5I4L

Crystal structure of Amicoumacin A bound to the yeast 80S ribosome


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Amicoumacin A induces cancer cell death by targeting the eukaryotic ribosome.

Prokhorova, I.V.Akulich, K.A.Makeeva, D.S.Osterman, I.A.Skvortsov, D.A.Sergiev, P.V.Dontsova, O.A.Yusupova, G.Yusupov, M.M.Dmitriev, S.E.

(2016) Sci Rep 6: 27720-27720

  • DOI: 10.1038/srep27720
  • Primary Citation of Related Structures:  
    5I4L

  • PubMed Abstract: 
  • Amicoumacin A is an antibiotic that was recently shown to target bacterial ribosomes. It affects translocation and provides an additional contact interface between the ribosomal RNA and mRNA. The binding site of amicoumacin A is formed by universally conserved nucleotides of rRNA ...

    Amicoumacin A is an antibiotic that was recently shown to target bacterial ribosomes. It affects translocation and provides an additional contact interface between the ribosomal RNA and mRNA. The binding site of amicoumacin A is formed by universally conserved nucleotides of rRNA. In this work, we showed that amicoumacin A inhibits translation in yeast and mammalian systems by affecting translation elongation. We determined the structure of the amicoumacin A complex with yeast ribosomes at a resolution of 3.1  Å. Toxicity measurement demonstrated that human cancer cell lines are more susceptible to the inhibition by this compound as compared to non-cancerous ones. This might be used as a starting point to develop amicoumacin A derivatives with clinical value.


