5MEI

Crystal structure of Agelastatin A bound to the 80S ribosome


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Inhibition of Eukaryotic Translation by the Antitumor Natural Product Agelastatin A.

McClary, B.Zinshteyn, B.Meyer, M.Jouanneau, M.Pellegrino, S.Yusupova, G.Schuller, A.Reyes, J.C.P.Lu, J.Guo, Z.Ayinde, S.Luo, C.Dang, Y.Romo, D.Yusupov, M.Green, R.Liu, J.O.

(2017) Cell Chem Biol 24: 605-613.e5

  • DOI: 10.1016/j.chembiol.2017.04.006

  • PubMed Abstract: 
  • Protein synthesis plays an essential role in cell proliferation, differentiation, and survival. Inhibitors of eukaryotic translation have entered the clinic, establishing the translation machinery as a promising target for chemotherapy. A recently di ...

    Protein synthesis plays an essential role in cell proliferation, differentiation, and survival. Inhibitors of eukaryotic translation have entered the clinic, establishing the translation machinery as a promising target for chemotherapy. A recently discovered, structurally unique marine sponge-derived brominated alkaloid, (-)-agelastatin A (AglA), possesses potent antitumor activity. Its underlying mechanism of action, however, has remained unknown. Using a systematic top-down approach, we show that AglA selectively inhibits protein synthesis. Using a high-throughput chemical footprinting method, we mapped the AglA-binding site to the ribosomal A site. A 3.5 Å crystal structure of the 80S eukaryotic ribosome from S. cerevisiae in complex with AglA was obtained, revealing multiple conformational changes of the nucleotide bases in the ribosome accompanying the binding of AglA. Together, these results have unraveled the mechanism of inhibition of eukaryotic translation by AglA at atomic level, paving the way for future structural modifications to develop AglA analogs into novel anticancer agents.


