8P85: 80S yeast ribosome

Name: PDB 8P85: 80S yeast ribosome in complex with Fluorolissoclimide
Published: 2025-06-25
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

80S yeast ribosome in complex with Fluorolissoclimide. Determined by X-ray diffraction at 2.9 Å resolution. Released 25 Jun 2025.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Saccharomyces cerevisiae
Chains: 157
Atoms: 404,943
Mol. weight: 6601.12 kDa
Ligands: OHX, MG, SPD, VDU
Released: 25 Jun 2025

Explore 8P85 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8P85 contains 984 α-helices and 1,064 β-strands across 149 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: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	5-13	9	107
α-helix	14-16	3
β-strand	25-31	7	107
α-helix	34-48	15
β-strand	56-64	9	107
β-strand	73-82	10	108
β-strand	87-96	10	108
α-helix	99-113	15
α-helix	118-120	3
β-strand	121-128	8	108
α-helix	138-141	4
β-strand	150-151	2	4
β-strand	164	1	38

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	118
α-helix	52-54	3
α-helix	55-57	3
β-strand	60-67	8	118
β-strand	71-80	10	118
β-strand	83-92	10	118
α-helix	93-95	3
β-strand	96-98	3	118
α-helix	103-121	19
α-helix	134-136	3
β-strand	139-142	4	268
β-strand	150	1	107

Chain 5: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	129
α-helix	20-24	5
α-helix	30-40	11
β-strand	42-43	2	130
β-strand	46-47	2	130
β-strand	54-58	5	129
β-strand	62-67	6	129
α-helix	73-86	14
β-strand	93-99	7	129
β-strand	102-107	6	129

Chain 6: 4 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	10-12	3
β-strand	17-18	2	147
β-strand	22-25	4	148
β-strand	27	1	149
β-strand	31-39	9	148
α-helix	48-50	3
β-strand	51-52	2	147
β-strand	57-61	5	148
β-strand	62	1	150
β-strand	63-65	3	148
β-strand	70	1	150
β-strand	73-80	8	148
β-strand	85-86	2	151
β-strand	92-95	4	151
β-strand	99-102	4	148
β-strand	103	1	152
β-strand	109	1	152
β-strand	114	1	149
β-strand	118	1	153
α-helix	120-123	4
α-helix	127-132	6
β-strand	136	1	153

Chain 7: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	160
β-strand	12-13	2	160
β-strand	19-22	4	151
β-strand	28-31	4	151
α-helix	34-41	8
α-helix	46-48	3
α-helix	53-58	6

Chain 8: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	40-42	3
α-helix	52-55	4
α-helix	59-62	4
β-strand	63-66	4	173
α-helix	70-79	10
β-strand	81-86	6	173
α-helix	92-103	12
β-strand	107-109	3	173
β-strand	112-115	4	173
β-strand	119-126	8	173
α-helix	132-139	8

Chain 9: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	12-21	10
α-helix	24-30	7
β-strand	32-34	3	179
β-strand	35	1	180
α-helix	36	1
α-helix	37-43	7
β-strand	47-49	3	179
β-strand	55-58	4	180
β-strand	67-69	3	180
β-strand	70-74	5	181
α-helix	75-77	3
β-strand	79-88	10	181
β-strand	94-99	6	181
α-helix	101-103	3
β-strand	104-108	5	180
α-helix	109-111	3
α-helix	113-121	9

Chain a: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	46-53	8
α-helix	62-66	5
α-helix	73-77	5
α-helix	79-84	6

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
16S ribosomal RNA	A, sR	RNA	1800	Saccharomyces cerevisiae
40S ribosomal protein S0-A	B, s0	protein	252	Saccharomyces cerevisiae	P32905 (AlphaFold model)
40S ribosomal protein S1-A	C, s1	protein	255	Saccharomyces cerevisiae	P33442 (AlphaFold model)
40S ribosomal protein S2	D, s2	protein	254	Saccharomyces cerevisiae	P25443 (AlphaFold model)
Small ribosomal subunit protein uS3	E, s3	protein	240	Saccharomyces cerevisiae	P05750 (AlphaFold model)
40S ribosomal protein S4-A	F, s4	protein	261	Saccharomyces cerevisiae	P0CX35
40S ribosomal protein S5	G, s5	protein	225	Saccharomyces cerevisiae	P26783
40S ribosomal protein S6-A	H, s6	protein	236	Saccharomyces cerevisiae	P0CX37
40S ribosomal protein S7-A	I, s7	protein	190	Saccharomyces cerevisiae	P26786
40S ribosomal protein S8-A	J, s8	protein	200	Saccharomyces cerevisiae	P0CX39
40S ribosomal protein S9-A	K, s9	protein	197	Saccharomyces cerevisiae	O13516
Small ribosomal subunit protein eS10A,Small ribosomal subunit protein eS10A,40S ribosomal protein…	L, c0	protein	105	Saccharomyces cerevisiae	Q08745

67 more molecules are not listed.

