5TBW: Chlorolissoclimide

Name: PDB 5TBW: Crystal structure of chlorolissoclimide bound to the yeast 80S ribosome
Published: 2017-07-26
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Crystal structure of chlorolissoclimide bound to the yeast 80S ribosome. Determined by X-ray diffraction at 3.0 Å resolution. Released 26 Jul 2017.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 159
Atoms: 409,612
Mol. weight: 6294.77 kDa
Ligands: MG, 7AL, ZN, OHX
Released: 26 Jul 2017

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

Secondary structure: helices and β-sheets

5TBW contains 1,022 α-helices and 1,022 β-strands across 151 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

Element	Residues	Length	Sheet
β-strand	5-13	9	239
α-helix	14-15	2
β-strand	25-31	7	239
α-helix	34-45	12
α-helix	53-55	3
β-strand	56-63	8	239
β-strand	73-82	10	240
β-strand	87-96	10	240
α-helix	99-114	16
α-helix	118-120	3
β-strand	121-128	8	240
α-helix	138-141	4
α-helix	142-144	3
β-strand	150-151	2	169
α-helix	157-159	3
β-strand	164	1	190

Chain 2: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	25-26	2
α-helix	28-31	4
β-strand	39-42	4	253
α-helix	52-54	3
α-helix	55-57	3
β-strand	60-67	8	253
β-strand	71-80	10	253
β-strand	83-92	10	253
β-strand	96-98	3	253
α-helix	103-120	18
α-helix	132-136	5
β-strand	139-142	4	106
α-helix	148	1
β-strand	149-150	2	239

Chain 5: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	258
α-helix	20-23	4
α-helix	30-40	11
β-strand	42-43	2	259
β-strand	46-47	2	259
β-strand	54-58	5	258
β-strand	62-67	6	258
α-helix	73-86	14
β-strand	94-99	6	258
β-strand	102-106	5	258

Chain 6: 3 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	17-18	2	277
β-strand	22-25	4	278
β-strand	27	1	279
β-strand	31	1	280
β-strand	33-39	7	278
α-helix	48-50	3
β-strand	51-52	2	277
β-strand	57-61	5	278
β-strand	65	1	280
β-strand	74-80	7	278
β-strand	85-86	2	281
β-strand	92-95	4	281
β-strand	99-102	4	278
β-strand	103	1	282
β-strand	109	1	282
β-strand	114	1	279
β-strand	118	1	283
α-helix	120-125	6
α-helix	127-131	5
β-strand	136	1	283

Chain 7: 6 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	295
β-strand	12-13	2	295
β-strand	19-22	4	281
β-strand	28-31	4	281
α-helix	34-41	8
α-helix	46-48	3
α-helix	53-58	6
α-helix	64-66	3
α-helix	87-89	3
α-helix	93-95	3

Chain 8: 7 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	31	1	117
α-helix	38-42	5
α-helix	52-55	4
α-helix	59-62	4
β-strand	63-66	4	307
α-helix	70-79	10
β-strand	81-86	6	307
α-helix	92-103	12
β-strand	107-114	8	307
β-strand	120-126	7	307
α-helix	127	1
α-helix	132-139	8

Chain 9: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	12-20	9
α-helix	24-30	7
β-strand	32-34	3	1
β-strand	35	1	2
α-helix	36	1
α-helix	37-43	7
β-strand	47-49	3	1
β-strand	55-58	4	2
β-strand	67-74	8	2
β-strand	79-83	5	2
β-strand	86-88	3	3
β-strand	94-96	3	3
α-helix	97-98	2
β-strand	99	1	2
α-helix	101-103	3
β-strand	104-108	5	2
α-helix	113-121	9

Chain a: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	44-53	10
β-strand	60	1	167
α-helix	62-66	5
α-helix	73-82	10
β-strand	90-91	2	167
β-strand	101-102	2	167

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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
25S ribosomal RNA	1, AR	RNA	3149	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
5S ribosomal RNA	3, AS	RNA	121	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
5.8S ribosomal RNA	4, AT	RNA	158	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
60S ribosomal protein L2-A	CD, j	protein	252	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P0CX45 (AlphaFold model)
60S ribosomal protein L3	CE, k	protein	386	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P14126 (AlphaFold model)
60S ribosomal protein L4-A	CF, l	protein	361	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P10664 (AlphaFold model)
60S ribosomal protein L5	CG, m	protein	296	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P26321 (AlphaFold model)
60S ribosomal protein L6-A	CH, n	protein	175	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Q02326
60S ribosomal protein L7-A	CI, o	protein	222	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P05737
60S ribosomal protein L8-A	CJ, p	protein	233	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P17076
60S ribosomal protein L9-A	CK, q	protein	191	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P05738
60S ribosomal protein L10	CL, r	protein	220	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P41805

71 more molecules are not listed.

