6TB3: Yeast 80S ribosome

yeast 80S ribosome in complex with the Not5 subunit of the CCR4-NOT complex. Determined by electron microscopy at 2.8 Å resolution. Released 22 Apr 2020.

Method: Electron microscopy
Resolution: 2.8 Å
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 83
Atoms: 205,032
Mol. weight: 3041.16 kDa
Ligands: SPD, ZN, MG
Released: 22 Apr 2020

Explore 6TB3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6TB3 contains 489 α-helices and 525 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 a: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	156
β-strand	8	1	156
α-helix	13-14	2
β-strand	15-16	2	157
β-strand	23-24	2	157
β-strand	32-39	8	158
β-strand	45-55	11	158
α-helix	57-61	5
α-helix	65-75	11

Chain A: 11 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	7-28	22
α-helix	30-32	3
β-strand	37-42	6	37
β-strand	45-52	8	37
α-helix	55-59	5
α-helix	61-63	3
α-helix	64-77	14
α-helix	79-80	2
β-strand	84-90	7	37
α-helix	94-96	3
α-helix	98-111	14
α-helix	115-128	14
β-strand	131-139	9	38
β-strand	141	1	39
β-strand	147	1	39
β-strand	150-155	6	38
α-helix	162-166	5
β-strand	168-177	10	38
β-strand	180-190	11	38
β-strand	207-208	2	40
α-helix	209-213	5
β-strand	222-223	2	41

Chain AA: 13 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	40-42	3
α-helix	47-49	3
α-helix	54-68	15
β-strand	70-71	2	134
α-helix	84-94	11
α-helix	102-118	17
α-helix	127-129	3
β-strand	133-134	2	135
α-helix	136-144	9
β-strand	150-154	5	135
α-helix	160-162	3
α-helix	165-173	9
β-strand	177-180	4	135
α-helix	183-189	7
β-strand	197-200	4	135
α-helix	208-221	14
α-helix	226-229	4
β-strand	234-235	2	134
α-helix	240-253	14

Chain AB: 3 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	11-15	5
β-strand	17	1	61
β-strand	22-25	4	62
β-strand	27	1	63
β-strand	33-39	7	62
β-strand	52	1	61
β-strand	57-64	8	62
β-strand	70	1	62
β-strand	73-80	8	62
β-strand	85-86	2	64
β-strand	92-94	3	64
β-strand	99-102	4	62
β-strand	103	1	65
β-strand	109	1	65
β-strand	114	1	63
β-strand	118	1	66
α-helix	120-123	4
α-helix	127-132	6
β-strand	136	1	66

Chain AC: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	22-25	4
α-helix	26-29	4
α-helix	32-34	3
α-helix	35-48	14
α-helix	52-63	12
α-helix	66-76	11
α-helix	80-99	20

Chain AD: 4 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	139
β-strand	6-11	6	140
β-strand	17-21	5	141
β-strand	24-28	5	141
β-strand	33-37	5	141
β-strand	44-47	4	140
β-strand	52-57	6	140
β-strand	60	1	139
α-helix	62-83	22
β-strand	86-93	8	142
α-helix	98-99	2
β-strand	100-104	5	143
β-strand	111-115	5	143
α-helix	117-119	3
β-strand	124-126	3	143
β-strand	133-136	4	142
β-strand	143-148	6	142
α-helix	151-163	13
β-strand	178-185	8	142

Chain AE: 6 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	71
β-strand	12-13	2	71
β-strand	19-22	4	64
β-strand	28-31	4	64
α-helix	34-41	8
α-helix	46-48	3
α-helix	53-58	6
α-helix	70-72	3
α-helix	87-95	9
α-helix	101-125	25

Chain AF: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	5-8	4
β-strand	16-17	2	151
β-strand	27-28	2	151
β-strand	33-34	2	151
α-helix	44-45	2
α-helix	51-57	7
α-helix	70-75	6

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
Saccharomyces cerevisiae S288C 18S ribosomal RNA (RDN18-1), rRNA	2	RNA	1798	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
mRNA	l	RNA	3	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
40S ribosomal protein S0-A	P	protein	206	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P32905 (AlphaFold model)
40S ribosomal protein S1-A	Q	protein	232	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P33442 (AlphaFold model)
40S ribosomal protein S15	E	protein	117	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Q01855 (AlphaFold model)
40S ribosomal protein S2	R	protein	216	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P25443 (AlphaFold model)
40S ribosomal protein S3	A	protein	222	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P05750
40S ribosomal protein S4-A	S	protein	258	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P0CX35
40S ribosomal protein S5	B	protein	206	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
40S ribosomal protein S6-A	T	protein	228	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P0CX37
40S ribosomal protein S7-A	U	protein	184	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P26786
40S ribosomal protein S8	V	protein	187	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	A0A0J9X221

71 more molecules are not listed.

