5ON6: Haemanthamine

Crystal structure of haemanthamine bound to the 80S ribosome. Determined by X-ray diffraction at 3.1 Å resolution. Released 28 Feb 2018.

Method
X-ray diffraction
Resolution
3.1 Å
Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains
160
Atoms
410,383
Mol. weight
6484.52 kDa
Ligands
OHX, MG, HN8, ZN
Released
28 Feb 2018

Explore 5ON6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5ON6 contains 1,030 α-helices and 1,060 β-strands across 152 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain 0: 8 helices, 8 β-strands

ElementResiduesLengthSheet
β-strand5-139255
α-helix14-152
β-strand25-317255
α-helix34-4815
α-helix53-553
β-strand56-638255
β-strand73-8210256
β-strand87-9610256
α-helix99-11416
α-helix118-1203
β-strand121-1288256
α-helix138-1414
α-helix142-1443
β-strand150-1512182
α-helix157-1593
β-strand1641200
Chain 2: 7 helices, 7 β-strands
ElementResiduesLengthSheet
α-helix25-262
α-helix28-314
β-strand39-424267
α-helix52-543
α-helix55-573
β-strand61-677267
β-strand71-8010267
β-strand83-9210267
β-strand96-983267
α-helix103-12119
α-helix134-1385
β-strand139-1413108
α-helix147-1482
β-strand149-1502255
Chain 5: 3 helices, 7 β-strands
ElementResiduesLengthSheet
β-strand13-186277
α-helix20-234
α-helix30-4011
β-strand421278
β-strand471278
β-strand54-585277
β-strand62-676277
α-helix73-8614
β-strand94-996277
β-strand102-1065277
Chain 7: 5 helices, 4 β-strands
ElementResiduesLengthSheet
β-strand4-52327
β-strand12-132327
β-strand19-224299
β-strand28-314299
α-helix34-418
α-helix46-483
α-helix53-586
α-helix64-674
α-helix87-893
Chain 8: 6 helices, 5 β-strands
ElementResiduesLengthSheet
β-strand311124
α-helix40-423
α-helix52-554
α-helix59-624
β-strand63-6641
α-helix70-7910
β-strand81-8661
α-helix92-10312
β-strand107-11591
β-strand119-12681
α-helix132-1398
Chain 9: 7 helices, 9 β-strands
ElementResiduesLengthSheet
α-helix12-209
α-helix24-307
β-strand32-34312
β-strand35113
α-helix361
α-helix37-437
β-strand47-49312
β-strand55-58413
β-strand67-69313
β-strand70-74514
α-helix75-773
β-strand79-881014
β-strand94-99614
α-helix101-1033
β-strand104-108513
α-helix113-1219
Chain a: 3 helices, 3 β-strands
ElementResiduesLengthSheet
α-helix44-518
β-strand601192
α-helix62-665
α-helix73-8210
β-strand90-912192
β-strand101-1022192
Chain AA: 5 helices, 5 β-strands
ElementResiduesLengthSheet
β-strand9-13527
β-strand22-29827
β-strand40-48927
α-helix49-524
α-helix59-657
β-strand69-76827
α-helix77-793
β-strand80-86727
α-helix90-923
α-helix104-12219

143 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
25S ribosomal RNA1, ARRNA3396Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
5S ribosomal RNA3, ASRNA121Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
5.8S ribosomal RNA4, ATRNA158Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
60S ribosomal protein L2-ACD, jprotein252Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P0CX45 (AlphaFold model)
60S ribosomal protein L3CE, kprotein386Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P14126 (AlphaFold model)
60S ribosomal protein L4-ACF, lprotein361Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P10664 (AlphaFold model)
60S ribosomal protein L5CG, mprotein296Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P26321 (AlphaFold model)
60S ribosomal protein L6-ACH, nprotein175Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Q02326
60S ribosomal protein L7-ACI, oprotein222Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P05737
60S ribosomal protein L8-ACJ, pprotein233Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P17076
60S ribosomal protein L9-ACK, qprotein191Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P05738
60S ribosomal protein L10CL, rprotein220Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P41805

71 more molecules are not listed.

