4V7R

Yeast 80S ribosome.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 0.341 
  • R-Value Work: 0.278 
  • R-Value Observed: 0.280 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of the eukaryotic ribosome.

Ben-Shem, A.Jenner, L.Yusupova, G.Yusupov, M.

(2010) Science 330: 1203-1209

  • DOI: 10.1126/science.1194294
  • Primary Citation of Related Structures:  
    4V7R

  • PubMed Abstract: 
  • Crystal structures of prokaryotic ribosomes have described in detail the universally conserved core of the translation mechanism. However, many facets of the translation process in eukaryotes are not shared with prokaryotes. The crystal structure of the yeast 80S ribosome determined at 4 ...

    Crystal structures of prokaryotic ribosomes have described in detail the universally conserved core of the translation mechanism. However, many facets of the translation process in eukaryotes are not shared with prokaryotes. The crystal structure of the yeast 80S ribosome determined at 4.15 angstrom resolution reveals the higher complexity of eukaryotic ribosomes, which are 40% larger than their bacterial counterparts. Our model shows how eukaryote-specific elements considerably expand the network of interactions within the ribosome and provides insights into eukaryote-specific features of protein synthesis. Our crystals capture the ribosome in the ratcheted state, which is essential for translocation of mRNA and transfer RNA (tRNA), and in which the small ribosomal subunit has rotated with respect to the large subunit. We describe the conformational changes in both ribosomal subunits that are involved in ratcheting and their implications in coordination between the two associated subunits and in mRNA and tRNA translocation.


    Organizational Affiliation

    IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), 1 rue Laurent Fries, BP10142, Illkirch F-67400, France. adam@igbmc.fr



