8PNN: 80S yeast ribosome

Name: PDB 8PNN: 80S yeast ribosome in complex with Bromolissoclimide
Published: 2025-05-28
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

80S yeast ribosome in complex with Bromolissoclimide. Determined by X-ray diffraction at 2.9 Å resolution. Released 28 May 2025.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Saccharomyces cerevisiae
Chains: 156
Atoms: 402,407
Mol. weight: 6564.04 kDa
Ligands: OHX, MG, ZN, ZWB
Released: 28 May 2025

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

Secondary structure: helices and β-sheets

8PNN contains 1,002 α-helices and 1,048 β-strands across 148 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: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	5-13	9	74
β-strand	25-31	7	74
α-helix	34-45	12
α-helix	53-55	3
β-strand	56-64	9	74
β-strand	73-82	10	75
β-strand	87-96	10	75
α-helix	99-114	16
α-helix	118-120	3
β-strand	121-128	8	75
α-helix	138-141	4
α-helix	142-144	3
β-strand	150-151	2	7
α-helix	157-159	3
β-strand	164	1	93

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	98
α-helix	52-54	3
α-helix	55-57	3
β-strand	61-67	7	98
β-strand	71-80	10	98
β-strand	83-92	10	98
α-helix	93-95	3
β-strand	96-98	3	98
α-helix	103-117	15
α-helix	132-136	5
β-strand	139-142	4	207
β-strand	149-150	2	74

Chain 5: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	213
α-helix	20-24	5
α-helix	30-40	11
β-strand	42-43	2	214
β-strand	46-47	2	214
β-strand	54-58	5	213
β-strand	62-67	6	213
α-helix	73-86	14
β-strand	94-99	6	213
β-strand	102-106	5	213

Chain 6: 3 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	17-18	2	300
β-strand	22-25	4	301
β-strand	27	1	302
β-strand	31	1	303
β-strand	33-36	4	301
α-helix	48-50	3
β-strand	51-52	2	300
β-strand	57-61	5	301
β-strand	62	1	304
β-strand	65	1	303
β-strand	70	1	304
β-strand	73-80	8	301
β-strand	85-86	2	51
β-strand	92-94	3	51
β-strand	99-102	4	301
β-strand	103	1	305
β-strand	109	1	305
β-strand	114	1	302
β-strand	118	1	306
α-helix	120-123	4
α-helix	127-132	6
β-strand	136	1	306

Chain 7: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	50
β-strand	12-13	2	50
β-strand	19-22	4	51
β-strand	28-31	4	51
α-helix	34-41	8
α-helix	46-48	3
α-helix	53-57	5

Chain 8: 7 helices, 4 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	130
α-helix	70-79	10
β-strand	81-86	6	130
α-helix	92-102	11
β-strand	107-115	9	130
β-strand	119-126	8	130
α-helix	127	1
α-helix	132-139	8

Chain 9: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	12-20	9
α-helix	24-30	7
β-strand	32-34	3	197
β-strand	35	1	198
α-helix	36	1
α-helix	37-43	7
β-strand	47-49	3	197
β-strand	55-58	4	198
β-strand	67-74	8	198
α-helix	75-77	3
β-strand	79-88	10	198
β-strand	94-99	6	198
α-helix	101-103	3
β-strand	104-108	5	198
α-helix	113-121	9

Chain a: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	46-53	8
α-helix	73-77	5
α-helix	80-83	4

