5TBW image
Entry Detail
PDB ID:
5TBW
Keywords:
Title:
Crystal structure of chlorolissoclimide bound to the yeast 80S ribosome
Biological Source:
PDB Version:
Deposition Date:
2016-09-13
Release Date:
2017-07-26
Method Details:
Experimental Method:
Resolution:
3.00 Å
R-Value Free:
0.22
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L20-A
Chain IDs:U (auth: 0), NB (auth: CU)
Chain Length:172
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polyribonucleotide
Description:25S ribosomal RNA
Chain IDs:A (auth: 1), TA (auth: AR)
Chain Length:3149
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L21-A
Chain IDs:V (auth: 2), OB (auth: CV)
Chain Length:159
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polyribonucleotide
Description:5S ribosomal RNA
Chain IDs:B (auth: 3), UA (auth: AS)
Chain Length:121
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polyribonucleotide
Description:5.8S ribosomal RNA
Chain IDs:C (auth: 4), VA (auth: AT)
Chain Length:158
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L22-A
Chain IDs:W (auth: 5), PB (auth: CW)
Chain Length:100
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L23-A
Chain IDs:X (auth: 6), QB (auth: CX)
Chain Length:136
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L24-A
Chain IDs:Y (auth: 7), RB (auth: CY)
Chain Length:98
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L25
Chain IDs:Z (auth: 8), SB (auth: CZ)
Chain Length:121
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L26-A
Chain IDs:AA (auth: 9), TB (auth: DA)
Chain Length:126
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polyribonucleotide
Description:18S ribosomal RNA
Chain IDs:NC (auth: A), VD (auth: sR)
Chain Length:70
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L27-A
Chain IDs:BA (auth: AA), UB (auth: DB)
Chain Length:135
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L28
Chain IDs:CA (auth: AB), VB (auth: DC)
Chain Length:148
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L29
Chain IDs:DA (auth: AC), WB (auth: DD)
Chain Length:58
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L30
Chain IDs:EA (auth: AD), XB (auth: DE)
Chain Length:97
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L31-A
Chain IDs:FA (auth: AE), YB (auth: DF)
Chain Length:109
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L32
Chain IDs:GA (auth: AF), ZB (auth: DG)
Chain Length:127
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L33-A
Chain IDs:HA (auth: AG), AC (auth: DH)
Chain Length:106
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L34-A
Chain IDs:IA (auth: AH), BC (auth: DI)
Chain Length:112
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L35-A
Chain IDs:JA (auth: AI), CC (auth: DJ)
Chain Length:119
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L36-A
Chain IDs:KA (auth: AJ), DC (auth: DK)
Chain Length:99
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L37-A
Chain IDs:LA (auth: AK), EC (auth: DL)
Chain Length:87
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L38
Chain IDs:MA (auth: AL), FC (auth: DM)
Chain Length:77
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L39
Chain IDs:NA (auth: AM), GC (auth: DN)
Chain Length:50
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:Ubiquitin-60S ribosomal protein L40
Chain IDs:OA (auth: AN), HC (auth: DO)
Chain Length:52
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L41-A
Chain IDs:PA (auth: AO), IC (auth: DP)
Chain Length:25
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L42-A
Chain IDs:QA (auth: AP), JC (auth: DQ)
Chain Length:105
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L43-A
Chain IDs:RA (auth: AQ), KC (auth: DR)
Chain Length:91
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S0-A
Chain IDs:OC (auth: B), XD (auth: s0)
Chain Length:97
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S1-A
Chain IDs:PC (auth: C), YD (auth: s1)
Chain Length:81
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S2
Chain IDs:QC (auth: D), ZD (auth: s2)
Chain Length:63
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S3
Chain IDs:RC (auth: E), AE (auth: s3)
Chain Length:53
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S4-A
Chain IDs:SC (auth: F), BE (auth: s4)
Chain Length:62
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S5
Chain IDs:TC (auth: G), CE (auth: s5)
Chain Length:71
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S6-A
Chain IDs:UC (auth: H), DE (auth: s6)
Chain Length:226
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S7-A
Chain IDs:VC (auth: I), EE (auth: s7)
Chain Length:168
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S8-A
Chain IDs:WC (auth: J), FE (auth: s8)
Chain Length:252
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S9-A
Chain IDs:XC (auth: K), GE (auth: s9)
Chain Length:386
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S10-A
Chain IDs:YC (auth: L), HE (auth: c0)
Chain Length:105
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S11-A
Chain IDs:ZC (auth: M), IE (auth: c1)
Chain Length:155
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S12
Chain IDs:AD (auth: N), JE (auth: c2)
Chain Length:143
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S13
Chain IDs:BD (auth: O), KE (auth: c3)
Chain Length:150
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S14-B
Chain IDs:CD (auth: P), LE (auth: c4)
Chain Length:128
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S15
Chain IDs:DD (auth: Q), ME (auth: c5)
Chain Length:135
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S16-A
Chain IDs:ED (auth: R), NE (auth: c6)
Chain Length:142
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S17-A
Chain IDs:FD (auth: S)
Chain Length:169
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S18-A
