5MEI

Crystal structure of Agelastatin A bound to the 80S ribosome

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


This is version 1.2 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
  • Primary Citation of Related Structures:  
    5MEI

  • 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 discovered, structurally unique marine sponge-derived brominated alkaloid, (-)-agelastatin A (AglA), possesses potent antitumor activity ...

    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; Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA. Electronic address: joliu@jhu.edu.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L2-ACD, j252Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL2A, RPL5B, YFR031C-A, YFR031BC
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Entity ID: 5
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60S ribosomal protein L3CE, k386Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL3, MAK8, TCM1, YOR063W, YOR29-14
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Entity ID: 6
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60S ribosomal protein L4-ACF, l361Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL4A, RPL2, RPL2A, YBR031W, YBR0315
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L5CG, m296Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL5, RPL1, RPL1A, YPL131W, LPI14W
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L6-ACH, n175Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL6A, RPL17A, YL16A, YML073C
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L7-ACI, o222Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL7A, RPL6A, RPL8A, YL8A, YGL076C
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L8-ACJ, p233Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL8A, MAK7, RPL4A, YHL033C
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Entity ID: 11
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60S ribosomal protein L9-ACK, q191Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL9A, RPL8A, RPL9, YGL147C
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Entity ID: 12
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60S ribosomal protein L10CL, r220Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL10, GRC5, QSR1, YLR075W
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Entity ID: 13
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60S ribosomal protein L11-BCM, s169Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL11B, RP39B, RPL16B, YGR085C
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Entity ID: 14
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60S ribosomal protein L13-ACN, t193Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL13A, YDL082W
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L14-ACO, u136Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL14A, YKL006W, YKL153
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Entity ID: 16
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60S ribosomal protein L15-ACP, v203Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL15A, RPL10A, RPL13A, YL10A, YLR029C
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L16-ACQ, w197Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL16A, RPL13, RPL21A, YIL133C
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Entity ID: 18
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60S ribosomal protein L17-ACR, x183Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL17A, RPL17, RPL20A, YKL180W
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Entity ID: 19
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60S ribosomal protein L18-ACS, y185Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL18A, RP28A, YOL120C
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Entity ID: 20
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60S ribosomal protein L19-ACT, z188Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL19A, RPL23A, YL14A, YBR084C-A, YBR084BC
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Entity ID: 21
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60S ribosomal protein L20-A0, CU172Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL20A, RPL18A, RPL18A2, YMR242C, YM9408.04C
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L21-A2, CV159Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL21A, URP1, YBR191W, YBR1401
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L22-A5, CW100Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL22A, YLR061W, L2168
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Entity ID: 24
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60S ribosomal protein L23-ACX, l2136Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL23A, RPL17A, RPL17AA, YBL087C, YBL0713
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Entity ID: 26
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60S ribosomal protein L24-A7, CY98Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL24A, RP29, RPL30A, YGL031C
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Entity ID: 27
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60S ribosomal protein L258, CZ121Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL25, YOL127W
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Entity ID: 28
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60S ribosomal protein L26-A9, DA126Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL26A, RPL26, RPL33A, YLR344W, L8300.4
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L27-AAA, DB135Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL27A, RPL27, YHR010W
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Entity ID: 30
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60S ribosomal protein L28AB, DC148Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL28, CYH2, YGL103W
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Entity ID: 31
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60S ribosomal protein L29AC, DD58Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL29, YL43, YFR032C-A, YFR032BW
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L30AD, DE97Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL30, RPL32, YGL030W
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Entity ID: 33
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60S ribosomal protein L31-AAE, DF109Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL31A, RPL34, RPL34A, YDL075W, D2478
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Entity ID: 34
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60S ribosomal protein L32AF, DG127Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL32, YBL092W, YBL0838
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Entity ID: 35
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60S ribosomal protein L33-AAG, DH106Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL33A, RPL37A, YPL143W, LPI4W, P2625
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Entity ID: 36
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60S ribosomal protein L34-AAH, DI112Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL34A, YER056C-A, YER056BC
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Entity ID: 37
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60S ribosomal protein L35-AAI, DJ119Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL35A, SOS1, YDL191W, D1249
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Entity ID: 38
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60S ribosomal protein L36-AAJ, DK99Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL36A, RPL39A, YMR194W, YM9646.06
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Entity ID: 39
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60S ribosomal protein L37-AAK, DL87Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL37A, RPL35A, YLR185W, L9470.6
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Entity ID: 40
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60S ribosomal protein L38AL, DM77Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL38, YLR325C, L8543.2
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Entity ID: 41
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60S ribosomal protein L39AM, DN50Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL39, RPL46, SPB2, YJL189W, J0360
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Entity ID: 42
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Ubiquitin-60S ribosomal protein L40AN, DO52Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL40A, UBI1, YIL148W
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Entity ID: 43
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60S ribosomal protein L41-BAO, DP25Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL41B, RPL47B, YL41B, YDL133C-A, YDL133BC, RPL41A, RPL47A, YL41A, YDL184C, D1290
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Entity ID: 44
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60S ribosomal protein L42-AAP, DQ105Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL42A, RPL41A, SCL41A, YNL162W, N1722
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Entity ID: 45
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60S ribosomal protein L43-AAQ, DR91Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL43A, YPR043W, YP9499.02
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Entity ID: 46
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Suppressor protein STM1i168Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: STM1, MPT4, STO1, YLR150W, L9634.1
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Entity ID: 47