139 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
5S ribosomal RNA	3, AS	RNA	121	Saccharomyces cerevisiae
60S ribosomal protein L28	AB, DC	protein	149	Saccharomyces cerevisiae	P02406 (AlphaFold model)
60S ribosomal protein L8-A	CJ, p	protein	256	Saccharomyces cerevisiae	P17076 (AlphaFold model)
60S ribosomal protein L35-A	AI, DJ	protein	120	Saccharomyces cerevisiae	P0CX84 (AlphaFold model)
40S ribosomal protein S15	Q, c5	protein	142	Saccharomyces cerevisiae	Q01855 (AlphaFold model)
40S ribosomal protein S6-A	H, s6	protein	236	Saccharomyces cerevisiae	P0CX37
5.8S ribosomal RNA	4, AT	RNA	158	Saccharomyces cerevisiae
60S ribosomal protein L29	AC, DD	protein	59	Saccharomyces cerevisiae	P05747
60S ribosomal protein L9-A	CK, q	protein	191	Saccharomyces cerevisiae	P05738
60S ribosomal protein L36-A	AJ, DK	protein	100	Saccharomyces cerevisiae	P05745
40S ribosomal protein S16-A	R, c6	protein	143	Saccharomyces cerevisiae	P0CX51
40S ribosomal protein S7-A	I, s7	protein	190	Saccharomyces cerevisiae	P26786

67 more molecules are not listed.

Sequence of entity 1 (3, AS), FASTA

>8PNN_1 5S ribosomal RNA (chains 3, AS)
GGUUGCGGCCAUAUCUACCAGAAAGCACCGUUUCCCGUCCGAUCAACUGUAGUUAAGCUG
GUAAGAGCCUGACCGAGUAGUGUAGUGGGUGACCAUACGCGAAACUCAGGUGCUGCAAUC
U

Sequence of entity 2 (AB, DC), FASTA

>8PNN_2 60S ribosomal protein L28 (chains AB, DC)
MPSRFTKTRKHRGHVSAGKGRIGKHRKHPGGRGMAGGQHHHRINMDKYHPGYFGKVGMRY
FHKQQAHFWKPVLNLDKLWTLIPEDKRDQYLKSASKETAPVIDTLAAGYGKILGKGRIPN
VPVIVKARFVSKLAEEKIRAAGGVVELIA

Sequence of entity 3 (CJ, p), FASTA

>8PNN_3 60S ribosomal protein L8-A (chains CJ, p)
MAPGKKVAPAPFGAKSTKSNKTRNPLTHSTPKNFGIGQAVQPKRNLSRYVKWPEYVRVQR
QKKILSIRLKVPPTIAQFQYTLDRNTAAETFKLFNKYRPETAAEKKERLTKEAAAVAEGK
SKQDASPKPYAVKYGLNHVVALIENKKAKLVLIANDVDPIELVVFLPALCKKMGVPYAIV
KGKARLGTLVNQKTSAVAALTEVRAEDEAALAKLVSTIDANFADKYDEVKKHWGGGILGN
KAQAKMDKRAKNSDSA

Sequence of entity 4 (AI, DJ), FASTA

>8PNN_4 60S ribosomal protein L35-A (chains AI, DJ)
MAGVKAYELRTKSKEQLASQLVDLKKELAELKVQKLSRPSLPKIKTVRKSIACVLTVINE
QQREAVRQLYKGKKYQPKDLRAKKTRALRRALTKFEASQVTEKQRKKQIAFPQRKYAIKA

Sequence of entity 5 (Q, c5), FASTA

>8PNN_5 40S ribosomal protein S15 (chains Q, c5)
MSQAVNAKKRVFKTHSYRGVDLEKLLEMSTEDFVKLAPARVRRRFARGMTSKPAGFMKKL
RAAKLAAPENEKPAPVRTHMRNMIIVPEMIGSVVGIYNGKAFNQVEIRPEMLGHYLGEFS
ITYTPVRHGRAGATTSRFIPLK

Sequence of entity 6 (H, s6), FASTA

>8PNN_6 40S ribosomal protein S6-A (chains H, s6)
MKLNISYPVNGSQKTFEIDDEHRIRVFFDKRIGQEVDGEAVGDEFKGYVFKISGGNDKQG
FPMKQGVLLPTRIKLLLTKNVSCYRPRRDGERKRKSVRGAIVGPDLAVLALVIVKKGEQE
LEGLTDTTVPKRLGPKRANNIRKFFGLSKEDDVRDFVIRREVTKGEKTYTKAPKIQRLVT
PQRLQRKRHQRALKVRNAQAQREAAAEYAQLLAKRLSERKAEKAEIRKRRASSLKA

