8UT0: 40S ribosomal protein S0-A

Name: PDB 8UT0: Eukaryotic 80S ribosome with Reh1, eIF5A and A/P site tRNA
Published: 2024-11-06
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Eukaryotic 80S ribosome with Reh1, eIF5A and A/P site tRNA. Determined by electron microscopy at 3.22 Å resolution. Released 6 Nov 2024.

Method: Electron microscopy
Resolution: 3.22 Å
Organism: Saccharomyces cerevisiae
Chains: 84
Atoms: 205,193
Mol. weight: 3172.44 kDa
Ligands: 3HE
Released: 6 Nov 2024

Explore 8UT0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8UT0 contains 546 α-helices and 541 β-strands across 77 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 AA: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	10-11	2
α-helix	12-15	4
α-helix	19-21	3
α-helix	44-53	10
β-strand	60	1	61
α-helix	62-69	8
α-helix	74-85	12
β-strand	90-93	4	61
β-strand	100-102	3	61

Chain E: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	5-14	10
β-strand	28-31	4	49
β-strand	59-61	3	50
α-helix	65-68	4
α-helix	71-74	4
β-strand	77-78	2	50
α-helix	83-85	3
α-helix	91-97	7
β-strand	103-104	2	50
α-helix	108-111	4
α-helix	112-114	3
α-helix	119-122	4
α-helix	140-147	8
β-strand	158-160	3	49
α-helix	170-176	7
β-strand	195-197	3	49
β-strand	200	1	51
β-strand	208	1	51

Chain La: 6 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	12-20	9
α-helix	24-30	7
β-strand	32-34	3	67
β-strand	35	1	68
α-helix	36	1
α-helix	37-43	7
β-strand	47-49	3	67
β-strand	55-58	4	68
β-strand	67-69	3	68
β-strand	70-72	3	69
β-strand	80	1	70
β-strand	81-82	2	69
β-strand	86-88	3	71
β-strand	94-96	3	71
β-strand	99	1	70
α-helix	101-103	3
β-strand	104-108	5	68
α-helix	113-122	10

Chain Lb: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	75
β-strand	22-29	8	75
β-strand	40-48	9	75
α-helix	49-52	4
α-helix	59-65	7
β-strand	69-76	8	75
β-strand	80-86	7	75
α-helix	98-102	5
α-helix	104-121	18
α-helix	128-131	4

Chain Lc: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	8-11	4
α-helix	42-48	7
α-helix	66-68	3
β-strand	72-73	2	81
α-helix	75-80	6
α-helix	84-92	9
β-strand	99-100	2	148
β-strand	101-103	3	82
α-helix	104-107	4
β-strand	111-112	2	81
β-strand	124-127	4	82
β-strand	129-130	2	81
α-helix	132-141	10
β-strand	144-147	4	82

Chain Ld: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	12-18	7
α-helix	23-26	4
α-helix	37-57	21

Chain LD: 10 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
α-helix	14-16	3
α-helix	34-38	5
β-strand	40-49	10	84
β-strand	58-64	7	84
β-strand	71-77	7	84
α-helix	78	1
β-strand	83	1	85
β-strand	87-91	5	84
β-strand	101-103	3	84
α-helix	104-106	3
β-strand	112-114	3	84
β-strand	116	1	86
β-strand	120	1	87
β-strand	122	1	87
β-strand	126	1	86
β-strand	134-140	7	84
β-strand	145-149	5	84
β-strand	155-159	5	84
β-strand	163-166	4	84
α-helix	174-176	3
α-helix	178-179	2
α-helix	182-189	8
α-helix	201-203	3
β-strand	224-225	2	88
α-helix	230	1
β-strand	237-238	2	88

Chain Le: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	11-19	9
β-strand	22-25	4	95
α-helix	27-35	9
β-strand	41-45	5	95
α-helix	50-63	14
β-strand	66-70	5	95
α-helix	74-81	8
β-strand	89-94	6	95

