6HHQ

Crystal structure of compound C45 bound to the yeast 80S ribosome


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Understanding the role of intermolecular interactions between lissoclimides and the eukaryotic ribosome.

Pellegrino, S.Meyer, M.Konst, Z.A.Holm, M.Voora, V.K.Kashinskaya, D.Zanette, C.Mobley, D.L.Yusupova, G.Vanderwal, C.D.Blanchard, S.C.Yusupov, M.

(2019) Nucleic Acids Res 47: 3223-3232

  • DOI: 10.1093/nar/gkz053
  • Primary Citation of Related Structures:  
    6HHQ

  • PubMed Abstract: 
  • Natural products that target the eukaryotic ribosome are promising therapeutics to treat a variety of cancers. It is therefore essential to determine their molecular mechanism of action to fully understand their mode of interaction with the target and to inform the development of new synthetic compounds with improved potency and reduced cytotoxicity ...

    Natural products that target the eukaryotic ribosome are promising therapeutics to treat a variety of cancers. It is therefore essential to determine their molecular mechanism of action to fully understand their mode of interaction with the target and to inform the development of new synthetic compounds with improved potency and reduced cytotoxicity. Toward this goal, we have previously established a short synthesis pathway that grants access to multiple congeners of the lissoclimide family. Here we present the X-ray co-crystal structure at 3.1 Å resolution of C45, a potent congener with two A-ring chlorine-bearing stereogenic centers with 'unnatural' configurations, with the yeast 80S ribosome, intermolecular interaction energies of the C45/ribosome complex, and single-molecule FRET data quantifying the impact of C45 on both human and yeast ribosomes. Together, these data provide new insights into the role of unusual non-covalent halogen bonding interactions involved in the binding of this synthetic compound to the 80S ribosome.


    Organizational Affiliation

    Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Russia.



