8Z70: State 1 (S1) of yeast 80S ribosome

Name: PDB 8Z70: State 1 (S1) of yeast 80S ribosome bound to 2 tRNAs during mRNA decoding
Published: 2024-12-11
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

State 1 (S1) of yeast 80S ribosome bound to 2 tRNAs during mRNA decoding. Determined by electron microscopy at 3.2 Å resolution. Released 11 Dec 2024.

Method: Electron microscopy
Resolution: 3.2 Å
Organisms: Saccharomyces cerevisiae S288C, Oryctolagus cuniculus
Chains: 81
Atoms: 206,049
Mol. weight: 3126.04 kDa
Released: 11 Dec 2024

Explore 8Z70 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Z70 contains 500 α-helices and 572 β-strands across 75 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 a: 7 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	12-20	9
α-helix	24-30	7
β-strand	32-34	3	83
β-strand	35	1	84
α-helix	36	1
α-helix	37-43	7
β-strand	47-49	3	83
β-strand	55-58	4	84
β-strand	67-69	3	84
β-strand	70-72	3	85
β-strand	80	1	86
β-strand	81-82	2	85
β-strand	86	1	87
β-strand	96	1	87
α-helix	97-98	2
β-strand	99	1	86
α-helix	101-103	3
β-strand	104-108	5	84
α-helix	113-122	10

Chain b: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	89
β-strand	22-28	7	89
β-strand	40-48	9	89
α-helix	49-52	4
α-helix	60-65	6
β-strand	69-76	8	89
α-helix	77-79	3
β-strand	80-86	7	89
α-helix	92-95	4
α-helix	104-123	20

Chain c: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	7-11	5
α-helix	42-47	6
β-strand	72-74	3	91
α-helix	76-78	3
α-helix	84-92	9
β-strand	99-100	2	188
β-strand	101-103	3	92
α-helix	104-107	4
β-strand	111-113	3	91
β-strand	124-127	4	92
β-strand	129-130	2	91
α-helix	132-141	10
β-strand	144-147	4	92

Chain d: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	12-18	7
β-strand	22	1	63
α-helix	23-26	4
α-helix	37-57	21

Chain D: 7 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
α-helix	29-31	3
α-helix	34-38	5
β-strand	40-49	10	106
β-strand	58-64	7	106
β-strand	71-77	7	106
β-strand	79	1	107
β-strand	83	1	17
β-strand	87-91	5	106
β-strand	103	1	108
α-helix	104-106	3
β-strand	112-114	3	109
β-strand	116	1	110
β-strand	126	1	110
β-strand	134-140	7	109
β-strand	145-149	5	109
β-strand	155-159	5	109
β-strand	163	1	108
β-strand	165-166	2	109
β-strand	169	1	107
α-helix	182-190	9
α-helix	201-203	3
β-strand	224-225	2	111
α-helix	229-230	2
β-strand	237-238	2	111

Chain e: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	10-20	11
β-strand	23-25	3	97
α-helix	28-36	9
β-strand	41-45	5	97
α-helix	50-63	14
β-strand	66-70	5	97
α-helix	74-81	8
β-strand	89-92	4	97

Chain E: 17 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	9-10	2
α-helix	27-28	2
α-helix	33-35	3
α-helix	40-41	2
β-strand	42-43	2	116
β-strand	45-60	16	117
β-strand	70-80	11	117
α-helix	82-83	2
β-strand	84-95	12	118
β-strand	98-106	9	118
α-helix	112-115	4
α-helix	116-118	3
α-helix	131-134	4
α-helix	135-137	3
α-helix	142-153	12
β-strand	157-163	7	118
β-strand	178-182	5	118
β-strand	183-184	2	116
α-helix	188-197	10
β-strand	202-203	2	118
α-helix	205-207	3
β-strand	214-220	7	117
α-helix	221-223	3
β-strand	226-227	2	119
α-helix	229-232	4
α-helix	235-239	5
β-strand	268-269	2	119
β-strand	274-285	12	117
α-helix	307	1
β-strand	311	1	120
β-strand	315	1	120
β-strand	321-326	6	117
β-strand	335-340	6	117
β-strand	356-359	4	117
α-helix	373-380	8