Sequence of entity 1 (1, AR), FASTA
>5ON6_1 25S ribosomal RNA (chains 1, AR)
GUUUGACCUCAAAUCAGGUAGGAGUACCCGCUGAACUUAAGCAUAUCAAUAAGCGGAGGA
AAAGAAACCAACCGGGAUUGCCUUAGUAACGGCGAGUGAAGCGGCAAAAGCUCAAAUUUG
AAAUCUGGUACCUUCGGUGCCCGAGUUGUAAUUUGGAGAGGGCAACUUUGGGGCCGUUCC
UUGUCUAUGUUCCUUGGAACAGGACGUCAUAGAGGGUGAGAAUCCCGUGUGGCGAGGAGU
GCGGUUCUUUGUAAAGUGCCUUCGAAGAGUCGAGUUGUUUGGGAAUGCAGCUCUAAGUGG
GUGGUAAAUUCCAUCUAAAGCUAAAUAUUGGCGAGAGACCGAUAGCGAACAAGUACAGUG
AUGGAAAGAUGAAAAGAACUUUGAAAAGAGAGUGAAAAAGUACGUGAAAUUGUUGAAAGG
GAAGGGCAUUUGAUCAGACAUGGUGUUUUGUGCCCUCUGCUCCUUGUGGGUAGGGGAAUC
UCGCAUUUCACUGGGCCAGCAUCAGUUUUGGUGGCAGGAUAAAUCCAUAGGAAUGUAGCU
UGCCUCGGUAAGUAUUAUAGCCUGUGGGAAUACUGCCAGCUGGGACUGAGGACUGCGACG
UAAGUCAAGGAUGCUGGCAUAAUGGUUAUAUGCCGCCCGUCUUGAAACACGGACCAAGGA
GUCUAACGUCUAUGCGAGUGUUUGGGUGUAAAACCCAUACGCGUAAUGAAAGUGAACGUA
GGUUGGGGCCUCGCAAGAGGUGCACAAUCGACCGAUCCUGAUGUCUUCGGAUGGAUUUGA
GUAAGAGCAUAGCUGUUGGGACCCGAAAGAUGGUGAACUAUGCCUGAAUAGGGUGAAGCC
AGAGGAAACUCUGGUGGAGGCUCGUAGCGGUUCUGACGUGCAAAUCGAUCGUCGAAUUUG
GGUAUAGGGGCGAAAGACUAAUCGAACCAUCUAGUAGCUGGUUCCUGCCGAAGUUUCCCU
CAGGAUAGCAGAAGCUCGUAUCAGUUUUAUGAGGUAAAGCGAAUGAUUAGAGGUUCCGGG
GUCGAAAUGACCUUGACCUAUUCUCAAACUUUAAAUAUGUAAGAAGUCCUUGUUACUUAA
UUGAACGUGGACAUUUGAAUGAAGAGCUUUUAGUGGGCCAUUUUUGGUAAGCAGAACUGG
CGAUGCGGGAUGAACCGAACGUAGAGUUAAGGUGCCGGAAUACACGCUCAUCAGACACCA
CAAAAGGUGUUAGUUCAUCUAGACAGCCGGACGGUGGCCAUGGAAGUCGGAAUCCGCUAA
GGAGUGUGUAACAACUCACCGGCCGAAUGAACUAGCCCUGAAAAUGGAUGGCGCUCAAGC
GUGUUACCUAUACUCUACCGUCAGGGUUGAUAUGAUGCCCUGACGAGUAGGCAGGCGUGG
AGGUCAGUGACGAAGCCUAGACCGUAAGGUCGGGUCGAACGGCCUCUAGUGCAGAUCUUG
GUGGUAGUAGCAAAUAUUCAAAUGAGAACUUUGAAGACUGAAGUGGGGAAAGGUUCCACG
UCAACAGCAGUUGGACGUGGGUUAGUCGAUCCUAAGAGAUGGGGAAGCUCCGUUUCAAAG
GCCUGAUUUUAUGCAGGCCACCAUCGAAAGGGAAUCCGGUUAAGAUUCCGGAACCUGGAU
AUGGAUUCUUCACGGUAACGUAACUGAAUGUGGAGACGUCGGCGCGAGCCCUGGGAGGAG
UUAUCUUUUCUUCUUAACAGCUUAUCACCCCGGAAUUGGUUUAUCCGGAGAUGGGGUCUU
AUGGCUGGAAGAGGCCAGCACCUUUGCUGGCUCCGGUGCGCUUGUGACGGCCCGUGAAAA
UCCACAGGAAGGAAUAGUUUUCAUGCCAGGUCGUACUGAUAACCGCAGCAGGUCUCCAAG