Chain IDs:GD (auth: T), PE (auth: c8)
Chain Length:145
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S19-A
Chain IDs:HD (auth: U), QE (auth: c9)
Chain Length:143
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S20
Chain IDs:ID (auth: V), RE (auth: d0)
Chain Length:110
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S21-A
Chain IDs:JD (auth: W), SE (auth: d1)
Chain Length:87
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S22-A
Chain IDs:KD (auth: X), TE (auth: d2)
Chain Length:129
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S23-A
Chain IDs:LD (auth: Y), UE (auth: d3)
Chain Length:144
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S24-A
Chain IDs:MD (auth: Z), VE (auth: d4)
Chain Length:134
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S25-A
Chain IDs:ND (auth: a), WE (auth: d5)
Chain Length:70
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S26-B
Chain IDs:OD (auth: b), XE (auth: d6)
Chain Length:97
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S27-A
Chain IDs:PD (auth: c), YE (auth: d7)
Chain Length:81
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S17-A
Chain IDs:OE (auth: c7)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S28-A
Chain IDs:QD (auth: d), ZE (auth: d8)
Chain Length:63
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S29-A
Chain IDs:RD (auth: e), AF (auth: d9)
Chain Length:53
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:Ubiquitin-40S ribosomal protein S31
Chain IDs:CF (auth: e1)
Chain Length:51
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S30-A
Chain IDs:SD (auth: f), BF (auth: e0)
Chain Length:62
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:Ubiquitin-40S ribosomal protein S31
Chain IDs:TD (auth: g)
Chain Length:71
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:Guanine nucleotide-binding protein subunit beta-like protein
Chain IDs:UD (auth: h), WD (auth: Rb)
Chain Length:226
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:Suppressor protein STM1
Chain IDs:SA (auth: i)
Chain Length:168
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L2-A
Chain IDs:D (auth: j), WA (auth: CD)
Chain Length:252
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L3
Chain IDs:E (auth: k), XA (auth: CE)
Chain Length:386
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L4-A
Chain IDs:F (auth: l), YA (auth: CF)
Chain Length:361
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L5
Chain IDs:G (auth: m), ZA (auth: CG)
Chain Length:296
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L6-A
Chain IDs:H (auth: n), AB (auth: CH)
Chain Length:175
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L7-A
Chain IDs:I (auth: o), BB (auth: CI)
Chain Length:222
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L8-A
Chain IDs:J (auth: p), CB (auth: CJ)
Chain Length:233
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S acidic ribosomal protein P0
Chain IDs:LC (auth: p0)
Chain Length:219
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L9-A
Chain IDs:K (auth: q), DB (auth: CK)
Chain Length:191
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L10
Chain IDs:L (auth: r), EB (auth: CL)
Chain Length:220
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L11-B
Chain IDs:M (auth: s), FB (auth: CM)
Chain Length:169
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:Suppressor protein STM1
Chain IDs:MC (auth: sM)
Chain Length:104
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L13-A
Chain IDs:N (auth: t), GB (auth: CN)
Chain Length:193
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L14-A
Chain IDs:O (auth: u), HB (auth: CO)
Chain Length:136
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L15-A
Chain IDs:P (auth: v), IB (auth: CP)
Chain Length:203
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L16-A
Chain IDs:Q (auth: w), JB (auth: CQ)
Chain Length:197
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L17-A
Chain IDs:R (auth: x), KB (auth: CR)
Chain Length:183
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L18-A
Chain IDs:S (auth: y), LB (auth: CS)
Chain Length:185
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L19-A
Chain IDs:T (auth: z), MB (auth: CT)
Chain Length:188
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Primary Citation
Synthesis facilitates an understanding of the structural basis for translation inhibition by the lissoclimides.
Nat Chem 9 1140 1149 (2017)
PMID: 29064494 DOI: 10.1038/nchem.2800

Abstact

The lissoclimides are unusual succinimide-containing labdane diterpenoids that were reported to be potent cytotoxins. Our short semisynthesis and analogue-oriented synthesis approaches provide a series of lissoclimide natural products and analogues that expand the structure-activity relationships (SARs) in this family. The semisynthesis approach yielded significant quantities of chlorolissoclimide (CL) to permit an evaluation against the National Cancer Institute's 60-cell line panel and allowed us to obtain an X-ray co-crystal structure of the synthetic secondary metabolite with the eukaryotic 80S ribosome. Although it shares a binding site with other imide-based natural product translation inhibitors, CL engages in a particularly interesting and novel face-on halogen-π interaction between the ligand's alkyl chloride and a guanine residue. Our analogue-oriented synthesis provides many more lissoclimide compounds, which were tested against aggressive human cancer cell lines and for protein synthesis inhibitory activity. Finally, computational modelling was used to explain the SARs of certain key compounds and set the stage for the structure-guided design of better translation inhibitors.

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Primary Citation of related structures