5I4L: Amicoumacin A

Name: PDB 5I4L: Crystal structure of Amicoumacin A bound to the yeast 80S ribosome
Published: 2016-06-22
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Crystal structure of Amicoumacin A bound to the yeast 80S ribosome. Determined by X-ray diffraction at 3.1 Å resolution. Released 22 Jun 2016.

Method: X-ray diffraction
Resolution: 3.1 Å
Organism: Saccharomyces cerevisiae S288c
Chains: 162
Atoms: 410,475
Mol. weight: 6467.21 kDa
Ligands: OHX, MG, ZN, UAM
Released: 22 Jun 2016

Explore 5I4L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5I4L contains 1,003 α-helices and 1,042 β-strands across 154 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 c0: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	5-17	13
β-strand	20-21	2	171
α-helix	39-52	14
β-strand	55-60	6	171
β-strand	63-68	6	171
α-helix	70-79	10

Chain C0: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	5-18	14
β-strand	20-22	3	158
α-helix	39-51	13
β-strand	55-58	4	158
β-strand	65-68	4	158
α-helix	70-79	10
α-helix	82-83	2

Chain c1: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	42-45	4
α-helix	46-50	5
β-strand	70-77	8	179
β-strand	83-94	12	179
β-strand	99-110	12	179
β-strand	120-132	13	179
β-strand	135-142	8	179

Chain C1: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	13-14	2
α-helix	46-49	4
β-strand	70-77	8	166
β-strand	83-94	12	166
α-helix	95-97	3
β-strand	99-110	12	166
β-strand	122-127	6	166
β-strand	137-142	6	166
α-helix	150-152	3

Chain c2: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	29-36	8
β-strand	41-43	3	192
α-helix	46-53	8
β-strand	59-61	3	192
α-helix	70-79	10
α-helix	94-99	6
β-strand	121-123	3	192
α-helix	135-141	7

Chain C2: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	27-37	11
β-strand	41-43	3	173
α-helix	45-52	8
β-strand	59-61	3	173
α-helix	70-79	10
α-helix	94-100	7
β-strand	121-123	3	173
α-helix	131-141	11

Chain c3: 6 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	30-42	13
α-helix	47-56	10
β-strand	58	1	46
α-helix	71-77	7
α-helix	86-104	19
α-helix	109-131	23
α-helix	143-150	8

Chain C3: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	30-43	14
α-helix	47-56	10
α-helix	63-66	4
α-helix	71-77	7
α-helix	86-104	19
α-helix	109-131	23
α-helix	136	1
α-helix	143-150	8

145 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
18S ribosomal RNA	2, 6	RNA	1800	Saccharomyces cerevisiae S288c
40S ribosomal protein S0-A	S0, s0	protein	206	Saccharomyces cerevisiae S288c	P32905 (AlphaFold model)
40S ribosomal protein S1-A	S1, s1	protein	216	Saccharomyces cerevisiae S288c	P33442 (AlphaFold model)
40S ribosomal protein S2	S2, s2	protein	217	Saccharomyces cerevisiae S288c	P25443 (AlphaFold model)
40S ribosomal protein S3	S3, s3	protein	223	Saccharomyces cerevisiae S288c	P05750 (AlphaFold model)
40S ribosomal protein S4-A	S4, s4	protein	260	Saccharomyces cerevisiae S288c	P0CX35
40S ribosomal protein S5	S5, s5	protein	206	Saccharomyces cerevisiae S288c	P26783
40S ribosomal protein S6-A	S6, s6	protein	226	Saccharomyces cerevisiae S288c	P0CX37
40S ribosomal protein S7-A	S7, s7	protein	186	Saccharomyces cerevisiae S288c	P26786
40S ribosomal protein S8-A	S8, s8	protein	200	Saccharomyces cerevisiae S288c	P0CX39
40S ribosomal protein S9-A	S9, s9	protein	185	Saccharomyces cerevisiae S288c	O13516
40S ribosomal protein S10-A	C0, c0	protein	98	Saccharomyces cerevisiae S288c	Q08745

73 more molecules are not listed.