GUGAACAGCCUCUAGUUGAUAGAAUAAUGUAGAUAAGGGAAGUCGGCAAAAUAGAUCCGU
AACUUCGGGAUAAGGAUUGGCUCUAAGGGUCGGGUAGUGAGGGCCUUGGUCAGACGCAGC
GGGCGUGCUUGUGGACUGCUUGGUGGGGCUUGCUCUGCUAGGCGGACUACUUGCGUGCCU
UGUUGUAGACGGCCUUGGUAGGUCUCUUGUAGACCGUCGCUUGCUACAAUUAACGAUCAA
CUUAGAACUGGUACGGACAAGGGGAAUCUGACUGUCUAAUUAAAACAUAGCAUUGCGAUG
GUCAGAAAGUGAUGUUGACGCAAUGUGAUUUCUGCCCAGUGCUCUGAAUGUCAAAGUGAA
GAAAUUCAACCAAGCGCGGGUAAACGGCGGGAGUAACUAUGACUCUCUUAAGGUAGCCAA
AUGCCUCGUCAUCUAAUUAGUGACGCGCAUGAAUGGAUUAACGAGAUUCCCACUGUCCCU
AUCUACUAUCUAGCGAAACCACAGCCAAGGGAACGGGCUUGGCAGAAUCAGCGGGGAAAG
AAGACCCUGUUGAGCUUGACUCUAGUUUGACAUUGUGAAGAGACAUAGAGGGUGUAGAAU
AAGUGGGAGCUUCGGCGCCAGUGAAAUACCACUACCUUUAUAGUUUCUUUACUUAUUCAA
UGAAGCGGAGCUGGAAUUCAUUUUCCACGUUCUAGCAUUCAAGGUCCCAUUCGGGGCUGA
UCCGGGUUGAAGACAUUGUCAGGUGGGGAGUUUGGCUGGGGCGGCACAUCUGUUAAACGA
UAACGCAGAUGUCCUAAGGGGGGCUCAUGGAGAACAGAAAUCUCCAGUAGAACAAAAGGG
UAAAAGCCCCCUUGAUUUUGAUUUUCAGUGUGAAUACAAACCAUGAAAGUGUGGCCUAUC
GAUCCUUUAGUCCCUCGGAAUUUGAGGCUAGAGGUGCCAGAAAAGUUACCACAGGGAUAA
CUGGCUUGUGGCAGUCAAGCGUUCAUAGCGACAUUGCUUUUUGAUUCUUCGAUGUCGGCU
CUUCCUAUCAUACCGAAGCAGAAUUCGGUAAGCGUUGGAUUGUUCACCCACUAAUAGGGA
ACGUGAGCUGGGUUUAGACCGUCGUGAGACAGGUUAGUUUUACCCUACUGAUGAAUGUUA
CCGCAAUAGUAAUUGAACUUAGUACGAGAGGAACAGUUCAUUCGGAUAAUUGGUUUUUGC
GGCUGUCUGAUCAGGCAUUGCCGCGAAGCUACCAUCCGCUGGAUUAUGGCUGAACGCCUC
UAAGUCAGAAUCCAUGCUAGAACGCGGUGAUUUCUUUGCUCCACACAAUAUAGAUGGAUA
CGAAUAAGGCGUCCUUGUGGCGUCGCUGAACCAUAGCAGGCUAGCAACGGUGCACUUGGC
GGAAAGGCCUUGGGUGCUUGCUGGCGAAUUGCAAUGUCAUUUUGCGUGGGGAUAAAUCAU
UUGUAUACGACUUAGAUGUACAACGGGGUAUUGUAAGCAGUAGAGUAGCCUUGUUGUUAC
GAUCUGCUGAGAUUAAGCCUUUGUUGUCUGAUUUGU
Sequence of entity 2 (3, AS), FASTA
>5ON6_2 5S ribosomal RNA (chains 3, AS)
GGUUGCGGCCAUAUCUACCAGAAAGCACCGUUUCCCGUCCGAUCAACUGUAGUUAAGCUG
GUAAGAGCCUGACCGAGUAGUGUAGUGGGUGACCAUACGCGAAACUCAGGUGCUGCAAUC
U
Sequence of entity 3 (4, AT), FASTA
>5ON6_3 5.8S ribosomal RNA (chains 4, AT)
AAACUUUCAACAACGGAUCUCUUGGUUCUCGCAUCGAUGAAGAACGCAGCGAAAUGCGAU