    Organizational Affiliation

    Department of Biochemistry, Biological Faculty, Lomonosov Moscow State University, Moscow, 119234 Russia.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S0-AB [auth S0],
CC [auth s0]
206Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS0ANAB1NAB1AYST1YGR214W
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S1-AC [auth S1],
DC [auth s1]
216Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS1APLC1RPS10AYLR441CL9753.9
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S2D [auth S2],
EC [auth s2]
217Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS2RPS4SUP38SUP44YGL123WG2893
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S3E [auth S3],
FC [auth s3]
223Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS3SUF14YNL178WN1653
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Find proteins for P05750 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S4-AF [auth S4],
GC [auth s4]
260Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS4ARPS7BYJR145CJ2186
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S5G [auth S5],
HC [auth s5]
206Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS5RPS2YJR123WJ2045
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S6-AH [auth S6],
IC [auth s6]
226Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS6ARPS101RPS10BYPL090CLPG18C
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S7-AI [auth S7],
JC [auth s7]
186Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS7ARPS30YOR096WYOR3177W
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S8-AJ [auth S8],
KC [auth s8]
200Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS8ARPS14AYBL072CYBL06.05YBL0613
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S9-AK [auth S9],
LC [auth s9]
185Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS9ARPS13AYS11AYPL081W
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S10-AL [auth C0],
MC [auth c0]
98Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS10AYOR293W
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Entity ID: 13
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40S ribosomal protein S11-AM [auth C1],
NC [auth c1]
156Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS11ARPS18AYDR025WYD9813.03
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Entity ID: 14
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40S ribosomal protein S12N [auth C2],
OC [auth c2]
124Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS12YOR369C
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S13O [auth C3],
PC [auth c3]
150Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS13RPS13CYDR064WD4252YD9609.18
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S14-BP [auth C4],
QC [auth c4]
128Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS14BCRY2YJL191WJ0354
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S15Q [auth C5],
RC [auth c5]
142Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS15RPS21YOL040C
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Entity ID: 18
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40S ribosomal protein S16-AR [auth C6],
SC [auth c6]
142Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS16ARP61RYMR143WYM9375.12
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Entity ID: 19
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40S ribosomal protein S17-AS [auth C7],
TC [auth c7]
136Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS17ARP51AYML024W
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S18-AT [auth C8],
UC [auth c8]
145Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS18AYDR450WD9461.35
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S19-AU [auth C9],
VC [auth c9]
143Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS19ARP55ARPS16AAYOL121C
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S20V [auth D0],
WC [auth d0]
110Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS20URP2YHL015W
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S21-AW [auth D1],
XC [auth d1]
87Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS21ARPS25RPS25ARPS26AYKR057W
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S22-AX [auth D2],
YC [auth d2]
129Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS22ARPS24RPS24AYJL190CJ0355
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S23-AY [auth D3],
ZC [auth d3]
144Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS23ARPS28AYGR118WG6178
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Entity ID: 26
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40S ribosomal protein S24-AZ [auth D4],
AD [auth d4]
134Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS24ARPS24EAYER074W
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S25-AAA [auth D5],
BD [auth d5]
70Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS25ARPS31AYGR027C
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S26-BBA [auth D6],
CD [auth d6]
97Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS26BYER131W
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Entity ID: 29
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40S ribosomal protein S27-ACA [auth D7],
DD [auth d7]
81Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS27AYKL156W
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Entity ID: 30
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40S ribosomal protein S28-ADA [auth D8],
ED [auth d8]
63Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS28ARPS33RPS33AYOR167CO3600
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S29-AEA [auth D9],
FD [auth d9]
53Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS29ARPS36AYS29AYLR388WL8084.11
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S30-AFA [auth E0],
GD [auth e0]
62Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS30AYLR287C-AL8003.23YLR287BC
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-40S ribosomal protein S31GA [auth E1],
HD [auth e1]
76Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS31RPS37UBI3YLR167WL9470.14
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein subunit beta-like proteinHA [auth SR],
ID [auth sR]
318Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ASC1CPC2YMR116CYM9718.15C
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Entity ID: 35
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Suppressor protein STM1,Suppressor protein STM1,Suppressor protein STM1IA [auth SM]176Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: STM1
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L2-AMA [auth L2],
ND [auth l2]
252Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL2ARPL5BYFR031C-AYFR031BC
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L3NA [auth L3],
OD [auth l3]
386Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL3MAK8TCM1YOR063WYOR29-14
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L4-AOA [auth L4],
PD [auth l4]
361Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL4ARPL2RPL2AYBR031WYBR0315
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L5PA [auth L5],
QD [auth l5]
296Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL5RPL1RPL1AYPL131WLPI14W
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L6-AQA [auth L6],
RD [auth l6]
176Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL6ARPL17AYL16AYML073C
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L7-ARA [auth L7],
SD [auth l7]
223Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL7ARPL6ARPL8AYL8AYGL076C
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L8-ASA [auth L8]233Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL8AMAK7RPL4AYHL033C
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L9-ATA [auth L9],
UD [auth l9]
191Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL9ARPL8ARPL9YGL147C
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L10UA [auth M0],
VD [auth m0]
221Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL10GRC5QSR1YLR075W
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L11-BVA [auth M1],
WD [auth m1]
169Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL11BRP39BRPL16BYGR085C
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L13-AWA [auth M3],
