ISDA

Deposition Date 2017-08-03

Release Date 2018-02-28

Last Version Date 2024-05-08

Entry Detail

PDB ID:

5ON6

Keywords:

RIBOSOME

Title:

Crystal structure of haemanthamine bound to the 80S ribosome

Biological Source:

Source Organism:

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Taxon ID: 559292)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

3.10 Å

R-Value Free:

0.25

R-Value Work:

0.22

R-Value Observed:

0.22

Space Group:

P 1 21 1

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L20-A
Gene (Uniprot):RPL20A
Chain IDs:U (auth: 0), PB (auth: CU)
Chain Length:172
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P0CX23 Pfam ID:PF01775

Polymer Type:polyribonucleotide
Molecule:25S ribosomal RNA
Chain IDs:A (auth: 1), UA (auth: AR)
Chain Length:3396
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L21-A
Gene (Uniprot):RPL21A
Chain IDs:V (auth: 2), QB (auth: CV)
Chain Length:159
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:Q02753 Pfam ID:PF01157

Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:B (auth: 3), VA (auth: AS)
Chain Length:121
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Polymer Type:polyribonucleotide
Molecule:5.8S ribosomal RNA
Chain IDs:C (auth: 4), WA (auth: AT)
Chain Length:158
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L22-A
Gene (Uniprot):RPL22A
Chain IDs:W (auth: 5), RB (auth: CW)
Chain Length:100
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P05749 Pfam ID:PF01776

Polymer Type:polyribonucleotide
Molecule:18S ribosomal RNA
Chain IDs:Y (auth: 6), PC (auth: A)
Chain Length:1800
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L24-A
Gene (Uniprot):RPL24A
Chain IDs:Z (auth: 7), TB (auth: CY)
Chain Length:98
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P04449 Pfam ID:PF01246

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L25
Gene (Uniprot):RPL25
Chain IDs:AA (auth: 8), UB (auth: CZ)
Chain Length:121
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P04456 Pfam ID:PF03939, PF00276

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L26-A
Gene (Uniprot):RPL26A
Chain IDs:BA (auth: 9), VB (auth: DA)
Chain Length:126
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P05743 Pfam ID:PF16906, PF00467

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L27-A
Gene (Uniprot):RPL27A
Chain IDs:CA (auth: AA), WB (auth: DB)
Chain Length:135
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P0C2H6 Pfam ID:PF01777

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L28
Gene (Uniprot):RPL28
Chain IDs:DA (auth: AB), XB (auth: DC)
Chain Length:148
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P02406 Pfam ID:PF00828

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L29
Gene (Uniprot):RPL29
Chain IDs:EA (auth: AC), YB (auth: DD)
Chain Length:58
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P05747 Pfam ID:PF01779

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L30
Gene (Uniprot):RPL30
Chain IDs:FA (auth: AD), ZB (auth: DE)
Chain Length:97
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P14120 Pfam ID:PF01248

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L31-A
Gene (Uniprot):RPL31A
Chain IDs:GA (auth: AE), AC (auth: DF)
Chain Length:109
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P0C2H8 Pfam ID:PF01198

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L32
Gene (Uniprot):RPL32
Chain IDs:HA (auth: AF), BC (auth: DG)
Chain Length:127
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P38061 Pfam ID:PF01655

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L33-A
Gene (Uniprot):RPL33A
Chain IDs:IA (auth: AG), CC (auth: DH)
Chain Length:106
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P05744 Pfam ID:PF01247

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L34-A
Gene (Uniprot):RPL34A
Chain IDs:JA (auth: AH), DC (auth: DI)
Chain Length:112
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P87262 Pfam ID:PF01199

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L35-A
Gene (Uniprot):RPL35A
Chain IDs:KA (auth: AI), EC (auth: DJ)
Chain Length:119
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P0CX84 Pfam ID:PF00831

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L36-A
Gene (Uniprot):RPL36A
Chain IDs:LA (auth: AJ), FC (auth: DK)
Chain Length:99
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P05745 Pfam ID:PF01158

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L37-A
Gene (Uniprot):RPL37A
Chain IDs:MA (auth: AK), GC (auth: DL)
Chain Length:87
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P49166 Pfam ID:PF01907

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L38
Gene (Uniprot):RPL38
Chain IDs:NA (auth: AL), HC (auth: DM)
Chain Length:77
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P49167 Pfam ID:PF01781