69 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	1800	Saccharomyces cerevisiae
40S ribosomal protein S0-A	SP	protein	206	Saccharomyces cerevisiae	P32905 (AlphaFold model)
40S ribosomal protein S1-A	SQ	protein	232	Saccharomyces cerevisiae	P33442 (AlphaFold model)
40S ribosomal protein S15	SE	protein	117	Saccharomyces cerevisiae	Q01855 (AlphaFold model)
40S ribosomal protein S2	SR	protein	216	Saccharomyces cerevisiae	P25443 (AlphaFold model)
40S ribosomal protein S3	SA	protein	222	Saccharomyces cerevisiae	P05750
40S ribosomal protein S4-A	SS	protein	258	Saccharomyces cerevisiae	P0CX35
40S ribosomal protein S5	SB	protein	206	Saccharomyces cerevisiae	P26783
40S ribosomal protein S6-A	ST	protein	228	Saccharomyces cerevisiae	P0CX37
40S ribosomal protein S7-A	SU	protein	184	Saccharomyces cerevisiae	P26786
40S ribosomal protein S8-A	SV	protein	187	Saccharomyces cerevisiae	P0CX39
40S ribosomal protein S9-A	SW	protein	184	Saccharomyces cerevisiae	O13516

72 more molecules are not listed.

Sequence of entity 1 (2), FASTA

>8UT0_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
UUUAGAGGAACUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA

Sequence of entity 2 (SP), FASTA

>8UT0_2 40S ribosomal protein S0-A (chains SP)
SLPATFDLTPEDAQLLLAANTHLGARNVQVHQEPYVFNARPDGVHVINVGKTWEKLVLAA
RIIAAIPNPEDVVAISSRTFGQRAVLKFAAHTGATPIAGRFTPGSFTNYITRSFKEPRLV
IVTDPRSDAQAIKEASYVNIPVIALTDLDSPSEFVDVAIPCNNRGKHSIGLIWYLLAREV
LRLRGALVDRTQPWSIMPDLYFYRDP

Sequence of entity 3 (SQ), FASTA

>8UT0_3 40S ribosomal protein S1-A (chains SQ)
AVGKNKRLSKGKKGQKKRVVDPFTRKEWFDIKAPSTFENRNVGKTLVNKSTGLKSASDAL
KGRVVEVCLADLQGSEDHSFRKIKLRVDEVQGKNLLTNFHGMDFTTDKLRSMVRKWQTLI
EANVTVKTSDDYVLRIFAIAFTRKQANQVKRHSYAQSSHIRAIRKVISEILTKEVQGSTL
AQLTSKLIPEVINKEIENATKDIFPLQNIHVRKVKLLKQPKFDVGALMALHG

Sequence of entity 4 (SE), FASTA

>8UT0_4 40S ribosomal protein S15 (chains SE)
KTHSYRGVDLEKLLEMSTEDFVKLAPARVRRRFARGMTSKPAGFMKKLRAAKLAAPENEK
PAPVRTHMRNMIIVPEMIGSVVGIYNGKAFNQVEIRPEMLGHYLGEFSITYTPVRHG

Sequence of entity 5 (SR), FASTA

>8UT0_5 40S ribosomal protein S2 (chains SR)
GWVPVTKLGRLVKAGKITTIEEIFLHSLPVKEFQIIDTLLPGLQDEVMNIKPVQKQTRAG
QRTRFKAVVVVGDSNGHVGLGIKTAKEVAGAIRAGIIIAKLSVIPIRRGYWGTNLGQPHS
LATKTTGKCGSVTVRLIPAPRGSGIVASPAVKKLLQLAGVEDVYTQSNGKTRTLENTLKA
AFVAIGNTYGFLTPNLWAEQPLPVSPLDIYSDEASA

Sequence of entity 6 (SA), FASTA

>8UT0_6 40S ribosomal protein S3 (chains SA)
LISKKRKLVADGVFYAELNEFFTRELAEEGYSGVEVRVTPTKTEVIIRATRTQDVLGENG
RRINELTLLVQKRFKYAPGTIVLYAERVQDRGLSAVAQAESMKFKLLNGLAIRRAAYGVV
RYVMESGAKGCEVVVSGKLRAARAKAMKFADGFLIHSGQPVNDFIDTATRHVLMRQGVLG
IKVKIMRDPAKSRTGPKALPDAVTIIEPKEEEPILAPSVKDY