Sequence of entity 1 (1, AR), FASTA

>5TBW_1 25S ribosomal RNA (chains 1, AR)
UUGACCUCAAAUCAGGUAGGAGUACCCGCUGAACUUAAGCAUAUCAAUAAGCGGAGGAAA
AGAAACCAACCGGGAUUGCCUUAGUAACGGCGAGUGAAGCGGCAAAAGCUCAAAUUUGAA
AUCUGGUACCUUCGGUGCCCGAGUUGUAAUUUGGAGAGGGCAACUUUGGGGCCGUUCCUU
GUCUAUGUUCCUUGGAACAGGACGUCAUAGAGGGUGAGAAUCCCGUGUGGCGAGGAGUGC
GGUUCUUUGUAAAGUGCCUUCGAAGAGUCGAGUUGUUUGGGAAUGCAGCUCUAAGUGGGU
GGUAAAUUCCAUCUAAAGCUAAAUAUUGGCGAGAGACCGAUAGCGAACAAGUACAGUGAU
GGAAAGAUGAAAAGAACUUUGAAAAGAGAGUGAAAAAGUACGUGAAAUUGUUGAAAGGGA
AGGGCAUUUGAUCAGACAGGCCAGCAUCAGUUUUGGUGGCAGGAUAAAUCCAUAGGAAUG
UAGCUUGCCUCGGUAAGUAUUAUAGCCUGUGGGAAUACUGCCAGCUGGGACUGAGGACUG
CGACGUAAGUCAAGGAUGCUGGCAUAAUGGUUAUAUGCCGCCCGUCUUGAAACACGGACC
AAGGAGUCUAACGUCUAUGCGAGUGUUUGGGUGUAAAACCCAUACGCGUAAUGAAAGUGA
ACGUAGGUUGGGGCCUCGCAAGAGGUGCACAAUCGACCGAUCCUGAUGUCUUCGGAUGGA
UUUGAGUAAGAGCAUAGCUGUUGGGACCCGAAAGAUGGUGAACUAUGCCUGAAUAGGGUG
AAGCCAGAGGAAACUCUGGUGGAGGCUCGUAGCGGUUCUGACGUGCAAAUCGAUCGUCGA
AUUUGGGUAUAGGGGCGAAAGACUAAUCGAACCAUCUAGUAGCUGGUUCCUGCCGAAGUU
UCCCUCAGGAUAGCAGAAGCUCGUAUCAGUUUUAUGAGGUAAAGCGAAUGAUUAGAGGUU
CCGGGGUCGAAAUGACCUUGACCUAUUCUCAAACUUUAAAUAUGUAAGAAGUCCUUGUUA
CUUAAUUGAACGUGGACAUUUGAAUGAAGAGCUUUUAGUGGGCCAUUUUUGGUAAGCAGA
ACUGGCGAUGCGGGAUGAACCGAACGUAGAGUUAAGGUGCCGGAAUACACGCUCAUCAGA
CACCACAAAAGGUGUUAGUUCAUCUAGACAGCCGGACGGUGGCCAUGGAAGUCGGAAUCC
GCUAAGGAGUGUGUAACAACUCACCGGCCGAAUGAACUAGCCCUGAAAAUGGAUGGCGCU
CAAGCGUGUUACCUAUACUCUACCGUCAGGGUUGAUAUGAUGCCCUGACGAGUAGGCAGG
CGUGGAGGUCAGUGACGAAGCCUAGACCGUAAGGUCGGGUCGAACGGCCUCUAGUGCAGA
UCUUGGUGGUAGUAGCAAAUAUUCAAAUGAGAACUUUGAAGACUGAAGUGGGGAAAGGUU
CCACGUCAACAGCAGUUGGACGUGGGUUAGUCGAUCCUAAGAGAUGGGGAAGCUCCGUUU
CAAAGGCCUGAUUUUAUGCAGGCCACCAUCGAAAGGGAAUCCGGUUAAGAUUCCGGAACC
UGGAUAUGGAUUCUUCACGGUAACGUAACUGAAUGUGGAGACGUCGGCGCGAGCCCUGGG