Sequence of entity 1 (A, sR), FASTA

>8P85_1 16S ribosomal RNA (chains A, sR)
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 (B, s0), FASTA

>8P85_2 40S ribosomal protein S0-A (chains B, s0)
MSLPATFDLTPEDAQLLLAANTHLGARNVQVHQEPYVFNARPDGVHVINVGKTWEKLVLA
ARIIAAIPNPEDVVAISSRTFGQRAVLKFAAHTGATPIAGRFTPGSFTNYITRSFKEPRL
VIVTDPRSDAQAIKEASYVNIPVIALTDLDSPSEFVDVAIPCNNRGKHSIGLIWYLLARE
VLRLRGALVDRTQPWSIMPDLYFYRDPEEVEQQVAEEATTEEAGEEEAKEEVTEEQAEAT
EWAEENADNVEW

Sequence of entity 3 (C, s1), FASTA

>8P85_3 40S ribosomal protein S1-A (chains C, s1)
MAVGKNKRLSKGKKGQKKRVVDPFTRKEWFDIKAPSTFENRNVGKTLVNKSTGLKSASDA
LKGRVVEVCLADLQGSEDHSFRKIKLRVDEVQGKNLLTNFHGMDFTTDKLRSMVRKWQTL
IEANVTVKTSDDYVLRIFAIAFTRKQANQVKRHSYAQSSHIRAIRKVISEILTKEVQGST
LAQLTSKLIPEVINKEIENATKDIFPLQNIHVRKVKLLKQPKFDVGALMALHGEGSGEEK
GKKVTGFKDEVLETV

Sequence of entity 4 (D, s2), FASTA

>8P85_4 40S ribosomal protein S2 (chains D, s2)
MSAPEAQQQKRGGFGGRNRGRPNRRGPRNTEEKGWVPVTKLGRLVKAGKITTIEEIFLHS
LPVKEFQIIDTLLPGLQDEVMNIKPVQKQTRAGQRTRFKAVVVVGDSNGHVGLGIKTAKE
VAGAIRAGIIIAKLSVIPIRRGYWGTNLGQPHSLATKTTGKCGSVTVRLIPAPRGSGIVA
SPAVKKLLQLAGVEDVYTQSNGKTRTLENTLKAAFVAIGNTYGFLTPNLWAEQPLPVSPL
DIYSDEASAQKKRF

Sequence of entity 5 (E, s3), FASTA

>8P85_5 Small ribosomal subunit protein uS3 (chains E, s3)
MVALISKKRKLVADGVFYAELNEFFTRELAEEGYSGVEVRVTPTKTEVIIRATRTQDVLG
ENGRRINELTLLVQKRFKYAPGTIVLYAERVQDRGLSAVAQAESMKFKLLNGLAIRRAAY
GVVRYVMESGAKGCEVVVSGKLRAARAKAMKFADGFLIHSGQPVNDFIDTATRHVLMRQG
VLGIKVKIMRDPAKSRTGPKALPDAVTIIEPKEEEPILAPSVKDYRPAEETEAQAEPVEA

Sequence of entity 6 (F, s4), FASTA

>8P85_6 40S ribosomal protein S4-A (chains F, s4)
MARGPKKHLKRLAAPHHWLLDKLSGCYAPRPSAGPHKLRESLPLIVFLRNRLKYALNGRE
VKAILMQRHVKVDGKVRTDTTYPAGFMDVITLDATNENFRLVYDVKGRFAVHRITDEEAS
YKLGKVKKVQLGKKGVPYVVTHDGRTIRYPDPNIKVNDTVKIDLASGKITDFIKFDAGKL
VYVTGGRNLGRIGTIVHKERHDGGFDLVHIKDSLDNTFVTRLNNVFVIGEQGKPYISLPK
GKGIKLSIAEERDRRRAQQGL