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L39
Gene (Uniprot):RPL39
Chain IDs:OA (auth: AM), IC (auth: DN)
Chain Length:50
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P04650 Pfam ID:PF00832

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ubiquitin-60S ribosomal protein L40
Gene (Uniprot):RPL40A
Chain IDs:PA (auth: AN), JC (auth: DO)
Chain Length:52
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P0CH08 Pfam ID:PF01020

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L41-B
Chain IDs:QA (auth: AO), KC (auth: DP)
Chain Length:25
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P0CX86 Pfam ID:PF05162

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L42-A
Gene (Uniprot):RPL42A
Chain IDs:RA (auth: AP), LC (auth: DQ)
Chain Length:105
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P0CX27 Pfam ID:PF00935

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L43-A
Gene (Uniprot):RPL43A
Chain IDs:SA (auth: AQ), MC (auth: DR)
Chain Length:91
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P0CX25 Pfam ID:PF01780

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S0-A
Gene (Uniprot):RPS0A
Chain IDs:QC (auth: B), XD (auth: s0)
Chain Length:206
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P32905 Pfam ID:PF00318

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S1-A
Gene (Uniprot):RPS1A
Chain IDs:RC (auth: C), YD (auth: s1)
Chain Length:216
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P33442 Pfam ID:PF01015

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S2
Gene (Uniprot):RPS2
Chain IDs:SC (auth: D), ZD (auth: s2)
Chain Length:217
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P25443 Pfam ID:PF00333, PF03719

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S3
Gene (Uniprot):RPS3
Chain IDs:TC (auth: E), AE (auth: s3)
Chain Length:53
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P05750 Pfam ID:PF07650, PF00189

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S4-A
Gene (Uniprot):RPS4A
Chain IDs:UC (auth: F), BE (auth: s4)
Chain Length:62
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P0CX35 Pfam ID:PF08071, PF01479, PF00900, PF00467, PF16121

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S5
Gene (Uniprot):RPS5
Chain IDs:VC (auth: G), CE (auth: s5)
Chain Length:71
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P26783 Pfam ID:PF00177

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S6-A
Gene (Uniprot):RPS6A
Chain IDs:WC (auth: H), DE (auth: s6)
Chain Length:318
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P0CX37 Pfam ID:PF01092

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S7-A
Gene (Uniprot):RPS7A
Chain IDs:XC (auth: I), EE (auth: s7)
Chain Length:186
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P26786 Pfam ID:PF01251

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S8-A
Gene (Uniprot):RPS8A
Chain IDs:YC (auth: J), FE (auth: s8)
Chain Length:252
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P0CX39 Pfam ID:PF01201

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S9-A
Gene (Uniprot):RPS9A
Chain IDs:ZC (auth: K), GE (auth: s9)
Chain Length:185
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:O13516 Pfam ID:PF00163, PF01479

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S10-A
Gene (Uniprot):RPS10A
Chain IDs:AD (auth: L), HE (auth: c0)
Chain Length:105
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:Q08745 Pfam ID:PF03501

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S11-A
Gene (Uniprot):RPS11A
Chain IDs:BD (auth: M), IE (auth: c1)
Chain Length:155
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P0CX47 Pfam ID:PF16205, PF00366

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S12
Gene (Uniprot):RPS12
Chain IDs:CD (auth: N), JE (auth: c2)
Chain Length:124
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P48589 Pfam ID:PF01248

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S13
Gene (Uniprot):RPS13
Chain IDs:DD (auth: O), KE (auth: c3)
Chain Length:150
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P05756 Pfam ID:PF08069, PF00312

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S14-B
Gene (Uniprot):RPS14B
Chain IDs:ED (auth: P), LE (auth: c4)
Chain Length:128
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P39516 Pfam ID:PF00411

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S15
Gene (Uniprot):RPS15
Chain IDs:FD (auth: Q), ME (auth: c5)
Chain Length:141
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:Q01855 Pfam ID:PF00203

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S16-A
Gene (Uniprot):RPS16A
Chain IDs:GD (auth: R), NE (auth: c6)
Chain Length:142
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P0CX51 Pfam ID:PF00380

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S17-A
Chain IDs:HD (auth: S), OE (auth: c7)
Chain Length:125
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P14127 Pfam ID:PF00833

