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 1.3 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: https://doi.org/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 4.15 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
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S0-AB [auth AA],
WB [auth CA]
252Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2C [auth AB],
XB [auth CB]
254Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3D [auth AC],
YB [auth CC]
240Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S5E [auth AD],
ZB [auth CD]
225Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9-AAC [auth CE],
F [auth AE]
197Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for O13516 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11BC [auth CF],
G [auth AF]
156Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13CC [auth CG],
H [auth AG]
151Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14-ADC [auth CH],
I [auth AH]
137Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15EC [auth CI],
J [auth AI]
142Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16FC [auth CJ],
K [auth AJ]
143Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17-AGC [auth CK],
L [auth AK]
136Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18HC [auth CL],
M [auth AL]
146Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19-AIC [auth CM],
N [auth AM]
144Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S20JC [auth CN],
O [auth AN]
121Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S22-AKC [auth CO],
P [auth AO]
130Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P0C0W1 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23LC [auth CP],
Q [auth AP]
145Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25-AMC [auth CQ],
R [auth AQ]
108Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q3E792 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28-ANC [auth CR],
S [auth AR]
67Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q3E7X9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S29-AOC [auth CS],
T [auth AS]
56Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P41057 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein subunit beta-like protein; RACK-1PC [auth CT],
U [auth AT]
319Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Unassigned secondary structureQC [auth Ca],
RB [auth Bo],
V [auth Aa]
20Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Unassigned secondary structureRC [auth Cb],
W [auth Ab]
105Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Unassigned secondary structureSC [auth Cc],
X [auth Ac]
93Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Unassigned secondary structureTC [auth Cd],
Y [auth Ad]
35Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Unassigned secondary structureHE [auth Dj],
MB [auth Bj],
Z [auth Ae]
21Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Unassigned secondary structureAA [auth Af]11Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Unassigned secondary structureBA [auth Ah],
UC [auth Ch]
41Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L1FA [auth BA],
YC [auth DA]
217Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L2GA [auth BB],
ZC [auth DB]
254Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3AD [auth DC],
HA [auth BC]
387Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4-ABD [auth DD],
IA [auth BD]
362Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5CD [auth DE],
JA [auth BE]
297Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6-ADD [auth DF],
KA [auth BF]
176Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7-AED [auth DG],
LA [auth BG]
244Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8-AFD [auth DH],
MA [auth BH]
256Saccharomyces cerevisiaeMutation(s): 0 
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Find proteins for P17076 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9-AGD [auth DI],
NA [auth BI]
191Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10HD [auth DJ],
OA [auth BJ]
221Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11-AID [auth DK],
PA [auth BK]
174Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14-ALD [auth DN],
QA [auth BN]
138Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L15-AMD [auth DO],
RA [auth BO]
204Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L16-AND [auth DP],
SA [auth BP]
199Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17-AOD [auth DQ],
TA [auth BQ]
184Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18PD [auth DR],
UA [auth BR]
186Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19QD [auth DS],
VA [auth BS]
189Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21-ARD [auth DT],
WA [auth BT]
160Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23SD [auth DU],
XA [auth BU]
137Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L24-ATD [auth DV],
YA [auth BV]
155Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L25UD [auth DW],
ZA [auth BW]
142Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26-AAB [auth BX],
VD [auth DX]
127Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P05743 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28BB [auth BY],
WD [auth DY]
149Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P02406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30CB [auth BZ],
XD [auth DZ]
105Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P14120 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31-ADB [auth Ba],
YD [auth Da]
113Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P0C2H8 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32EB [auth Bb],
ZD [auth Db]
130Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P38061 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35AE [auth Dc],
FB [auth Bc]
120Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37-ABE [auth Dd],
GB [auth Bd]
88Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P49166 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39CE [auth De],
HB [auth Be]
51Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L42DE [auth Df],
IB [auth Bf]
106Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L43EE [auth Dg],
JB [auth Bg]
92Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
Unassigned secondary structureFE [auth Dh],
KB [auth Bh]
44Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
Unassigned secondary structureGE [auth Di],
LB [auth Bi]
12Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
Unassigned secondary structureIE [auth Dk],
NB [auth Bk]
16Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
Unassigned secondary structureOB [auth Bl]19Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
Unassigned secondary structurePB [auth Bm]9Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
Unassigned secondary structureQB [auth Bn]27Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
Unassigned secondary structureSB [auth Bp]8Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
Unassigned secondary structureTB [auth Bq]17Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
Unassigned secondary structureUB [auth Br]23Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L12JD [auth DL]165Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
60S acidic ribosomal protein P0KD [auth DM]312Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P05317 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 1
MoleculeChains LengthOrganismImage
18S ribosomal RNAA [auth A1],
VB [auth C1]
1,800Saccharomyces cerevisiae
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Entity ID: 29
MoleculeChains LengthOrganismImage
25S ribosomal RNACA [auth B1],
VC [auth D1]
3,396Saccharomyces cerevisiae S288C
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Entity ID: 30
MoleculeChains LengthOrganismImage
5S ribosomal RNADA [auth B2],
WC [auth D2]
121Saccharomyces cerevisiae
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Entity ID: 31
MoleculeChains LengthOrganismImage
5.8S ribosomal RNAEA [auth B3],
XC [auth D3]
158Saccharomyces cerevisiae
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OHX
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