ACGUAAUGUGAAUUGCAGAAUUCCGUGAAUCAUCGAAUCUUUGAACGCACAUUGCGCCCC
UUGGUAUUCCAGGGGGCAUGCCUGUUUGAGCGUCAUUU
Sequence of entity 4 (CD, j), FASTA
>5ON6_4 60S ribosomal protein L2-A (chains CD, j)
GRVIRNQRKGAGSIFTSHTRLRQGAAKLRTLDYAERHGYIRGIVKQIVHDSGRGAPLAKV
VFRDPYKYRLREEIFIANEGVHTGQFIYAGKKASLNVGNVLPLGSVPEGTIVSNVEEKPG
DRGALARASGNYVIIIGHNPDENKTRVRLPSGAKKVISSDARGVIGVIAGGGRVDKPLLK
AGRAFHKYRLKRNSWPKTRGVAMNPVDHPHGGGNHQHIGKASTISRGAVSGQKAGLIAAR
RTGLLRGSQKTQ
Sequence of entity 5 (CE, k), FASTA
>5ON6_5 60S ribosomal protein L3 (chains CE, k)
SHRKYEAPRHGHLGFLPRKRAASIRARVKAFPKDDRSKPVALTSFLGYKAGMTTIVRDLD
RPGSKFHKREVVEAVTVVDTPPVVVVGVVGYVETPRGLRSLTTVWAEHLSDEVKRRFYKN
WYKSKKKAFTKYSAKYAQDGAGIERELARIKKYASVVRVLVHTQIRKTPLAQKKAHLAEI
QLNGGSISEKVDWAREHFEKTVAVDSVFEQNEMIDAIAVTKGHGFEGVTHRWGTKKLPRK
THRGLRKVACIGAWHPAHVMWSVARAGQRGYHSRTSINHKIYRVGKGDDEANGATSFDRT
KKTITPMGGFVHYGEIKNDFIMVKGCIPGNRKRIVTLRKSLYTNTSRKALEEVSLKWIDT
ASKFGKGRFQTPAEKHAFMGTLKKDL
Sequence of entity 6 (CF, l), FASTA
>5ON6_6 60S ribosomal protein L4-A (chains CF, l)
SRPQVTVHSLTGEATANALPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYAVSEKAGHQTS
AESWGTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFAPTKTWRKWNVKVNHNEKRYA
TASAIAATAVASLVLARGHRVEKIPEIPLVVSTDLESIQKTKEAVAALKAVGAHSDLLKV
LKSKKLRAGKGKYRNRRWTQRRGPLVVYAEDNGIVKALRNVPGVETANVASLNLLQLAPG
AHLGRFVIWTEAAFTKLDQVWGSETVASSKVGYTLPSHIISTSDVTRIINSSEIQSAIRP
AGQATQKRTHVLKKNPLKNKQVLLRLNPYAKVFAAEKLGSKKAEKTGTKPAAVFTETLKH
D
Sequence of entity 7 (CG, m), FASTA
>5ON6_7 60S ribosomal protein L5 (chains CG, m)
AFQKDAKSSAYSSRFQTPFRRRREGKTDYYQRKRLVTQHKAKYNTPKYRLVVRFTNKDII
CQIISSTITGDVVLAAAYSHELPRYGITHGLTNWAAAYATGLLIARRTLQKLGLDETYKG
VEEVEGEYELTEAVEDGPRPFKVFLDIGLQRTTTGARVFGALKGASDGGLYVPHSENRFP
GWDFETEEIDPELLRSYIFGGHVSQYMEELADDDEERFSELFKGYLADDIDADSLEDIYT
SAHEAIRADPAFKPTEKKFTKEQYAAESKKYRQTKLSKEERAARVAAKIAALAGQQ
Sequence of entity 8 (CH, n), FASTA
>5ON6_8 60S ribosomal protein L6-A (chains CH, n)
SAQKAPKWYPSEDVAALKKTRKAARPQKLRASLVPGTVLILLAGRFRGKRVVYLKHLEDN