YD [auth m3]
194Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL13AYDL082W
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L14-AXA [auth M4],
ZD [auth m4]
137Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL14AYKL006WYKL153
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L15-AYA [auth M5],
AE [auth m5]
203Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL15ARPL10ARPL13AYL10AYLR029C
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L16-AZA [auth M6],
BE [auth m6]
197Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL16ARPL13RPL21AYIL133C
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L17-AAB [auth M7],
CE [auth m7]
183Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL17ARPL17RPL20AYKL180W
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L18-ABB [auth M8],
DE [auth m8]
185Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL18ARP28AYOL120C
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L19-ACB [auth M9],
EE [auth m9]
188Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL19ARPL23AYL14AYBR084C-AYBR084BC
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L20-ADB [auth N0],
FE [auth n0]
172Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL20ARPL18ARPL18A2YMR242CYM9408.04C
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L21-AEB [auth N1],
GE [auth n1]
159Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL21AURP1YBR191WYBR1401
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L22-AFB [auth N2],
HE [auth n2]
100Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL22AYLR061WL2168
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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L23-AGB [auth N3],
IE [auth n3]
136Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL23ARPL17ARPL17AAYBL087CYBL0713
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Entity ID: 60
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60S ribosomal protein L24-AHB [auth N4]98Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL24ARP29RPL30AYGL031C
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Entity ID: 61
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60S ribosomal protein L25IB [auth N5],
KE [auth n5]
121Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL25YOL127W
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Entity ID: 62
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L26-AJB [auth N6],
LE [auth n6]
126Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL26ARPL26RPL33AYLR344WL8300.4
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Entity ID: 63
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L27-AKB [auth N7],
ME [auth n7]
135Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL27ARPL27YHR010W
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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L28LB [auth N8],
NE [auth n8]
148Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL28CYH2YGL103W
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Entity ID: 65
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L29MB [auth N9],
OE [auth n9]
58Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL29YL43YFR032C-AYFR032BW
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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L30NB [auth O0],
PE [auth o0]
100Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL30RPL32YGL030W
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Entity ID: 67
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L31-AOB [auth O1],
QE [auth o1]
109Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL31ARPL34RPL34AYDL075WD2478
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Entity ID: 68
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60S ribosomal protein L32PB [auth O2],
RE [auth o2]
127Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL32YBL092WYBL0838
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Entity ID: 69
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L33-AQB [auth O3],
SE [auth o3]
106Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL33ARPL37AYPL143WLPI4WP2625
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Entity ID: 70
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60S ribosomal protein L34-ARB [auth O4],
TE [auth o4]
112Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL34AYER056C-AYER056BC
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Entity ID: 71
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L35-ASB [auth O5],
UE [auth o5]
119Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL35ASOS1YDL191WD1249
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Entity ID: 72
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60S ribosomal protein L36-ATB [auth O6],
VE [auth o6]
99Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL36ARPL39AYMR194WYM9646.06
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Entity ID: 73
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L37-AUB [auth O7],
WE [auth o7]
87Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL37ARPL35AYLR185WL9470.6
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Entity ID: 74
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60S ribosomal protein L38VB [auth O8],
XE [auth o8]
77Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL38YLR325CL8543.2
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Entity ID: 75
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L39WB [auth O9],
YE [auth o9]
50Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL39RPL46SPB2YJL189WJ0360
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Entity ID: 76
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Ubiquitin-60S ribosomal protein L40XB [auth Q0],
ZE [auth q0]
52Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL40AUBI1YIL148W
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Entity ID: 77
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60S ribosomal protein L41-AYB [auth Q1],
AF [auth q1]
25Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL41ARPL47AYL41AYDL184CD1290
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Entity ID: 78
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L42-AZB [auth Q2],
BF [auth q2]
105Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL42ARPL41ASCL41AYNL162WN1722
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Entity ID: 79
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L43-AAC [auth Q3],
CF [auth q3]
91Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL43AYPR043WYP9499.02
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Entity ID: 80
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Suppressor protein STM1,Suppressor protein STM1,Suppressor protein STM1JD [auth sM]159Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: STM1
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Entity ID: 81
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L8-ATD [auth l8]231Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL8AMAK7RPL4AYHL033C
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Entity ID: 82
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60S ribosomal protein L12XD [auth m2]155Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 83
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L24-AJE [auth n4]135Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL24ARP29RPL30AYGL031C
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Entity ID: 84
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60S acidic ribosomal protein P0DF [auth p0]312Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPP0L10ERPA0RPL10ERPLA0YLR340WL8300.8
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Find proteins for P05317 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P05317
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UniProt GroupP05317
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Entity ID: 85
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein P1 alpha, P2 betaEF [auth p1],
FF [auth p2]
47Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
18S ribosomal RNAA [auth 2],
BC [auth 6]
1800Saccharomyces cerevisiae S288C
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