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-ACDj252Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL2ARPL5BYFR031C-AYFR031BC
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Entity ID: 5
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60S ribosomal protein L3CEk386Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL3MAK8TCM1YOR063WYOR29-14
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Entity ID: 6
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60S ribosomal protein L4-ACFl361Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL4ARPL2RPL2AYBR031WYBR0315
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L5CGm296Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL5RPL1RPL1AYPL131WLPI14W
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L6-ACHn175Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL6ARPL17AYL16AYML073C
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Entity ID: 9
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60S ribosomal protein L7-ACIo222Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL7ARPL6ARPL8AYL8AYGL076C
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Entity ID: 10
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60S ribosomal protein L8-ACJp233Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL8AMAK7RPL4AYHL033C
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Entity ID: 11
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60S ribosomal protein L9-ACKq191Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL9ARPL8ARPL9YGL147C
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Entity ID: 12
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60S ribosomal protein L10CLr220Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL10GRC5QSR1YLR075W
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Entity ID: 13
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60S ribosomal protein L11-BCMs169Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL11BRP39BRPL16BYGR085C
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Entity ID: 14
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60S ribosomal protein L13-ACNt193Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL13AYDL082W
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Entity ID: 15
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60S ribosomal protein L14-ACOu136Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL14AYKL006WYKL153
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L15-ACPv203Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL15ARPL10ARPL13AYL10AYLR029C
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Entity ID: 17
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60S ribosomal protein L16-ACQw197Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL16ARPL13RPL21AYIL133C
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Entity ID: 18
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60S ribosomal protein L17-ACRx183Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL17ARPL17RPL20AYKL180W
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Entity ID: 19
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60S ribosomal protein L18-ACSy185Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL18ARP28AYOL120C
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Entity ID: 20
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60S ribosomal protein L19-ACTz188Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL19ARPL23AYL14AYBR084C-AYBR084BC
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Entity ID: 21
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60S ribosomal protein L20-A0CU172Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL20ARPL18ARPL18A2YMR242CYM9408.04C
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Entity ID: 22
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60S ribosomal protein L21-A2CV159Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL21AURP1YBR191WYBR1401
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Entity ID: 23
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60S ribosomal protein L22-A5CW100Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL22AYLR061WL2168
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Entity ID: 24
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60S ribosomal protein L23-ACXl2136Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL23ARPL17ARPL17AAYBL087CYBL0713
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Entity ID: 26
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60S ribosomal protein L24-A7CY98Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL24ARP29RPL30AYGL031C
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Entity ID: 27
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60S ribosomal protein L258CZ121Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL25YOL127W
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Entity ID: 28
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60S ribosomal protein L26-A9DA126Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL26ARPL26RPL33AYLR344WL8300.4
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Entity ID: 29
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60S ribosomal protein L27-AAADB135Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL27ARPL27YHR010W
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Entity ID: 30
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60S ribosomal protein L28ABDC148Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL28CYH2YGL103W
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Entity ID: 31
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60S ribosomal protein L29ACDD58Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL29YL43YFR032C-AYFR032BW
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Entity ID: 32
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60S ribosomal protein L30ADDE97Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL30RPL32YGL030W
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Entity ID: 33
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60S ribosomal protein L31-AAEDF109Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL31ARPL34RPL34AYDL075WD2478
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Entity ID: 34
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60S ribosomal protein L32AFDG127Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL32YBL092WYBL0838
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Entity ID: 35
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60S ribosomal protein L33-AAGDH106Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL33ARPL37AYPL143WLPI4WP2625
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Entity ID: 36
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60S ribosomal protein L34-AAHDI112Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL34AYER056C-AYER056BC
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Entity ID: 37
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60S ribosomal protein L35-AAIDJ119Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL35ASOS1YDL191WD1249
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Entity ID: 38
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60S ribosomal protein L36-AAJDK99Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL36ARPL39AYMR194WYM9646.06
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Entity ID: 39
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60S ribosomal protein L37-AAKDL87Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL37ARPL35AYLR185WL9470.6
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Entity ID: 40
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60S ribosomal protein L38ALDM77Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL38YLR325CL8543.2
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Entity ID: 41
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60S ribosomal protein L39AMDN50Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL39RPL46SPB2YJL189WJ0360
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Entity ID: 42
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Ubiquitin-60S ribosomal protein L40ANDO52Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL40AUBI1YIL148W
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Entity ID: 43
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60S ribosomal protein L41-BAODP25Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL41BRPL47BYL41BYDL133C-AYDL133BCRPL41ARPL47AYL41AYDL184CD1290
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Entity ID: 44
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60S ribosomal protein L42-AAPDQ105Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL42ARPL41ASCL41AYNL162WN1722
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Entity ID: 45
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60S ribosomal protein L43-AAQDR91Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL43AYPR043WYP9499.02