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S18-A
Gene (Uniprot):RPS18A
Chain IDs:ID (auth: T), PE (auth: c8)
Chain Length:145
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P0CX55 Pfam ID:PF00416

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S19-A
Gene (Uniprot):RPS19A
Chain IDs:JD (auth: U), QE (auth: c9)
Chain Length:143
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P07280 Pfam ID:PF01090

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S20
Gene (Uniprot):RPS20
Chain IDs:KD (auth: V), RE (auth: d0)
Chain Length:110
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P38701 Pfam ID:PF00338

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S21-A
Gene (Uniprot):RPS21A
Chain IDs:LD (auth: W), SE (auth: d1)
Chain Length:87
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P0C0V8 Pfam ID:PF01249

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S22-A
Gene (Uniprot):RPS22A
Chain IDs:MD (auth: X), TE (auth: d2)
Chain Length:129
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P0C0W1 Pfam ID:PF00410

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S23-A
Gene (Uniprot):RPS23A
Chain IDs:ND (auth: Y), UE (auth: d3)
Chain Length:144
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P0CX29 Pfam ID:PF00164

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S24-A
Gene (Uniprot):RPS24A
Chain IDs:OD (auth: Z), VE (auth: d4)
Chain Length:134
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P0CX31 Pfam ID:PF01282

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S25-A
Gene (Uniprot):RPS25A
Chain IDs:PD (auth: a), WE (auth: d5)
Chain Length:1800
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:Q3E792 Pfam ID:PF03297

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S26-B
Gene (Uniprot):RPS26B
Chain IDs:QD (auth: b), XE (auth: d6)
Chain Length:206
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P39939 Pfam ID:PF01283

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S27-A
Gene (Uniprot):RPS27A
Chain IDs:RD (auth: c), YE (auth: d7)
Chain Length:216
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P35997 Pfam ID:PF01667

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S28-A
Gene (Uniprot):RPS28A
Chain IDs:SD (auth: d), ZE (auth: d8)
Chain Length:217
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:Q3E7X9 Pfam ID:PF01200

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S29-A
Gene (Uniprot):RPS29A
Chain IDs:TD (auth: e), AF (auth: d9)
Chain Length:53
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P41057 Pfam ID:PF00253

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ubiquitin-40S ribosomal protein S31
Gene (Uniprot):RPS31
Chain IDs:CF (auth: e1)
Chain Length:51
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P05759 Pfam ID:PF01599

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S30-A
Gene (Uniprot):RPS30A
Chain IDs:UD (auth: f), BF (auth: e0)
Chain Length:62
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P0CX33 Pfam ID:PF04758

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ubiquitin-40S ribosomal protein S31
Gene (Uniprot):RPS31
Chain IDs:VD (auth: g)
Chain Length:71
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P05759 Pfam ID:PF01599

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Guanine nucleotide-binding protein subunit beta-like protein
Gene (Uniprot):ASC1
Chain IDs:WD (auth: h), DF (auth: sR)
Chain Length:318
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P38011 Pfam ID:PF00400

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Suppressor protein STM1
Gene (Uniprot):STM1
Chain IDs:TA (auth: i)
Chain Length:186
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P39015 Pfam ID:PF09598

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L2-A
Gene (Uniprot):RPL2A
Chain IDs:D (auth: j), XA (auth: CD)
Chain Length:252
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P0CX45 Pfam ID:PF00181, PF03947

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L3
Gene (Uniprot):RPL3
Chain IDs:E (auth: k), YA (auth: CE)
Chain Length:386
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P14126 Pfam ID:PF00297

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L4-A
Gene (Uniprot):RPL4A
Chain IDs:F (auth: l), ZA (auth: CF)
Chain Length:361
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P10664 Pfam ID:PF00573, PF14374

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L23-A
Gene (Uniprot):RPL23A
Chain IDs:X (auth: lR), SB (auth: CX)
Chain Length:136
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P0CX41 Pfam ID:PF00238

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L5
Gene (Uniprot):RPL5
Chain IDs:G (auth: m), AB (auth: CG)
Chain Length:296
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P26321 Pfam ID:PF17144, PF14204

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L12
Chain IDs:HB (auth: m2)
Chain Length:150
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L6-A
Gene (Uniprot):RPL6A
Chain IDs:H (auth: n), BB (auth: CH)
Chain Length:175
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:Q02326 Pfam ID:PF01159