    Organizational Affiliation

    Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; The SJ Yan and HJ Mao Laboratory of Chemical Biology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L2-A
j, CD
252Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL2A (RPL5B)
Find proteins for P0CX45 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L3
k, CE
386Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL3 (MAK8, TCM1)
Find proteins for P14126 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P14126
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L4-A
l, CF
361Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL4A (RPL2, RPL2A)
Find proteins for P10664 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L5
m, CG
296Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL5 (RPL1, RPL1A)
Find proteins for P26321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P26321
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L6-A
n, CH
175Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL6A (RPL17A, YL16A)
Find proteins for Q02326 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q02326
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L7-A
o, CI
222Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL7A (RPL6A, RPL8A, YL8A)
Find proteins for P05737 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L8-A
p, CJ
233Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL8A (MAK7, RPL4A)
Find proteins for P17076 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P17076
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L9-A
q, CK
191Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL9A (RPL8A, RPL9)
Find proteins for P05738 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L10
r, CL
220Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL10 (GRC5, QSR1)
Find proteins for P41805 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L11-B
s, CM
169Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL11B (RP39B, RPL16B)
Find proteins for Q3E757 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L13-A
t, CN
193Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL13A
Find proteins for Q12690 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L14-A
u, CO
136Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL14A
Find proteins for P36105 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L15-A
v, CP
203Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL15A (RPL10A, RPL13A, YL10A)
Find proteins for P05748 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L16-A
w, CQ
197Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL16A (RPL13, RPL21A)
Find proteins for P26784 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L17-A
x, CR
183Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL17A (RPL17, RPL20A)
Find proteins for P05740 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18-A
y, CS
185Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL18A (RP28A)
Find proteins for P0CX49 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL18A
Go to UniProtKB:  P0CX49
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L19-A
z, CT
188Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL19A (RPL23A, YL14A)
Find proteins for P0CX82 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L20-A
0, CU
172Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL20A (RPL18A, RPL18A2)
Find proteins for P0CX23 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX23
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L21-A
2, CV
159Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL21A (URP1)
Find proteins for Q02753 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L22-A
5, CW
100Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL22A
Find proteins for P05749 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L23-A
l2, CX
136Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL23A (RPL17A, RPL17AA)
Find proteins for P0CX41 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L24-A
7, CY
98Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL24A (RP29, RPL30A)
Find proteins for P04449 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L25
8, CZ
121Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL25
Find proteins for P04456 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P04456
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L26-A
9, DA
126Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL26A (RPL26, RPL33A)
Find proteins for P05743 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L27-A
AA, DB
135Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL27A (RPL27)
Find proteins for P0C2H6 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L28
AB, DC
148Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL28 (CYH2)
Find proteins for P02406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL28
Go to UniProtKB:  P02406
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L29
AC, DD
58Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL29 (YL43)
Find proteins for P05747 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P05747
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L30
AD, DE
97Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL30 (RPL32)
Find proteins for P14120 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL30
Go to UniProtKB:  P14120
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L31-A
AE, DF
109Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL31A (RPL34, RPL34A)
Find proteins for P0C2H8 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0C2H8
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L32
AF, DG
127Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL32
Find proteins for P38061 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P38061
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L33-A
AG, DH
106Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL33A (RPL37A)
Find proteins for P05744 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05744
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L34-A
AH, DI
112Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL34A
Find proteins for P87262 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P87262
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L35-A
AI, DJ
119Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL35A (SOS1)
Find proteins for P0CX84 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL35A
Go to UniProtKB:  P0CX84
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L36-A
AJ, DK
99Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL36A (RPL39A)
Find proteins for P05745 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL36A
Go to UniProtKB:  P05745
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L37-A
AK, DL
87Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL37A (RPL35A)
Find proteins for P49166 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL37A
Go to UniProtKB:  P49166
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L38
AL, DM
77Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL38
Find proteins for P49167 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL38
Go to UniProtKB:  P49167
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L39
AM, DN
50Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL39 (RPL46, SPB2)
Find proteins for P04650 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL39
Go to UniProtKB:  P04650
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-60S ribosomal protein L40
AN, DO
52Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL40A (UBI1)
Find proteins for P0CH08 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CH08
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L41-B
AO, DP
25Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL41B (RPL47B, YL41B)
Find proteins for P0CX87 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX87
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L42-A
AP, DQ
105Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL42A (RPL41A, SCL41A)
Find proteins for P0CX27 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX27
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L43-A
AQ, DR
91Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL43A
Find proteins for P0CX25 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX25
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
Suppressor protein STM1
i
168Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: STM1 (MPT4, STO1)
Find proteins for P39015 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P39015
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
60S acidic ribosomal protein P0
p0
220Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPP0 (L10E, RPA0, RPL10E, RPLA0)
Find proteins for P05317 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05317
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
Suppressor protein STM1,Suppressor protein STM1,Suppressor protein Stm1 - Mol B
sM
104Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: STM1 (MPT4, STO1)
Find proteins for P39015 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P39015
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S0-A
B, s0
206Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS0A (NAB1, NAB1A, YST1)
Find proteins for P32905 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32905
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S1-A
C, s1
216Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS1A (PLC1, RPS10A)
Find proteins for P33442 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S2
D, s2
217Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS2 (RPS4, SUP38, SUP44)
Find proteins for P25443 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPS2
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S3
E, s3
223Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS3 (SUF14)
Find proteins for P05750 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S4-A
F, s4
260Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS4A (RPS7B)
Find proteins for P0CX35 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S5
G, s5
206Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS5 (RPS2)
Find proteins for P26783 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPS5
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S6-A
H, s6
226Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS6A (RPS101, RPS10B)
Find proteins for P0CX37 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S7-A
I, s7
186Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS7A (RPS30)
Find proteins for P26786 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S8-A
J, s8
199Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS8A (RPS14A)
Find proteins for P0CX39 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S9-A
K, s9
185Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS9A (RPS13A, YS11A)
Find proteins for O13516 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S10-A
L, c0
105Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS10A
Find proteins for Q08745 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S11-A
M, c1
155Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS11A (RPS18A)
Find proteins for P0CX47 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S12
N, c2
124Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS12
Find proteins for P48589 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P48589
Entity ID: 62
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S13
O, c3
150Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS13 (RPS13C)
Find proteins for P05756 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P05756
Entity ID: 63
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S14-B
P, c4
128Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS14B (CRY2)
Find proteins for P39516 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S15
Q, c5
141Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS15 (RPS21)
Find proteins for Q01855 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  Q01855
Entity ID: 65
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S16-A
R, c6
142Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS16A (RP61R)
Find proteins for P0CX51 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S17-B
S
125Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS17B (RP51B)
Find proteins for P14127 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 67
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S18-A
T, c8
145Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS18A
Find proteins for P0CX55 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 68
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S19-A
U, c9
143Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS19A (RP55A, RPS16AA)
Find proteins for P07280 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 69
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S20
V, d0
110Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS20 (URP2)
Find proteins for P38701 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 70
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S21-A
W, d1
87Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS21A (RPS25, RPS25A, RPS26A)
Find proteins for P0C0V8 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 71
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S22-A
X, d2
129Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS22A (RPS24, RPS24A)
Find proteins for P0C0W1 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S23-A
Y, d3
144Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS23A (RPS28A)
Find proteins for P0CX29 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 73
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S24-A
Z, d4
134Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS24A (RPS24EA)
Find proteins for P0CX31 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 74
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S25-A
a, d5
70Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS25A (RPS31A)
Find proteins for Q3E792 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q3E792
Entity ID: 75
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S26-B
b, d6
97Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS26B
Find proteins for P39939 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P39939
Entity ID: 76
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S27-A
c, d7
81Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS27A
Find proteins for P35997 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPS27A
Go to UniProtKB:  P35997
Entity ID: 77
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S28-A
d, d8
63Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS28A (RPS33, RPS33A)
Find proteins for Q3E7X9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q3E7X9
Entity ID: 78
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S29-A
e, d9
53Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS29A (RPS36A, YS29A)
Find proteins for P41057 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P41057
Entity ID: 79
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S30-A
f, e0
62Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS30A
Find proteins for P0CX33 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX33
Entity ID: 80
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-40S ribosomal protein S31
g
71Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS31 (RPS37, UBI3)
Find proteins for P05759 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05759
Entity ID: 81
MoleculeChainsSequence LengthOrganismDetails
Guanine nucleotide-binding protein subunit beta-like protein
h, sR
318Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: ASC1 (CPC2)
Find proteins for P38011 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38011
Entity ID: 82
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S17-A
c7
121Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS17A (RP51A)
Find proteins for P02407 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P02407
Entity ID: 83
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-40S ribosomal protein S31
e1
51Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS31 (RPS37, UBI3)
Find proteins for P05759 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05759
Entity ID: 1
MoleculeChainsLengthOrganism
25S ribosomal RNA1,AR3396Saccharomyces cerevisiae S288C
Entity ID: 2
MoleculeChainsLengthOrganism
5S ribosomal RNA3,AS121Saccharomyces cerevisiae S288C
Entity ID: 3
MoleculeChainsLengthOrganism
5.8S ribosomal RNA4,AT158Saccharomyces cerevisiae S288C
Entity ID: 25
MoleculeChainsLengthOrganism
18S ribosomal RNA6,A1800Saccharomyces cerevisiae S288C
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
AK, AN, AP, AQ, b, c, d6, d7, d9, DL, DO, DQ, DR, e, e1, g
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
OHX
Query on OHX