AGGAGUUAUCUUUUCUUCUUAACAGCUUAUCACCCCGGAAUUGGUUUAUCCGGAGAUGGG
GUCUUAUGGCUGGAAGAGGCCAGCACCUUUGCUGGCUCCGGUGCGCUUGUGACGGCCCGU
GAAAAUCCACAGGAAGGAAUAGUUUUCAUGCCAGGUCGUACUGAUAACCGCAGCAGGUCU
CCAAGGUGAACAGCCUCUAGUUGAUAGAAUAAUGUAGAUAAGGGAAGUCGGCAAAAUAGA
UCCGUAACUUCGGGAUAAGGAUUGGCUCUAAGGGUCGGGUACGAUCAACUUAGAACUGGU
ACGGACAAGGGGAAUCUGACUGUCUAAUUAAAACAUAGCAUUGCGAUGGUCAGAAAGUGA
UGUUGACGCAAUGUGAUUUCUGCCCAGUGCUCUGAAUGUCAAAGUGAAGAAAUUCAACCA
AGCGCGGGUAAACGGCGGGAGUAACUAUGACUCUCUUAAGGUAGCCAAAUGCCUCGUCAU
CUAAUUAGUGACGCGCAUGAAUGGAUUAACGAGAUUCCCACUGUCCCUAUCUACUAUCUA
GCGAAACCACAGCCAAGGGAACGGGCUUGGCAGAAUCAGCGGGGAAAGAAGACCCUGUUG
AGCUUGACUCUAGUUUGACAUUGUGAAGAGACAUAGUUUCUUUACUUAUUCAAUGAAGCG
GAGCUGGAAUUCAUUUUCCACGUUCUAGCAUUCAAGGUCCCAUUCGGGGCUGAUCCGGGU
UGAAGACAUUGUCAGGUGGGGAGUUUGGCUGGGGCGGCACAUCUGUUAAACGAUAACGCA
GAUGUCCUAAGGGGGGCUCAUGGAGAACAGAAAUCUCCAGUAGAACAAAAGGGUAAAAGC
CCCCUUGAUUUUGAUUUUCAGUGUGAAUACAAACCAUGAAAGUGUGGCCUAUCGAUCCUU
UAGUCCCUCGGAAUUUGAGGCUAGAGGUGCCAGAAAAGUUACCACAGGGAUAACUGGCUU
GUGGCAGUCAAGCGUUCAUAGCGACAUUGCUUUUUGAUUCUUCGAUGUCGGCUCUUCCUA
UCAUACCGAAGCAGAAUUCGGUAAGCGUUGGAUUGUUCACCCACUAAUAGGGAACGUGAG
CUGGGUUUAGACCGUCGUGAGACAGGUUAGUUUUACCCUACUGAUGAAUGUUACCGCAAU
AGUAAUUGAACUUAGUACGAGAGGAACAGUUCAUUCGGAUAAUUGGUUUUUGCGGCUGUC
UGAUCAGGCAUUGCCGCGAAGCUACCAUCCGCUGGAUUAUGGCUGAACGCCUCUAAGUCA
GAAUCCAUGCUAGAACGCGGUGAUUUCUUUGCUCCACACAAUAUAGAUGGAUACGAAUAA
GGCGUCCUUGUGGCGUCGCUGAACCAUAGCAGGCUAGCAACGGUGCACUUGGCGGAAAGG
CCUUGGGUGCUUGCUGGCGAAUUGCAAUGUCAUUUUGCGUGGGGAUAAAUCAUUUGUAUA
CGACUUAGAUGUACAACGGGGUAUUGUAAGCAGUAGAGUAGCCUUGUUGUUACGAUCUGC
UGAGAUUAAGCCUUUGUUGUCUGAUUUGU

Sequence of entity 2 (3, AS), FASTA

>5TBW_2 5S ribosomal RNA (chains 3, AS)
GGUUGCGGCCAUAUCUACCAGAAAGCACCGUUUCCCGUCCGAUCAACUGUAGUUAAGCUG
GUAAGAGCCUGACCGAGUAGUGUAGUGGGUGACCAUACGCGAAACUCAGGUGCUGCAAUC
U