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Entity ID: 4
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60S ribosomal protein L2-AWA [auth CD], D [auth j]254Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L3XA [auth CE], E [auth k]387Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L4-AYA [auth CF], F [auth l]362Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L5ZA [auth CG], G [auth m]297Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L6-AAB [auth CH], H [auth n]176Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L7-ABB [auth CI], I [auth o]244Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L8-ACB [auth CJ], J [auth p]256Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L9-ADB [auth CK], K [auth q]191Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L10EB [auth CL], L [auth r]221Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L11-BFB [auth CM], M [auth s]174Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L13-AGB [auth CN], N [auth t]199Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L14-AHB [auth CO], O [auth u]138Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L15-AIB [auth CP], P [auth v]204Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L16-AJB [auth CQ], Q [auth w]199Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L17-AKB [auth CR], R [auth x]184Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L18-ALB [auth CS], S [auth y]186Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L19-AMB [auth CT], T [auth z]189Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L20-AU [auth 0], NB [auth CU]172Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L21-AV [auth 2], OB [auth CV]160Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L22-AW [auth 5], PB [auth CW]121Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L23-AX [auth 6], QB [auth CX]137Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L24-AY [auth 7], RB [auth CY]155Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L25Z [auth 8], SB [auth CZ]142Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L26-AAA [auth 9], TB [auth DA]127Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L27-ABA [auth AA], UB [auth DB]136Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L28CA [auth AB], VB [auth DC]149Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L29DA [auth AC], WB [auth DD]59Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L30EA [auth AD], XB [auth DE]105Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L31-AFA [auth AE], YB [auth DF]113Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L32GA [auth AF], ZB [auth DG]130Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L33-AHA [auth AG], AC [auth DH]107Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L34-AIA [auth AH], BC [auth DI]121Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L35-AJA [auth AI], CC [auth DJ]120Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L36-AKA [auth AJ], DC [auth DK]100Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L37-ALA [auth AK], EC [auth DL]88Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L38MA [auth AL], FC [auth DM]78Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L39NA [auth AM], GC [auth DN]51Saccharomyces cerevisiaeMutation(s): 0 
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Ubiquitin-60S ribosomal protein L40OA [auth AN], HC [auth DO]128Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L41-BPA [auth AO], IC [auth DP]25Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L42-AQA [auth AP], JC [auth DQ]106Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L43-ARA [auth AQ], KC [auth DR]92Saccharomyces cerevisiaeMutation(s): 0 
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Suppressor protein STM1SA [auth i], MC [auth sM]273Saccharomyces cerevisiaeMutation(s): 0 
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60S acidic ribosomal protein P0LC [auth p0]312Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S0-AOC [auth B], XD [auth s0]252Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S1-APC [auth C], YD [auth s1]255Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S2QC [auth D], ZD [auth s2]254Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S3RC [auth E], AE [auth s3]240Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S4-ASC [auth F], BE [auth s4]261Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S5TC [auth G], CE [auth s5]225Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S6-AUC [auth H], DE [auth s6]236Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S7-AVC [auth I], EE [auth s7]190Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S8-AWC [auth J], FE [auth s8]200Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S9-AXC [auth K], GE [auth s9]197Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S10-AYC [auth L], HE [auth c0]105Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S11-AZC [auth M], IE [auth c1]156Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S12AD [auth N], JE [auth c2]143Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S13BD [auth O], KE [auth c3]151Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 62
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40S ribosomal protein S14-BCD [auth P], LE [auth c4]138Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 63
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40S ribosomal protein S15DD [auth Q], ME [auth c5]142Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 64
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40S ribosomal protein S16-AED [auth R], NE [auth c6]143Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 65
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40S ribosomal protein S17-AFD [auth S], OE [auth c7]136Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 66
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40S ribosomal protein S18-AGD [auth T], PE [auth c8]146Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 67
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40S ribosomal protein S19-AHD [auth U], QE [auth c9]144Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 68
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40S ribosomal protein S20ID [auth V], RE [auth d0]121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 69
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40S ribosomal protein S21-AJD [auth W], SE [auth d1]87Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 70
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40S ribosomal protein S22-AKD [auth X], TE [auth d2]130Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 71
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40S ribosomal protein S23-ALD [auth Y], UE [auth d3]145Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 72
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40S ribosomal protein S24-AMD [auth Z], VE [auth d4]135Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 73
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40S ribosomal protein S25-AND [auth a], WE [auth d5]108Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 74
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40S ribosomal protein S26-BOD [auth b], XE [auth d6]119Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 75
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40S ribosomal protein S27-APD [auth c], YE [auth d7]82Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 76
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40S ribosomal protein S28-AQD [auth d], ZE [auth d8]67Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 77
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40S ribosomal protein S29-AAF [auth d9], RD [auth e]56Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 78
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40S ribosomal protein S30-ABF [auth e0], SD [auth f]63Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 79
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Ubiquitin-40S ribosomal protein S31CF [auth e1], TD [auth g]152Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 80
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Guanine nucleotide-binding protein subunit beta-like proteinWD [auth Rb], UD [auth h]319Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 1
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25S ribosomal RNAA [auth 1], TA [auth AR]3396Saccharomyces cerevisiae
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Entity ID: 2
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5S ribosomal RNAB [auth 3], UA [auth AS]121Saccharomyces cerevisiae
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Entity ID: 3
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5.8S ribosomal RNAC [auth 4], VA [auth AT]158Saccharomyces cerevisiae
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Entity ID: 47
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18S ribosomal RNANC [auth A]1797Saccharomyces cerevisiae
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Entity ID: 81
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18S ribosomal RNAVD [auth sR]1800Saccharomyces cerevisiae
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Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G5B
Query on G5B

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UKA [auth 1], VWB [auth AR](3~{R})-3-[(1~{S})-2-[(1~{S},4~{a}~{R},6~{S},7~{S},8~{a}~{R})-6,7-bis(chloranyl)-5,5,8~{a}-trimethyl-2-methylidene-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]-1-oxidanyl-ethyl]pyrrolidine-2,5-dione
C20 H29 Cl2 N O3
PPKXULKLJJFMKB-RHKPTJIRSA-N
 Ligand Interaction
OHX
Query on OHX

Download Ideal Coordinates CCD File