Sequence of entity 1 (2, 6), FASTA

>5I4L_1 18S ribosomal RNA (chains 2, 6)
UAUCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCU
AAGUAUAAGCAAUUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUCGUUUAU
UUGAUAGUUCCUUUACUACAUGGUAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCUUAA
AAUCUCGACCCUUUGGAAGAGAUGUAUUUAUUAGAUAAAAAAUCAAUGUCUUCGGACUCU
UUGAUGAUUCAUAAUAACUUUUCGAAUCGCAUGGCCUUGUGCUGGCGAUGGUUCAUUCAA
AUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUUUCAACGGGUAA
CGGGGAAUAAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGA
AGGCAGCAGGCGCGCAAAUUACCCAAUCCUAAUUCAGGGAGGUAGUGACAAUAAAUAACG
AUACAGGGCCCAUUCGGGUCUUGUAAUUGGAAUGAGUACAAUGUAAAUACCUUAACGAGG
AACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAU
AUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAACUUUGGGCCCGGUUGGCCGGUCCG
AUUUUUUCGUGUACUGGAUUUCCAACGGGGCCUUUCCUUCUGGCUAACCUUGAGUCCUUG
UGGCUCUUGGCGAACCAGGACUUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUA
UUGCUCGAAUAUAUUAGCAUGGAAUAAUAGAAUAGGACGUUUGGUUCUAUUUUGUUGGUU
UCUAGGACCAUCGUAAUGAUUAAUAGGGACGGUCGGGGGCAUCAGUAUUCAAUUGUCAGA
GGUGAAAUUCUUGGAUUUAUUGAAGACUAACUACUGCGAAAGCAUUUGCCAAGGACGUUU
UCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUCAGAUACCGUCGUAGUCUUAA
CCAUAAACUAUGCCGACUAGGGAUCGGGUGGUGUUUUUUUAAUGACCCACUCGGCACCUU
ACGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAG
GAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGG
GAAACUCACCAGGUCCAGACACAAUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUUU
GUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGCUUAAUUGCGAU
AACGAACGAGACCUUAACCUACUAAAUAGUGGUGCUAGCAUUUGCUGGUUAUCCACUUCU
UAGAGGGACUAUCGGUUUCAAGCCGAUGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCC
CUUAGACGUUCUGGGCCGCACGCGCGCUACACUGACGGAGCCAGCGAGUCUAACCUUGGC
CGAGAGGUCUUGGUAAUCUUGUGAAACUCCGUCGUGCUGGGGAUAGAGCAUUGUAAUUAU
UGCUCUUCAACGAGGAAUUCCUAGUAAGCGCAAGUCAUCAGCUUGCGUUGAUUACGUCCC
UGCCCUUUGUACACACCGCCCGUCGCUAGUACCGAUUGAAUGGCUUAGUGAGGCCUCAGG
AUCUGCUUAGAGAAGGGGGCAACUCCAUCUCAGAGCGGAGAAUUUGGACAAACUUGGUCA
UUUAGAGGAACUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA

Sequence of entity 2 (S0, s0), FASTA

>5I4L_2 40S ribosomal protein S0-A (chains S0, s0)
SLPATFDLTPEDAQLLLAANTHLGARNVQVHQEPYVFNARPDGVHVINVGKTWEKLVLAA
RIIAAIPNPEDVVAISSRTFGQRAVLKFAAHTGATPIAGRFTPGSFTNYITRSFKEPRLV
IVTDPRSDAQAIKEASYVNIPVIALTDLDSPSEFVDVAIPCNNRGKHSIGLIWYLLAREV
LRLRGALVDRTQPWSIMPDLYFYRDP

Sequence of entity 3 (S1, s1), FASTA

>5I4L_3 40S ribosomal protein S1-A (chains S1, s1)
VVDPFTRKEWFDIKAPSTFENRNVGKTLVNKSTGLKSASDALKGRVVEVCLADLQGSEDH
SFRKIKLRVDEVQGKNLLTNFHGMDFTTDKLRSMVRKWQTLIEANVTVKTSDDYVLRIFA
IAFTRKQANQVKRHSYAQSSHIRAIRKVISEILTKEVQGSTLAQLTSKLIPEVINKEIEN
ATKDIFPLQNIHVRKVKLLKQPKFDVGALMALHGEG

Sequence of entity 4 (S2, s2), FASTA

>5I4L_4 40S ribosomal protein S2 (chains S2, s2)
GWVPVTKLGRLVKAGKITTIEEIFLHSLPVKEFQIIDTLLPGLQDEVMNIKPVQKQTRAG
QRTRFKAVVVVGDSNGHVGLGIKTAKEVAGAIRAGIIIAKLSVIPIRRGYWGTNLGQPHS
LATKTTGKCGSVTVRLIPAPRGSGIVASPAVKKLLQLAGVEDVYTQSNGKTRTLENTLKA
AFVAIGNTYGFLTPNLWAEQPLPVSPLDIYSDEASAQ

Sequence of entity 5 (S3, s3), FASTA

>5I4L_5 40S ribosomal protein S3 (chains S3, s3)
ALISKKRKLVADGVFYAELNEFFTRELAEEGYSGVEVRVTPTKTEVIIRATRTQDVLGEN
GRRINELTLLVQKRFKYAPGTIVLYAERVQDRGLSAVAQAESMKFKLLNGLAIRRAAYGV
VRYVMESGAKGCEVVVSGKLRAARAKAMKFADGFLIHSGQPVNDFIDTATRHVLMRQGVL
GIKVKIMRDPAKSRTGPKALPDAVTIIEPKEEEPILAPSVKDY