Sequence of entity 7 (4, AT), FASTA

>8PNN_7 5.8S ribosomal RNA (chains 4, AT)
AAACUUUCAACAACGGAUCUCUUGGUUCUCGCAUCGAUGAAGAACGCAGCGAAAUGCGAU
ACGUAAUGUGAAUUGCAGAAUUCCGUGAAUCAUCGAAUCUUUGAACGCACAUUGCGCCCC
UUGGUAUUCCAGGGGGCAUGCCUGUUUGAGCGUCAUUU

Sequence of entity 8 (AC, DD), FASTA

>8PNN_8 60S ribosomal protein L29 (chains AC, DD)
MAKSKNHTAHNQTRKAHRNGIKKPKTYKYPSLKGVDPKFRRNHKHALHGTAKALAAAKK

Sequence of entity 9 (CK, q), FASTA

>8PNN_9 60S ribosomal protein L9-A (chains CK, q)
MKYIQTEQQIEVPEGVTVSIKSRIVKVVGPRGTLTKNLKHIDVTFTKVNNQLIKVAVHNG
GRKHVAALRTVKSLVDNMITGVTKGYKYKMRYVYAHFPINVNIVEKDGAKFIEVRNFLGD
KKIRNVPVRDGVTIEFSTNVKDEIVLSGNSVEDVSQNAADLQQICRVRNKDIRKFLDGIY
VSHKGFITEDL

Sequence of entity 10 (AJ, DK), FASTA

>8PNN_10 60S ribosomal protein L36-A (chains AJ, DK)
MTVKTGIAIGLNKGKKVTSMTPAPKISYKKGAASNRTKFVRSLVREIAGLSPYERRLIDL
IRNSGEKRARKVAKKRLGSFTRAKAKVEEMNNIIAASRRH

Sequence of entity 11 (R, c6), FASTA

>8PNN_11 40S ribosomal protein S16-A (chains R, c6)
MSAVPSVQTFGKKKSATAVAHVKAGKGLIKVNGSPITLVEPEILRFKVYEPLLLVGLDKF
SNIDIRVRVTGGGHVSQVYAIRQAIAKGLVAYHQKYVDEQSKNELKKAFTSYDRTLLIAD
SRRPEPKKFGGKGARSRFQKSYR

Sequence of entity 12 (I, s7), FASTA

>8PNN_12 40S ribosomal protein S7-A (chains I, s7)
MSAPQAKILSQAPTELELQVAQAFVELENSSPELKAELRPLQFKSIREIDVAGGKKALAI
FVPVPSLAGFHKVQTKLTRELEKKFQDRHVIFLAERRILPKPSRTSRQVQKRPRSRTLTA
VHDKILEDLVFPTEIVGKRVRYLVGGNKIQKVLLDSKDVQQIDYKLESFQAVYNKLTGKQ
IVFEIPSETH

Ligands and cofactors

ID	Name	Formula	Copies
OHX	osmium (III) hexammine	H12 N6 Os	935
MG	Magnesium ion	Mg	1490
ZN	Zinc ion	Zn	15
ZWB	(3~{R})-3-[(1~{S})-2-[(1~{R},3~{S},4~{a}~{S},7~{S},8~{a}~{S})-7-bromanyl-5,5,8~…	C20 H30 Br N O4	2
SPD	Spermidine	C7 H19 N3	4

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

Primary citation

Synthesis of Differentially Halogenated Lissoclimide Analogues To Probe Ribosome E-Site Binding. Terrosu, S., Nurullina, L., Supantanapong, N. et al. ACS Chem Biol (2025) 20:858-869. DOI 10.1021/acschembio.4c00825 · PubMed

Other PDB entries of the same protein (UniProt P02406 (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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