Sequence of entity 7 (SS), FASTA

>8UT0_7 40S ribosomal protein S4-A (chains SS)
ARGPKKHLKRLAAPHHWLLDKLSGCYAPRPSAGPHKLRESLPLIVFLRNRLKYALNGREV
KAILMQRHVKVDGKVRTDTTYPAGFMDVITLDATNENFRLVYDVKGRFAVHRITDEEASY
KLGKVKKVQLGKKGVPYVVTHDGRTIRYPDPNIKVNDTVKIDLASGKITDFIKFDAGKLV
YVTGGRNLGRIGTIVHKERHDGGFDLVHIKDSLDNTFVTRLNNVFVIGEQGKPYISLPKG
KGIKLSIAEERDRRRAQQ

Sequence of entity 8 (SB), FASTA

>8UT0_8 40S ribosomal protein S5 (chains SB)
FTPVVLATPIPEEVQQAQTEIKLFNKWSFEEVEVKDASLVDYVQVRQPIFVAHTAGRYAN
KRFRKAQCPIIERLTNSLMMNGRNNGKKLKAVRIIKHTLDIINVLTDQNPIQVVVDAITN
TGPREDTTRVGGGGAARRQAVDVSPLRRVNQAIALLTIGAREAAFRNIKTIAETLAEELI
NAAKGSSTSYAIKKKDELERVAKSNR

Sequence of entity 9 (ST), FASTA

>8UT0_9 40S ribosomal protein S6-A (chains ST)
MKLNISYPVNGSQKTFEIDDEHRIRVFFDKRIGQEVDGEAVGDEFKGYVFKISGGNDKQG
FPMKQGVLLPTRIKLLLTKNVSCYRPRRDGERKRKSVRGAIVGPDLAVLALVIVKKGEQE
LEGLTDTTVPKRLGPKRANNIRKFFGLSKEDDVRDFVIRREVTKGEKTYTKAPKIQRLVT
PQRLQRKRHQRALKVRNAQAQREAAAEYAQLLAKRLSERKAEKAEIRK

Sequence of entity 10 (SU), FASTA

>8UT0_10 40S ribosomal protein S7-A (chains SU)
PQAKILSQAPTELELQVAQAFVELENSSPELKAELRPLQFKSIREIDVAGGKKALAIFVP
VPSLAGFHKVQTKLTRELEKKFQDRHVIFLAERRILPKPSRTSRQVQKRPRSRTLTAVHD
KILEDLVFPTEIVGKRVRYLVGGNKIQKVLLDSKDVQQIDYKLESFQAVYNKLTGKQIVF
EIPS

Sequence of entity 11 (SV), FASTA

>8UT0_11 40S ribosomal protein S8-A (chains SV)
GISRDSRHKRSATGAKRAQFRKKRKFELGRQPANTKIGAKRIHSVRTRGGNKKYRALRIE
TGNFSWASEGISKKTRIAGVVYHPSNNELVRTNTLTKAAIVQIDATPFRQWFEAHYGQTL
GKKSKNAERKWAARAASAKIESSVESQFSAGRLYACISSRPGQSGRCDGYILEGEELAFY
LRRLTAK

Sequence of entity 12 (SW), FASTA

>8UT0_12 40S ribosomal protein S9-A (chains SW)
PRAPRTYSKTYSTPKRPYESSRLDAELKLAGEFGLKNKKEIYRISFQLSKIRRAARDLLT
RDEKDPKRLFEGNALIRRLVRVGVLSEDKKKLDYVLALKVEDFLERRLQTQVYKLGLAKS
VHHARVLITQRHIAVGKQIVNIPSFMVRLDSEKHIDFAPTSPFGGARPGRVARRNAARKA
EASG

Ligands and cofactors

ID	Name	Formula	Copies
3HE	4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2…	C15 H23 N O4	1

Primary citation

The assembly factor Reh1 is released from the ribosome during its initial round of translation. Musalgaonkar, S., Yelland, J.N., Chitale, R. et al. Nat Commun (2025) 16:1278-1278. DOI 10.1038/s41467-025-55844-8 · 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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