Chain f: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	9-15	7	112
α-helix	16-19	4
α-helix	25-27	3
α-helix	28-44	17
β-strand	49-51	3	112
α-helix	53-59	7
β-strand	70-79	10	112
β-strand	89-95	7	112
β-strand	107-108	2	112
α-helix	109-110	2

67 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 rRNA	2	RNA	1799	Saccharomyces cerevisiae S288C
Small ribosomal subunit protein uS3	SA	protein	222	Saccharomyces cerevisiae S288C	P05750 (AlphaFold model)
Small ribosomal subunit protein uS7	SB	protein	206	Saccharomyces cerevisiae S288C	P26783 (AlphaFold model)
Small ribosomal subunit protein eS10A	SC	protein	92	Saccharomyces cerevisiae S288C	Q08745 (AlphaFold model)
Small ribosomal subunit protein eS12	SD	protein	121	Saccharomyces cerevisiae S288C	P48589 (AlphaFold model)
Small ribosomal subunit protein uS19	SE	protein	117	Saccharomyces cerevisiae S288C	Q01855
Small ribosomal subunit protein uS9A	SF	protein	141	Saccharomyces cerevisiae S288C	P0CX51
Small ribosomal subunit protein eS17A	SG	protein	121	Saccharomyces cerevisiae S288C	P02407
Small ribosomal subunit protein uS13A	SH	protein	145	Saccharomyces cerevisiae S288C	P0CX55
Small ribosomal subunit protein eS19A	SI	protein	143	Saccharomyces cerevisiae S288C	P07280
Small ribosomal subunit protein uS10	SJ	protein	100	Saccharomyces cerevisiae S288C	P38701
Small ribosomal subunit protein eS25A	SK	protein	108	Saccharomyces cerevisiae S288C	Q3E792

69 more molecules are not listed.

Sequence of entity 1 (2), FASTA

>8Z70_1 18S rRNA (chains 2)
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
UUUAGAGGAACUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUU

Sequence of entity 2 (SA), FASTA

>8Z70_2 Small ribosomal subunit protein uS3 (chains SA)
LISKKRKLVADGVFYAELNEFFTRELAEEGYSGVEVRVTPTKTEVIIRATRTQDVLGENG
RRINELTLLVQKRFKYAPGTIVLYAERVQDRGLSAVAQAESMKFKLLNGLAIRRAAYGVV
RYVMESGAKGCEVVVSGKLRAARAKAMKFADGFLIHSGQPVNDFIDTATRHVLMRQGVLG
IKVKIMRDPAKSRTGPKALPDAVTIIEPKEEEPILAPSVKDY

Sequence of entity 3 (SB), FASTA

>8Z70_3 Small ribosomal subunit protein uS7 (chains SB)
FTPVVLATPIPEEVQQAQTEIKLFNKWSFEEVEVKDASLVDYVQVRQPIFVAHTAGRYAN
KRFRKAQCPIIERLTNSLMMNGRNNGKKLKAVRIIKHTLDIINVLTDQNPIQVVVDAITN
TGPREDTTRVGGGGAARRQAVDVSPLRRVNQAIALLTIGAREAAFRNIKTIAETLAEELI
NAAKGSSTSYAIKKKDELERVAKSNR

Sequence of entity 4 (SC), FASTA

>8Z70_4 Small ribosomal subunit protein eS10A (chains SC)
MLMPKEDRNKIHQYLFQEGVVVAKKDFNQAKHEEIDTKNLYVIKALQSLTSKGYVKTQFS
WQYYYYTLTEEGVEYLREYLNLPEHIVPGTYI