Sequence of entity 6 (S4, s4), FASTA

>5I4L_6 40S ribosomal protein S4-A (chains S4, s4)
ARGPKKHLKRLAAPHHWLLDKLSGCYAPRPSAGPHKLRESLPLIVFLRNRLKYALNGREV
KAILMQRHVKVDGKVRTDTTYPAGFMDVITLDATNENFRLVYDVKGRFAVHRITDEEASY
KLGKVKKVQLGKKGVPYVVTHDGRTIRYPDPNIKVNDTVKIDLASGKITDFIKFDAGKLV
YVTGGRNLGRIGTIVHKERHDGGFDLVHIKDSLDNTFVTRLNNVFVIGEQGKPYISLPKG
KGIKLSIAEERDRRRAQQGL

Sequence of entity 7 (S5, s5), FASTA

>5I4L_7 40S ribosomal protein S5 (chains S5, s5)
FTPVVLATPIPEEVQQAQTEIKLFNKWSFEEVEVKDASLVDYVQVRQPIFVAHTAGRYAN
KRFRKAQCPIIERLTNSLMMNGRNNGKKLKAVRIIKHTLDIINVLTDQNPIQVVVDAITN
TGPREDTTRVGGGGAARRQAVDVSPLRRVNQAIALLTIGAREAAFRNIKTIAETLAEELI
NAAKGSSTSYAIKKKDELERVAKSNR

Sequence of entity 8 (S6, s6), FASTA

>5I4L_8 40S ribosomal protein S6-A (chains S6, s6)
MKLNISYPVNGSQKTFEIDDEHRIRVFFDKRIGQEVDGEAVGDEFKGYVFKISGGNDKQG
FPMKQGVLLPTRIKLLLTKNVSCYRPRRDGERKRKSVRGAIVGPDLAVLALVIVKKGEQE
LEGLTDTTVPKRLGPKRANNIRKFFGLSKEDDVRDFVIRREVTKGEKTYTKAPKIQRLVT
PQRLQRKRHQRALKVRNAQAQREAAAEYAQLLAKRLSERKAEKAEI

Sequence of entity 9 (S7, s7), FASTA

>5I4L_9 40S ribosomal protein S7-A (chains S7, s7)
SAPQAKILSQAPTELELQVAQAFVELENSSPELKAELRPLQFKSIREIDVAGGKKALAIF
VPVPSLAGFHKVQTKLTRELEKKFQDRHVIFLAERRILPKPSRTSRQVQKRPRSRTLTAV
HDKILEDLVFPTEIVGKRVRYLVGGNKIQKVLLDSKDVQQIDYKLESFQAVYNKLTGKQI
VFEIPS

Sequence of entity 10 (S8, s8), FASTA

>5I4L_10 40S ribosomal protein S8-A (chains S8, s8)
MGISRDSRHKRSATGAKRAQFRKKRKFELGRQPANTKIGAKRIHSVRTRGGNKKYRALRI
ETGNFSWASEGISKKTRIAGVVYHPSNNELVRTNTLTKAAIVQIDATPFRQWFEAHYGQT
LGKKKNVKEEETVAKSKNAERKWAARAASAKIESSVESQFSAGRLYACISSRPGQSGRCD
GYILEGEELAFYLRRLTAKK

Sequence of entity 11 (S9, s9), FASTA

>5I4L_11 40S ribosomal protein S9-A (chains S9, s9)
PRAPRTYSKTYSTPKRPYESSRLDAELKLAGEFGLKNKKEIYRISFQLSKIRRAARDLLT
RDEKDPKRLFEGNALIRRLVRVGVLSEDKKKLDYVLALKVEDFLERRLQTQVYKLGLAKS
VHHARVLITQRHIAVGKQIVNIPSFMVRLDSEKHIDFAPTSPFGGARPGRVARRNAARKA
EASGE

Sequence of entity 12 (C0, c0), FASTA

>5I4L_12 40S ribosomal protein S10-A (chains C0, c0)
MLMPKEDRNKIHQYLFQEGVVVAKKDFNQAKHEEIDTKNLYVIKALQSLTSKGYVKTQFS
WQYYYYTLTEEGVEYLREYLNLPEHIVPGTYIQERNPT

Ligands and cofactors

ID	Name	Formula	Copies
OHX	osmium (III) hexammine	H12 N6 Os	993
MG	Magnesium ion	Mg	1019
ZN	Zinc ion	Zn	16
UAM	Amicoumacin A	C20 H29 N3 O7	1

Primary citation

Amicoumacin A induces cancer cell death by targeting the eukaryotic ribosome. Prokhorova, I.V., Akulich, K.A., Makeeva, D.S. et al. Sci Rep (2016) 6:27720-27720. DOI 10.1038/srep27720 · PubMed

Other PDB entries of the same protein (UniProt P32905 (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…
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,…
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
8EVP 2.38 Å, Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome…
9DP7 2.38 Å, Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome…
7ZW0 2.4 Å, FAP-80S Complex - Rotated state
8BN3 2.4 Å, Yeast 80S, ES7s delta, eIF5A, Stm1 containing

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