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S0-AB [auth AA],
WB [auth CA]
252Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S2C [auth AB],
XB [auth CB]
254Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S3D [auth AC],
YB [auth CC]
240Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S5E [auth AD],
ZB [auth CD]
225Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S9-AF [auth AE],
AC [auth CE]
197Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S11G [auth AF],
BC [auth CF]
156Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S13H [auth AG],
CC [auth CG]
151Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S14-AI [auth AH],
DC [auth CH]
137Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S15J [auth AI],
EC [auth CI]
142Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S16K [auth AJ],
FC [auth CJ]
143Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S17-AL [auth AK],
GC [auth CK]
136Saccharomyces cerevisiaeMutation(s): 0 
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Find proteins for P02407 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S18M [auth AL],
HC [auth CL]
146Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S19-AN [auth AM],
IC [auth CM]
144Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S20O [auth AN],
JC [auth CN]
121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S22-AP [auth AO],
KC [auth CO]
130Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 17
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40S ribosomal protein S23Q [auth AP],
LC [auth CP]
145Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S25-AR [auth AQ],
MC [auth CQ]
108Saccharomyces cerevisiaeMutation(s): 0 
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Find proteins for Q3E792 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S28-AS [auth AR],
NC [auth CR]
67Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S29-AT [auth AS],
OC [auth CS]
56Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein subunit beta-like protein; RACK-1U [auth AT],
PC [auth CT]
319Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Unassigned secondary structureV [auth Aa],
RB [auth Bo],
QC [auth Ca]
20Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 23
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Unassigned secondary structureW [auth Ab],
RC [auth Cb]
105Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Unassigned secondary structureX [auth Ac],
SC [auth Cc]
93Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Unassigned secondary structureY [auth Ad],
TC [auth Cd]
35Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
Unassigned secondary structureZ [auth Ae],
MB [auth Bj],
HE [auth Dj]
21Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
Unassigned secondary structureAA [auth Af]11Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
Unassigned secondary structureBA [auth Ah],
UC [auth Ch]
41Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L1FA [auth BA],
YC [auth DA]
217Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L2GA [auth BB],
ZC [auth DB]
254Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L3HA [auth BC],
AD [auth DC]
387Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L4-AIA [auth BD],
BD [auth DD]
362Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L5JA [auth BE],
CD [auth DE]
297Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L6-AKA [auth BF],
DD [auth DF]
176Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L7-ALA [auth BG],
ED [auth DG]
244Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L8-AMA [auth BH],
FD [auth DH]
256Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L9-ANA [auth BI],
GD [auth DI]
191Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L10OA [auth BJ],
HD [auth DJ]
221Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 42
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60S ribosomal protein L11-APA [auth BK],
ID [auth DK]
174Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 43
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60S ribosomal protein L14-AQA [auth BN],
LD [auth DN]
138Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 44
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60S ribosomal protein L15-ARA [auth BO],
MD [auth DO]
204Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L16-ASA [auth BP],
ND [auth DP]
199Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 46
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60S ribosomal protein L17-ATA [auth BQ],
OD [auth DQ]
184Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L18UA [auth BR],
PD [auth DR]
186Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L19VA [auth BS],
QD [auth DS]
189Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 49
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60S ribosomal protein L21-AWA [auth BT],
RD [auth DT]
160Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L23XA [auth BU],
SD [auth DU]
137Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 51
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60S ribosomal protein L24-AYA [auth BV],
TD [auth DV]
155Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 52
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60S ribosomal protein L25ZA [auth BW],
UD [auth DW]
142Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 53
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60S ribosomal protein L26-AAB [auth BX],
VD [auth DX]
127Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 54
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60S ribosomal protein L28BB [auth BY],
WD [auth DY]
149Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L30CB [auth BZ],
XD [auth DZ]
105Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L31-ADB [auth Ba],
YD [auth Da]
113Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L32EB [auth Bb],
ZD [auth Db]
130Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L35FB [auth Bc],
AE [auth Dc]
120Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L37-AGB [auth Bd],
BE [auth Dd]
88Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P49166 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L39HB [auth Be],
CE [auth De]
51Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L42IB [auth Bf],
DE [auth Df]
106Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 62
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L43JB [auth Bg],
EE [auth Dg]
92Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 63
MoleculeChainsSequence LengthOrganismDetailsImage
Unassigned secondary structureKB [auth Bh],
FE [auth Dh]
44Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetailsImage
Unassigned secondary structureLB [auth Bi],
GE [auth Di]
12Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 65
MoleculeChainsSequence LengthOrganismDetailsImage
Unassigned secondary structureNB [auth Bk],
IE [auth Dk]
16Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetailsImage
Unassigned secondary structureOB [auth Bl]19Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 67
MoleculeChainsSequence LengthOrganismDetailsImage
Unassigned secondary structurePB [auth Bm]9Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 68
MoleculeChainsSequence LengthOrganismDetailsImage
Unassigned secondary structureQB [auth Bn]27Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 69
MoleculeChainsSequence LengthOrganismDetailsImage
Unassigned secondary structureSB [auth Bp]8Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 70
MoleculeChainsSequence LengthOrganismDetailsImage
Unassigned secondary structureTB [auth Bq]17Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 71
MoleculeChainsSequence LengthOrganismDetailsImage
Unassigned secondary structureUB [auth Br]23Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L12JD [auth DL]165Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 73
MoleculeChainsSequence LengthOrganismDetailsImage
60S acidic ribosomal protein P0KD [auth DM]312Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChainsLengthOrganismImage
18S ribosomal RNAA [auth A1],
VB [auth C1]
1800Saccharomyces cerevisiae
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Entity ID: 29
MoleculeChainsLengthOrganismImage
25S ribosomal RNACA [auth B1],
VC [auth D1]
3396Saccharomyces cerevisiae S288C
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Entity ID: 30
MoleculeChainsLengthOrganismImage
5S ribosomal RNADA [auth B2],
WC [auth D2]
121Saccharomyces cerevisiae
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Entity ID: 31
MoleculeChainsLengthOrganismImage
5.8S ribosomal RNAEA [auth B3],
XC [auth D3]
158Saccharomyces cerevisiae
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OHX
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