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Entity ID: 46
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Suppressor protein STM1i168Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: STM1MPT4STO1YLR150WL9634.1
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Entity ID: 47
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60S acidic ribosomal protein P0p0220Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPP0L10ERPA0RPL10ERPLA0YLR340WL8300.8
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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: STM1MPT4STO1YLR150WL9634.1
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Entity ID: 49
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40S ribosomal protein S0-ABs0206Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS0ANAB1NAB1AYST1YGR214W
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Entity ID: 50
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40S ribosomal protein S1-ACs1216Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS1APLC1RPS10AYLR441CL9753.9
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Entity ID: 51
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40S ribosomal protein S2Ds2217Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS2RPS4SUP38SUP44YGL123WG2893
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Entity ID: 52
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40S ribosomal protein S3Es3223Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS3SUF14YNL178WN1653
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Entity ID: 53
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40S ribosomal protein S4-AFs4260Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS4ARPS7BYJR145CJ2186
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Entity ID: 54
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40S ribosomal protein S5Gs5206Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS5RPS2YJR123WJ2045
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Entity ID: 55
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40S ribosomal protein S6-AHs6226Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS6ARPS101RPS10BYPL090CLPG18C
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Entity ID: 56
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40S ribosomal protein S7-AIs7186Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS7ARPS30YOR096WYOR3177W
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Entity ID: 57
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40S ribosomal protein S8-AJs8199Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS8ARPS14AYBL072CYBL06.05YBL0613
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Entity ID: 58
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40S ribosomal protein S9-AKs9185Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS9ARPS13AYS11AYPL081W
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Entity ID: 59
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40S ribosomal protein S10-ALc0105Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS10AYOR293W
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Entity ID: 60
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40S ribosomal protein S11-AMc1155Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS11ARPS18AYDR025WYD9813.03
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Entity ID: 61
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40S ribosomal protein S12Nc2124Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS12YOR369C
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Entity ID: 62
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40S ribosomal protein S13Oc3150Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS13RPS13CYDR064WD4252YD9609.18
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Entity ID: 63
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40S ribosomal protein S14-BPc4128Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS14BCRY2YJL191WJ0354
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Entity ID: 64
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40S ribosomal protein S15Qc5141Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS15RPS21YOL040C
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Entity ID: 65
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40S ribosomal protein S16-ARc6142Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS16ARP61RYMR143WYM9375.12
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Entity ID: 66
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40S ribosomal protein S17-BS125Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS17BRP51BYDR447C
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Entity ID: 67
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40S ribosomal protein S18-ATc8145Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS18AYDR450WD9461.35
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Entity ID: 68
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40S ribosomal protein S19-AUc9143Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS19ARP55ARPS16AAYOL121C
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Entity ID: 69
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40S ribosomal protein S20Vd0110Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS20URP2YHL015W
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Entity ID: 70
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40S ribosomal protein S21-AWd187Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS21ARPS25RPS25ARPS26AYKR057W
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Entity ID: 71
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40S ribosomal protein S22-AXd2129Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS22ARPS24RPS24AYJL190CJ0355
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Entity ID: 72
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40S ribosomal protein S23-AYd3144Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS23ARPS28AYGR118WG6178
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Entity ID: 73
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40S ribosomal protein S24-AZd4134Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS24ARPS24EAYER074W
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Entity ID: 74
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40S ribosomal protein S25-Aad570Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS25ARPS31AYGR027C
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Entity ID: 75
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S26-Bbd697Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS26BYER131W
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Entity ID: 76
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40S ribosomal protein S27-Acd781Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS27AYKL156W
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Entity ID: 77
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40S ribosomal protein S28-Add863Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS28ARPS33RPS33AYOR167CO3600
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Entity ID: 78
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S29-Ad9e53Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS29ARPS36AYS29AYLR388WL8084.11
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Entity ID: 79
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40S ribosomal protein S30-Ae0f62Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS30AYLR287C-AL8003.23YLR287BC
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Entity ID: 80
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Ubiquitin-40S ribosomal protein S31g71Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS31RPS37UBI3YLR167WL9470.14
Find proteins for P05759 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 81
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Guanine nucleotide-binding protein subunit beta-like proteinhsR318Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ASC1CPC2YMR116CYM9718.15C
Find proteins for P38011 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 82
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S17-Ac7121Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS17ARP51AYML024W
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Entity ID: 83
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-40S ribosomal protein S31e151Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS31RPS37UBI3YLR167WL9470.14
Find proteins for P05759 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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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

Download Ideal Coordinates CCD File 
1, AR
Agelastatin A
C12 H13 Br N4 O3
MPASKXAEPUAMBS-WJOUQXRDSA-N
 Ligand Interaction
OHX
Query on OHX

Download Ideal Coordinates CCD File