Sequence of entity 5 (SD), FASTA

>8Z70_5 Small ribosomal subunit protein eS12 (chains SD)
TIEDALKVVLRTALVHDGLARGLRESTKALTRGEALLVVLVSSVTEANIIKLVEGLANDP
ENKVPLIKVADAKQLGEWAGLGKIDREGNARKVVGASVVVVKNWGAETDELSMIMEHFSQ
Q

Sequence of entity 6 (SE), FASTA

>8Z70_6 Small ribosomal subunit protein uS19 (chains SE)
KTHSYRGVDLEKLLEMSTEDFVKLAPARVRRRFARGMTSKPAGFMKKLRAAKLAAPENEK
PAPVRTHMRNMIIVPEMIGSVVGIYNGKAFNQVEIRPEMLGHYLGEFSITYTPVRHG

Sequence of entity 7 (SF), FASTA

>8Z70_7 Small ribosomal subunit protein uS9A (chains SF)
AVPSVQTFGKKKSATAVAHVKAGKGLIKVNGSPITLVEPEILRFKVYEPLLLVGLDKFSN
IDIRVRVTGGGHVSQVYAIRQAIAKGLVAYHQKYVDEQSKNELKKAFTSYDRTLLIADSR
RPEPKKFGGKGARSRFQKSYR

Sequence of entity 8 (SG), FASTA

>8Z70_8 Small ribosomal subunit protein eS17A (chains SG)
GRVRTKTVKRASKALIERYYPKLTLDFQTNKRLCDEIATIQSKRLRNKIAGYTTHLMKRI
QKGPVRGISFKLQEEERERKDQYVPEVSALDLSRSNGVLNVDNQTSDLVKSLGLKLPLSV
I

Sequence of entity 9 (SH), FASTA

>8Z70_9 Small ribosomal subunit protein uS13A (chains SH)
SLVVQEQGSFQHILRLLNTNVDGNIKIVYALTTIKGVGRRYSNLVCKKADVDLHKRAGEL
TQEELERIVQIMQNPTHYKIPAWFLNRQNDITDGKDYHTLANNVESKLRDDLERLKKIRA
HRGIRHFWGLRVRGQHTKTTGRRRA

Sequence of entity 10 (SI), FASTA

>8Z70_10 Small ribosomal subunit protein eS19A (chains SI)
PGVSVRDVAAQDFINAYASFLQRQGKLEVPGYVDIVKTSSGNEMPPQDAEGWFYKRAASV
ARHIYMRKQVGVGKLNKLYGGAKSRGVRPYKHIDASGSINRKVLQALEKIGIVEISPKGG
RRISENGQRDLDRIAAQTLEEDE

Sequence of entity 11 (SJ), FASTA

>8Z70_11 Small ribosomal subunit protein uS10 (chains SJ)
IKIRITLTSTKVKQLENVSSNIVKNAEQHNLVKKGPVRLPTKVLKISTRKTPNGEGSKTW
ETYEMRIHKRYIDLEAPVQIVKRITQITIEPGVDVEVVVA

Sequence of entity 12 (SK), FASTA

>8Z70_12 Small ribosomal subunit protein eS25A (chains SK)
MPPKQQLSKAAKAAAALAGGKKSKKKWSKKSMKDRAQHAVILDQEKYDRILKEVPTYRYV
SVSVLVDRLKIGGSLARIALRHLEKEGIIKPISKHSKQAIYTRATASE

Primary citation

Capturing eukaryotic ribosome dynamics in situ at high resolution. Cheng, J., Wu, C., Li, J. et al. Nat Struct Mol Biol (2025) 32:698-708. DOI 10.1038/s41594-024-01454-9 · PubMed

Other PDB entries of the same protein (UniProt P05750 (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…
8T2Y 2.2 Å, Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA,…
8ZHC 2.3 Å, pre-frameshift complex of yeast 80S ribosome with eRF1 and mRNA of WNV
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
8T2Z 2.4 Å, Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA,…
8T2X 2.46 Å, Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, A-site tRNA, messenger…
9DOV 2.49 Å, Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome…
7ZUX 2.5 Å, Collided ribosome in a disome unit from S. cerevisiae

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