TLLISGPFKVNGVPLRRVNARYVIATSTKVSVEGVNVEKFNVEYFAKEKLTKKEKKEANL
FPEQQNKEIKAERVEDQKVVDKALIAEIKKTPLLKQYLSASFSLKNGDKPHMLKF
Sequence of entity 9 (CI, o), FASTA
>5ON6_9 60S ribosomal protein L7-A (chains CI, o)
AEQVAAERAARKAANKEKRAIILERNAAYQKEYETAERNIIQAKRDAKAAGSYYVEAQHK
LVFVVRIKGINKIPPKPRKVLQLLRLTRINSGTFVKVTKATLELLKLIEPYVAYGYPSYS
TIRQLVYKRGFGKINKQRVPLSDNAIIEANLGKYGILSIDDLIHEIITVGPHFKQANNFL
WPFKLSNPSGGWGVPRKFKHFIQGGSFGNREEFINKLVKSMN
Sequence of entity 10 (CJ, p), FASTA
>5ON6_10 60S ribosomal protein L8-A (chains CJ, p)
NPLTHSTPKNFGIGQAVQPKRNLSRYVKWPEYVRVQRQKKILSIRLKVPPTIAQFQYTLD
RNTAAETFKLFNKYRPETAAEKKERLTKEAAAVAEGKSKQDASPKPYAVKYGLNHVVALI
ENKKAKLVLIANDVDPIELVVFLPALCKKMGVPYAIVKGKARLGTLVNQKTSAVAALTEV
RAEDEAALAKLVSTIDANFADKYDEVKKHWGGGILGNKAQAKMDKRAKNSDSA
Sequence of entity 11 (CK, q), FASTA
>5ON6_11 60S ribosomal protein L9-A (chains CK, q)
MKYIQTEQQIEVPEGVTVSIKSRIVKVVGPRGTLTKNLKHIDVTFTKVNNQLIKVAVHNG
GRKHVAALRTVKSLVDNMITGVTKGYKYKMRYVYAHFPINVNIVEKDGAKFIEVRNFLGD
KKIRNVPVRDGVTIEFSTNVKDEIVLSGNSVEDVSQNAADLQQICRVRNKDIRKFLDGIY
VSHKGFITEDL
Sequence of entity 12 (CL, r), FASTA
>5ON6_12 60S ribosomal protein L10 (chains CL, r)
ARRPARCYRYQKNKPYPKSRYNRAVPDSKIRIYDLGKKKATVDEFPLCVHLVSNELEQLS
SEALEAARICANKYMTTVSGRDAFHLRVRVHPFHVLRINKMLSCAGADRLQQGMRGAWGK
PHGLAARVDIGQIIFSVRTKDSNKDVVVEGLRRARYKFPGQQKIILSKKWGFTNLDRPEY
LKKREAGEVKDDGAFVKFLSKKGSLENNIREFPEYFAAQA

Ligands and cofactors

IDNameFormulaCopies
OHXosmium (III) hexammineH12 N6 Os1064
MGMagnesium ionMg1461
HN8HaemanthamineC17 H19 N O42
ZNZinc ionZn16

Water and common crystallization additives (GOL) are not listed.

Primary citation

The Amaryllidaceae Alkaloid Haemanthamine Binds the Eukaryotic Ribosome to Repress Cancer Cell Growth. Pellegrino, S., Meyer, M., Zorbas, C. et al. Structure (2018) 26:416-425.e4. DOI 10.1016/j.str.2018.01.009 · PubMed

Other PDB entries of the same protein (UniProt P0CX45 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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