Download SDF File 
Download CCD File 
1, 2, 3, 4, 6, A, AC, AE, AG, AK, AP, AR, AS, AT, c3, c5, c8, CE, CF, CG, CK, CL, CM, CO, CP, CV, CX, CZ, d9, DD, DG, DH, DI, DL, e, H, h, J, k, l, M, O, Q, r, s8, sR, T, v, x, y, z
osmium (III) hexammine
osmium(6+) hexaazanide
H12 N6 Os
OWCQTVJQFLTQTE-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
1, 3, 4, 6, 9, A, AB, AF, AH, AK, AP, AR, AS, AT, b, c6, c9, CD, CE, CF, CI, CK, CO, CP, CQ, CR, CU, CX, D, d3, d5, d6, d9, DA, DC, DD, DE, DF, DG, DH, DI, DO, DP, DR, F, i, j, k, l, l2, o, r, s, s1, s2, s6, s8, sM, t, v, w, x, Y, z
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
7MB
Query on 7MB

Download SDF File 
Download CCD File 
1, AR
Agelastatin A
C12 H13 Br N4 O3
MPASKXAEPUAMBS-WJOUQXRDSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
sM
L-PEPTIDE LINKINGC4 H9 N O2

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.195 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 304.080α = 90.00
b = 286.550β = 99.05
c = 436.550γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
NIHUnited StatesR37 GM052964
ERCFrance294312

Revision History 

  • Version 1.0: 2017-06-28
    Type: Initial release
  • Version 1.1: 2017-07-05
    Type: Structure summary