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L7-A
Gene (Uniprot):RPL7A
Chain IDs:I (auth: o), CB (auth: CI)
Chain Length:222
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P05737 Pfam ID:PF08079, PF00327

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L8-A
Gene (Uniprot):RPL8A
Chain IDs:J (auth: p), DB (auth: CJ)
Chain Length:233
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P17076 Pfam ID:PF01248

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S acidic ribosomal protein P0
Gene (Uniprot):RPP0
Chain IDs:OC (auth: p0)
Chain Length:311
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P05317 Pfam ID:PF00466, PF17777, PF00428

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L9-A
Gene (Uniprot):RPL9A
Chain IDs:K (auth: q), EB (auth: CK)
Chain Length:191
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P05738 Pfam ID:PF00347

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L10
Gene (Uniprot):RPL10
Chain IDs:L (auth: r), FB (auth: CL)
Chain Length:220
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P41805 Pfam ID:PF00252

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L11-B
Gene (Uniprot):RPL11B
Chain IDs:M (auth: s), GB (auth: CM)
Chain Length:169
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:Q3E757 Pfam ID:PF00281, PF00673

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Suppressor protein STM1,Suppressor protein STM1
Gene (Uniprot):STM1
Chain IDs:NC (auth: sM)
Chain Length:104
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P39015 Pfam ID:PF09598

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13-A
Gene (Uniprot):RPL13A
Chain IDs:N (auth: t), IB (auth: CN)
Chain Length:193
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:Q12690 Pfam ID:PF01294

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L14-A
Gene (Uniprot):RPL14A
Chain IDs:O (auth: u), JB (auth: CO)
Chain Length:136
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P36105 Pfam ID:PF00467, PF01929

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L15-A
Gene (Uniprot):RPL15A
Chain IDs:P (auth: v), KB (auth: CP)
Chain Length:203
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P05748 Pfam ID:PF00827

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L16-A
Gene (Uniprot):RPL16A
Chain IDs:Q (auth: w), LB (auth: CQ)
Chain Length:197
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P26784 Pfam ID:PF00572

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L17-A
Gene (Uniprot):RPL17A
Chain IDs:R (auth: x), MB (auth: CR)
Chain Length:183
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P05740 Pfam ID:PF00237

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18-A
Gene (Uniprot):RPL18A
Chain IDs:S (auth: y), NB (auth: CS)
Chain Length:185
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P0CX49 Pfam ID:PF17135

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L19-A
Gene (Uniprot):RPL19A
Chain IDs:T (auth: z), OB (auth: CT)
Chain Length:188
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt ID:P0CX82 Pfam ID:PF01280

Ligand Molecules

GOL

HN8

OHX

Primary Citation

The Amaryllidaceae Alkaloid Haemanthamine Binds the Eukaryotic Ribosome to Repress Cancer Cell Growth.

Pellegrino, S, Meyer, M, Zorbas, C, Bouchta, S.A, Saraf, K, Pelly, S.C, Yusupova, G, Evidente, A, Mathieu, V, Kornienko, A, Lafontaine, D.L.J, Yusupov, M.Show

Structure 26 416 425.e4 (2018)

PMID: 29429877 DOI: 10.1016/j.str.2018.01.009

Abstact

Alkaloids isolated from the Amaryllidaceae plants have potential as therapeutics for treating human diseases. Haemanthamine has been studied as a novel anticancer agent due to its ability to overcome cancer cell resistance to apoptosis. Biochemical experiments have suggested that hemanthamine targets the ribosome. However, a structural characterization of its mechanism has been missing. Here we present the 3.1 Å resolution X-ray structure of haemanthamine bound to the Saccharomyces cerevisiae 80S ribosome. This structure reveals that haemanthamine targets the A-site cleft on the large ribosomal subunit rearranging rRNA to halt the elongation phase of translation. Furthermore, we provide evidence that haemanthamine and other Amaryllidaceae alkaloids also inhibit specifically ribosome biogenesis, triggering nucleolar stress response and leading to p53 stabilization in cancer cells. Together with a computer-aided interpretation of existing structure-activity relationships of Amaryllidaceae alkaloids congeners, we provide a rationale for designing molecules with enhanced potencies and reduced toxicities.

Legend

Protein

Chemical

Disease

Primary Citation of related structures