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60S acidic ribosomal protein P0p0220Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPP0, L10E, RPA0, RPL10E, RPLA0, YLR340W, L8300.8
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Entity ID: 48
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Suppressor protein STM1,Suppressor protein STM1,Suppressor protein Stm1 - Mol BsM104Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: STM1, MPT4, STO1, YLR150W, L9634.1
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Entity ID: 49
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40S ribosomal protein S0-AB, s0206Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS0A, NAB1, NAB1A, YST1, YGR214W
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Entity ID: 50
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40S ribosomal protein S1-AC, s1216Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS1A, PLC1, RPS10A, YLR441C, L9753.9
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Entity ID: 51
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40S ribosomal protein S2D, s2217Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS2, RPS4, SUP38, SUP44, YGL123W, G2893
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Entity ID: 52
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40S ribosomal protein S3E, s3223Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS3, SUF14, YNL178W, N1653
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Entity ID: 53
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40S ribosomal protein S4-AF, s4260Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS4A, RPS7B, YJR145C, J2186
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Entity ID: 54
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40S ribosomal protein S5G, s5206Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS5, RPS2, YJR123W, J2045
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Entity ID: 55
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40S ribosomal protein S6-AH, s6226Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS6A, RPS101, RPS10B, YPL090C, LPG18C
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Entity ID: 56
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40S ribosomal protein S7-AI, s7186Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS7A, RPS30, YOR096W, YOR3177W
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Entity ID: 57
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40S ribosomal protein S8-AJ, s8199Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS8A, RPS14A, YBL072C, YBL06.05, YBL0613
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Entity ID: 58
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40S ribosomal protein S9-AK, s9185Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS9A, RPS13A, YS11A, YPL081W
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Entity ID: 59
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40S ribosomal protein S10-AL, c0105Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS10A, YOR293W
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Entity ID: 60
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40S ribosomal protein S11-AM, c1155Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS11A, RPS18A, YDR025W, YD9813.03
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Entity ID: 61
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40S ribosomal protein S12N, c2124Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS12, YOR369C
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Entity ID: 62
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40S ribosomal protein S13O, c3150Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS13, RPS13C, YDR064W, D4252, YD9609.18
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Entity ID: 63
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40S ribosomal protein S14-BP, c4128Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS14B, CRY2, YJL191W, J0354
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Entity ID: 64
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40S ribosomal protein S15Q, c5141Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS15, RPS21, YOL040C
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Entity ID: 65
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40S ribosomal protein S16-AR, c6142Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS16A, RP61R, YMR143W, YM9375.12
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Entity ID: 66
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40S ribosomal protein S17-BS125Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS17B, RP51B, YDR447C
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Entity ID: 67
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40S ribosomal protein S18-AT, c8145Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS18A, YDR450W, D9461.35
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Entity ID: 68
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40S ribosomal protein S19-AU, c9143Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS19A, RP55A, RPS16AA, YOL121C
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Entity ID: 69
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40S ribosomal protein S20V, d0110Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS20, URP2, YHL015W
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Entity ID: 70
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40S ribosomal protein S21-AW, d187Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS21A, RPS25, RPS25A, RPS26A, YKR057W
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Entity ID: 71
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40S ribosomal protein S22-AX, d2129Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS22A, RPS24, RPS24A, YJL190C, J0355
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Entity ID: 72
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40S ribosomal protein S23-AY, d3144Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS23A, RPS28A, YGR118W, G6178
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Entity ID: 73
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40S ribosomal protein S24-AZ, d4134Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS24A, RPS24EA, YER074W
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Entity ID: 74
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40S ribosomal protein S25-Aa, d570Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS25A, RPS31A, YGR027C
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Entity ID: 75
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40S ribosomal protein S26-Bb, d697Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS26B, YER131W
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Entity ID: 76
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40S ribosomal protein S27-Ac, d781Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS27A, YKL156W
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Entity ID: 77
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40S ribosomal protein S28-Ad, d863Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS28A, RPS33, RPS33A, YOR167C, O3600
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Entity ID: 78
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40S ribosomal protein S29-Ad9, e53Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS29A, RPS36A, YS29A, YLR388W, L8084.11
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Entity ID: 79
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40S ribosomal protein S30-Ae0, f62Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS30A, YLR287C-A, L8003.23, YLR287BC
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Entity ID: 80
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Ubiquitin-40S ribosomal protein S31g71Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS31, RPS37, UBI3, YLR167W, L9470.14
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Entity ID: 81
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Guanine nucleotide-binding protein subunit beta-like proteinh, sR318Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ASC1, CPC2, YMR116C, YM9718.15C
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Entity ID: 82
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40S ribosomal protein S17-Ac7121Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS17A, RP51A, YML024W
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Entity ID: 83
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Ubiquitin-40S ribosomal protein S31e151Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS31, RPS37, UBI3, YLR167W, L9470.14
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Entity ID: 1
MoleculeChainsLengthOrganismImage
25S ribosomal RNA1, AR3396Saccharomyces cerevisiae S288C
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Entity ID: 2
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5S ribosomal RNA3, AS121Saccharomyces cerevisiae S288C
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Entity ID: 3
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5.8S ribosomal RNA4, AT158Saccharomyces cerevisiae S288C
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Entity ID: 25
MoleculeChainsLengthOrganismImage
18S ribosomal RNA6, A1800Saccharomyces cerevisiae S288C
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7MB
Query on 7MB
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1, AR
Agelastatin A
C12 H13 Br N4 O3
MPASKXAEPUAMBS-WJOUQXRDSA-N		 Ligand Interaction
OHX
Query on OHX
Download Ideal Coordinates CCD File