomal RNAB1123Canis lupus familiaris
Entity ID: 26
MoleculeChainsLengthOrganism
28S Ribosomal RNAB02903Canis lupus familiaris
Entity ID: 27
MoleculeChainsLengthOrganism
RNA Expansion segment ES3BA21Canis lupus familiaris
Entity ID: 28
MoleculeChainsLengthOrganism
RNA Expansion segment ES4BB27Canis lupus familiaris
Entity ID: 29
MoleculeChainsLengthOrganism
RNA Expansion segment ES5BC17Canis lupus familiaris
Entity ID: 30
MoleculeChainsLengthOrganism
RNA Expansion segment ES7 part IBD16Canis lupus familiaris
Entity ID: 31
MoleculeChainsLengthOrganism
RNA Expansion segment ES7 part IIBE54Canis lupus familiaris
Entity ID: 32
MoleculeChainsLengthOrganism
RNA Expansion segment ES7 part IIIBF120Canis lupus familiaris
Entity ID: 33
MoleculeChainsLengthOrganism
RNA Expansion segment ES9BG48Canis lupus familiaris
Entity ID: 34
MoleculeChainsLengthOrganism
RNA Expansion segment ES12BH25Canis lupus familiaris
Entity ID: 35
MoleculeChainsLengthOrganism
RNA Expansion segment ES15 part IBI72Canis lupus familiaris
Entity ID: 36
MoleculeChainsLengthOrganism
RNA Expansion segment ES15 part IIBJ30Canis lupus familiaris
Entity ID: 37
MoleculeChainsLengthOrganism
RNA Expansion segment ES19BK26Canis lupus familiaris
Entity ID: 38
MoleculeChainsLengthOrganism
RNA Expansion segment ES20BL20Canis lupus familiaris
Entity ID: 39
MoleculeChainsLengthOrganism
RNA Expansion segment ES24BM19Canis lupus familiaris
Entity ID: 40
MoleculeChainsLengthOrganism
RNA Expansion segment ES27BN78Canis lupus familiaris
Entity ID: 41
MoleculeChainsLengthOrganism
RNA Expansion segment ES30BO20Canis lupus familiaris
Entity ID: 42
MoleculeChainsLengthOrganism
RNA Expansion segment ES31 part IBP15Canis lupus familiaris
Entity ID: 43
MoleculeChainsLengthOrganism
RNA Expansion segment ES31 part IIBQ30Canis lupus familiaris
Entity ID: 44
MoleculeChainsLengthOrganism
RNA Expansion segment ES39 part IBR30Canis lupus familiaris
Entity ID: 45
MoleculeChainsLengthOrganism
RNA Expansion segment ES39 part IIBS38Canis lupus familiaris
Entity ID: 46
MoleculeChainsLengthOrganism
RNA Expansion segment ES39 part IIIBT30Canis lupus familiaris
Entity ID: 47
MoleculeChainsLengthOrganism
RNA Expansion segment ES41BU16Canis lupus familiaris
Entity ID: 48
MoleculeChainsLengthOrganism
RNA Expansion segment ES9 part2BV22Canis lupus familiaris
Entity ID: 49
MoleculeChainsLengthOrganism
RNA Expansion segment ES10BW16Canis lupus familiaris
Entity ID: 50
MoleculeChainsLengthOrganism
RNA helicesBX113Canis lupus familiaris
Entity ID: 51
MoleculeChainsLengthOrganism
5S Ribosomal RNABY115Canis lupus familiaris
Entity ID: 52
MoleculeChainsLengthOrganism
E site t-RNABZ72Canis lupus familiaris
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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: 2015-03-25
    Type: Other