Sequence of entity 7 (G, s5), FASTA

>8P85_7 40S ribosomal protein S5 (chains G, s5)
MSDTEAPVEVQEDFEVVEEFTPVVLATPIPEEVQQAQTEIKLFNKWSFEEVEVKDASLVD
YVQVRQPIFVAHTAGRYANKRFRKAQCPIIERLTNSLMMNGRNNGKKLKAVRIIKHTLDI
INVLTDQNPIQVVVDAITNTGPREDTTRVGGGGAARRQAVDVSPLRRVNQAIALLTIGAR
EAAFRNIKTIAETLAEELINAAKGSSTSYAIKKKDELERVAKSNR

Sequence of entity 8 (H, s6), FASTA

>8P85_8 40S ribosomal protein S6-A (chains H, s6)
MKLNISYPVNGSQKTFEIDDEHRIRVFFDKRIGQEVDGEAVGDEFKGYVFKISGGNDKQG
FPMKQGVLLPTRIKLLLTKNVSCYRPRRDGERKRKSVRGAIVGPDLAVLALVIVKKGEQE
LEGLTDTTVPKRLGPKRANNIRKFFGLSKEDDVRDFVIRREVTKGEKTYTKAPKIQRLVT
PQRLQRKRHQRALKVRNAQAQREAAAEYAQLLAKRLSERKAEKAEIRKRRASSLKA

Sequence of entity 9 (I, s7), FASTA

>8P85_9 40S ribosomal protein S7-A (chains I, s7)
MSAPQAKILSQAPTELELQVAQAFVELENSSPELKAELRPLQFKSIREIDVAGGKKALAI
FVPVPSLAGFHKVQTKLTRELEKKFQDRHVIFLAERRILPKPSRTSRQVQKRPRSRTLTA
VHDKILEDLVFPTEIVGKRVRYLVGGNKIQKVLLDSKDVQQIDYKLESFQAVYNKLTGKQ
IVFEIPSETH

Sequence of entity 10 (J, s8), FASTA

>8P85_10 40S ribosomal protein S8-A (chains J, s8)
MGISRDSRHKRSATGAKRAQFRKKRKFELGRQPANTKIGAKRIHSVRTRGGNKKYRALRI
ETGNFSWASEGISKKTRIAGVVYHPSNNELVRTNTLTKAAIVQIDATPFRQWFEAHYGQT
LGKKKNVKEEETVAKSKNAERKWAARAASAKIESSVESQFSAGRLYACISSRPGQSGRCD
GYILEGEELAFYLRRLTAKK

Sequence of entity 11 (K, s9), FASTA

>8P85_11 40S ribosomal protein S9-A (chains K, s9)
MPRAPRTYSKTYSTPKRPYESSRLDAELKLAGEFGLKNKKEIYRISFQLSKIRRAARDLL
TRDEKDPKRLFEGNALIRRLVRVGVLSEDKKKLDYVLALKVEDFLERRLQTQVYKLGLAK
SVHHARVLITQRHIAVGKQIVNIPSFMVRLDSEKHIDFAPTSPFGGARPGRVARRNAARK
AEASGEAADEADEADEE

Sequence of entity 12 (L, c0), FASTA

>8P85_12 Small ribosomal subunit protein eS10A,Small ribosomal subunit protein eS10A,40S ribosomal protein S10-A (chains L, c0)
MLMPKEDRNKIHQYLFQEGVVVAKKDFNQAKHEEIDTKNLYVIKALQSLTSKGYVKTQFS
WQYYYYTLTEEGVEYLREYLNLPEHIVPGTYIQERNPTQRPQRRY

Ligands and cofactors

ID	Name	Formula	Copies
OHX	osmium (III) hexammine	H12 N6 Os	1003
MG	Magnesium ion	Mg	1502
SPD	Spermidine	C7 H19 N3	2
VDU	fluorolissoclimide	C20 H30 F N O4	2
ZN	Zinc ion	Zn	17
5XU	(2~{S})-2-azanylpropanal	C3 H7 N O	5

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

Primary citation

Role of Protein eL42 in the Ribosome Binding of Synthetic Analogues of Natural Lissoclimides. Terrosu, S., Yusupov, M. To be published.

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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