Sequence of entity 3 (4, AT), FASTA

>5TBW_3 5.8S ribosomal RNA (chains 4, AT)
AAACUUUCAACAACGGAUCUCUUGGUUCUCGCAUCGAUGAAGAACGCAGCGAAAUGCGAU
ACGUAAUGUGAAUUGCAGAAUUCCGUGAAUCAUCGAAUCUUUGAACGCACAUUGCGCCCC
UUGGUAUUCCAGGGGGCAUGCCUGUUUGAGCGUCAUUU

Sequence of entity 4 (CD, j), FASTA

>5TBW_4 60S ribosomal protein L2-A (chains CD, j)
GRVIRNQRKGAGSIFTSHTRLRQGAAKLRTLDYAERHGYIRGIVKQIVHDSGRGAPLAKV
VFRDPYKYRLREEIFIANEGVHTGQFIYAGKKASLNVGNVLPLGSVPEGTIVSNVEEKPG
DRGALARASGNYVIIIGHNPDENKTRVRLPSGAKKVISSDARGVIGVIAGGGRVDKPLLK
AGRAFHKYRLKRNSWPKTRGVAMNPVDHPHGGGNHQHIGKASTISRGAVSGQKAGLIAAR
RTGLLRGSQKTQ

Sequence of entity 5 (CE, k), FASTA

>5TBW_5 60S ribosomal protein L3 (chains CE, k)
SHRKYEAPRHGHLGFLPRKRAASIRARVKAFPKDDRSKPVALTSFLGYKAGMTTIVRDLD
RPGSKFHKREVVEAVTVVDTPPVVVVGVVGYVETPRGLRSLTTVWAEHLSDEVKRRFYKN
WYKSKKKAFTKYSAKYAQDGAGIERELARIKKYASVVRVLVHTQIRKTPLAQKKAHLAEI
QLNGGSISEKVDWAREHFEKTVAVDSVFEQNEMIDAIAVTKGHGFEGVTHRWGTKKLPRK
THRGLRKVACIGAWHPAHVMWSVARAGQRGYHSRTSINHKIYRVGKGDDEANGATSFDRT
KKTITPMGGFVHYGEIKNDFIMVKGCIPGNRKRIVTLRKSLYTNTSRKALEEVSLKWIDT
ASKFGKGRFQTPAEKHAFMGTLKKDL

Sequence of entity 6 (CF, l), FASTA

>5TBW_6 60S ribosomal protein L4-A (chains CF, l)
SRPQVTVHSLTGEATANALPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYAVSEKAGHQTS
AESWGTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFAPTKTWRKWNVKVNHNEKRYA
TASAIAATAVASLVLARGHRVEKIPEIPLVVSTDLESIQKTKEAVAALKAVGAHSDLLKV
LKSKKLRAGKGKYRNRRWTQRRGPLVVYAEDNGIVKALRNVPGVETANVASLNLLQLAPG
AHLGRFVIWTEAAFTKLDQVWGSETVASSKVGYTLPSHIISTSDVTRIINSSEIQSAIRP
AGQATQKRTHVLKKNPLKNKQVLLRLNPYAKVFAAEKLGSKKAEKTGTKPAAVFTETLKH
D

Sequence of entity 7 (CG, m), FASTA

>5TBW_7 60S ribosomal protein L5 (chains CG, m)
AFQKDAKSSAYSSRFQTPFRRRREGKTDYYQRKRLVTQHKAKYNTPKYRLVVRFTNKDII
CQIISSTITGDVVLAAAYSHELPRYGITHGLTNWAAAYATGLLIARRTLQKLGLDETYKG
VEEVEGEYELTEAVEDGPRPFKVFLDIGLQRTTTGARVFGALKGASDGGLYVPHSENRFP
GWDFETEEIDPELLRSYIFGGHVSQYMEELADDDEERFSELFKGYLADDIDADSLEDIYT
SAHEAIRADPAFKPTEKKFTKEQYAAESKKYRQTKLSKEERAARVAAKIAALAGQQ

Sequence of entity 8 (CH, n), FASTA

>5TBW_8 60S ribosomal protein L6-A (chains CH, n)
SAQKAPKWYPSEDVAALKKTRKAARPQKLRASLVPGTVLILLAGRFRGKRVVYLKHLEDN
TLLISGPFKVNGVPLRRVNARYVIATSTKVSVEGVNVEKFNVEYFAKEKLTKKEKKEANL
FPEQQNKEIKAERVEDQKVVDKALIAEIKKTPLLKQYLSASFSLKNGDKPHMLKF

Sequence of entity 9 (CI, o), FASTA

>5TBW_9 60S ribosomal protein L7-A (chains CI, o)
AEQVAAERAARKAANKEKRAIILERNAAYQKEYETAERNIIQAKRDAKAAGSYYVEAQHK
LVFVVRIKGINKIPPKPRKVLQLLRLTRINSGTFVKVTKATLELLKLIEPYVAYGYPSYS
TIRQLVYKRGFGKINKQRVPLSDNAIIEANLGKYGILSIDDLIHEIITVGPHFKQANNFL
WPFKLSNPSGGWGVPRKFKHFIQGGSFGNREEFINKLVKSMN

Sequence of entity 10 (CJ, p), FASTA

>5TBW_10 60S ribosomal protein L8-A (chains CJ, p)
NPLTHSTPKNFGIGQAVQPKRNLSRYVKWPEYVRVQRQKKILSIRLKVPPTIAQFQYTLD
RNTAAETFKLFNKYRPETAAEKKERLTKEAAAVAEGKSKQDASPKPYAVKYGLNHVVALI
ENKKAKLVLIANDVDPIELVVFLPALCKKMGVPYAIVKGKARLGTLVNQKTSAVAALTEV
RAEDEAALAKLVSTIDANFADKYDEVKKHWGGGILGNKAQAKMDKRAKNSDSA

Sequence of entity 11 (CK, q), FASTA

>5TBW_11 60S ribosomal protein L9-A (chains CK, q)
MKYIQTEQQIEVPEGVTVSIKSRIVKVVGPRGTLTKNLKHIDVTFTKVNNQLIKVAVHNG
GRKHVAALRTVKSLVDNMITGVTKGYKYKMRYVYAHFPINVNIVEKDGAKFIEVRNFLGD
KKIRNVPVRDGVTIEFSTNVKDEIVLSGNSVEDVSQNAADLQQICRVRNKDIRKFLDGIY
VSHKGFITEDL

Sequence of entity 12 (CL, r), FASTA

>5TBW_12 60S ribosomal protein L10 (chains CL, r)
ARRPARCYRYQKNKPYPKSRYNRAVPDSKIRIYDLGKKKATVDEFPLCVHLVSNELEQLS
SEALEAARICANKYMTTVSGRDAFHLRVRVHPFHVLRINKMLSCAGADRLQQGMRGAWGK
PHGLAARVDIGQIIFSVRTKDSNKDVVVEGLRRARYKFPGQQKIILSKKWGFTNLDRPEY
LKKREAGEVKDDGAFVKFLSKKGSLENNIREFPEYFAAQA

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1394
7AL	Chlorolissoclimide	C20 H30 Cl N O4	2
ZN	Zinc ion	Zn	16
OHX	osmium (III) hexammine	H12 N6 Os	1074

Primary citation

Synthesis facilitates an understanding of the structural basis for translation inhibition by the lissoclimides. Konst, Z.A., Szklarski, A.R., Pellegrino, S. et al. Nat Chem (2017) 9:1140-1149. DOI 10.1038/nchem.2800 · PubMed

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

9PN5 1.75 Å, Composite map of hypomethylated 80S ribosome treated with hygromycin B
8CCS 1.97 Å, 80S S. cerevisiae ribosome with ligands in hybrid-1 pre-translocation (PRE-H1) complex
8CDR 2.04 Å, Translocation intermediate 2 (TI-2) of 80S S. cerevisiae ribosome with ligands and eEF2…
8CEH 2.05 Å, Translocation intermediate 4 (TI-4) of 80S S. cerevisiae ribosome with ligands and eEF2…
8P8N 2.15 Å, Mouse RPL39 integrated into the yeast 60S ribosomal subunit
8PFR 2.15 Å, Mouse RPL39L integrated into the yeast 60S ribosomal subunit
8EVT 2.2 Å, Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome…
8T2Y 2.2 Å, Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA,…
8P8U 2.23 Å, Yeast 60S ribosomal subunit
8CGN 2.28 Å, Non-rotated 80S S. cerevisiae ribosome with ligands
8ZHC 2.3 Å, pre-frameshift complex of yeast 80S ribosome with eRF1 and mRNA of WNV
7UOO 2.34 Å, Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state

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