Sequence of entity 1 (2), FASTA

>6TB3_1 Saccharomyces cerevisiae S288C 18S ribosomal RNA (RDN18-1), rRNA (chains 2)
UAUCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCU
AAGUAUAAGCAAUUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUCGUUUAU
UUGAUAGUUCCUUUACUACAUGGUAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCUUAA
AAUCUCGACCCUUUGGAAGAGAUGUAUUUAUUAGAUAAAAAAUCAAUGUCUUCGGACUCU
UUGAUGAUUCAUAAUAACUUUUCGAAUCGCAUGGCCUUGUGCUGGCGAUGGUUCAUUCAA
AUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUUUCAACGGGUAA
CGGGGAAUAAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGA
AGGCAGCAGGCGCGCAAAUUACCCAAUCCUAAUUCAGGGAGGUAGUGACAAUAAAUAACG
AUACAGGGCCCAUUCGGGUCUUGUAAUUGGAAUGAGUACAAUGUAAAUACCUUAACGAGG
AACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAU
AUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAACUUUGGGCCCGGUUGGCCGGUCCG
AUUUUUCGUGUACUGGAUUUCCAACGGGGCCUUUCCUUCUGGCUAACCUUGAGUCCUUGU
GGCUCUUGGCGAACCAGGACUUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUAU
UGCUCGAAUAUAUUAGCAUGGAAUAAUAGAAUAGGACGUUUGGUUCUAUUUUGUUGGUUU
CUAGGACCAUCGUAAUGAUUAAUAGGGACGGUCGGGGGCAUCAGUAUUCAAUUGUCAGAG
GUGAAAUUCUUGGAUUUAUUGAAGACUAACUACUGCGAAAGCAUUUGCCAAGGACGUUUU
CAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUCAGAUACCGUCGUAGUCUUAAC
CAUAAACUAUGCCGACUAGGGAUCGGGUGGUGUUUUUUUAAUGACCCACUCGGCACCUUA
CGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGG
AAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGG
AAACUCACCAGGUCCAGACACAAUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUUUG
UGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGCUUAAUUGCGAUA
ACGAACGAGACCUUAACCUACUAAAUAGUGGUGCUAGCAUUUGCUGGUUAUCCACUUCUU
AGAGGGACUAUCGGUUUCAAGCCGAUGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCC
UUAGACGUUCUGGGCCGCACGCGCGCUACACUGACGGAGCCAGCGAGUCUAACCUUGGCC
GAGAGGUCUUGGUAAUCUUGUGAAACUCCGUCGUGCUGGGGAUAGAGCAUUGUAAUUAUU
GCUCUUCAACGAGGAAUUCCUAGUAAGCGCAAGUCAUCAGCUUGCGUUGAUUACGUCCCU
GCCCUUUGUACACACCGCCCGUCGCUAGUACCGAUUGAAUGGCUUAGUGAGGCCUCAGGA
UCUGCUUAGAGAAGGGGGCAACUCCAUCUCAGAGCGGAGAAUUUGGACAAACUUGGUCAU
UUAGAGGAACUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUU

Sequence of entity 2 (l), FASTA

>6TB3_2 mRNA (chains l)
AUG

Sequence of entity 3 (P), FASTA

>6TB3_3 40S ribosomal protein S0-A (chains P)
SLPATFDLTPEDAQLLLAANTHLGARNVQVHQEPYVFNARPDGVHVINVGKTWEKLVLAA
RIIAAIPNPEDVVAISSRTFGQRAVLKFAAHTGATPIAGRFTPGSFTNYITRSFKEPRLV
IVTDPRSDAQAIKEASYVNIPVIALTDLDSPSEFVDVAIPCNNRGKHSIGLIWYLLAREV
LRLRGALVDRTQPWSIMPDLYFYRDP

Sequence of entity 4 (Q), FASTA

>6TB3_4 40S ribosomal protein S1-A (chains Q)
AVGKNKRLSKGKKGQKKRVVDPFTRKEWFDIKAPSTFENRNVGKTLVNKSTGLKSASDAL
KGRVVEVCLADLQGSEDHSFRKIKLRVDEVQGKNLLTNFHGMDFTTDKLRSMVRKWQTLI
EANVTVKTSDDYVLRIFAIAFTRKQANQVKRHSYAQSSHIRAIRKVISEILTKEVQGSTL
AQLTSKLIPEVINKEIENATKDIFPLQNIHVRKVKLLKQPKFDVGALMALHG

Sequence of entity 5 (E), FASTA

>6TB3_5 40S ribosomal protein S15 (chains E)
KTHSYRGVDLEKLLEMSTEDFVKLAPARVRRRFARGMTSKPAGFMKKLRAAKLAAPENEK
PAPVRTHMRNMIIVPEMIGSVVGIYNGKAFNQVEIRPEMLGHYLGEFSITYTPVRHG

Sequence of entity 6 (R), FASTA

>6TB3_6 40S ribosomal protein S2 (chains R)
GWVPVTKLGRLVKAGKITTIEEIFLHSLPVKEFQIIDTLLPGLQDEVMNIKPVQKQTRAG
QRTRFKAVVVVGDSNGHVGLGIKTAKEVAGAIRAGIIIAKLSVIPIRRGYWGTNLGQPHS
LATKTTGKCGSVTVRLIPAPRGSGIVASPAVKKLLQLAGVEDVYTQSNGKTRTLENTLKA
AFVAIGNTYGFLTPNLWAEQPLPVSPLDIYSDEASA

Sequence of entity 7 (A), FASTA

>6TB3_7 40S ribosomal protein S3 (chains A)
LISKKRKLVADGVFYAELNEFFTRELAEEGYSGVEVRVTPTKTEVIIRATRTQDVLGENG
RRINELTLLVQKRFKYAPGTIVLYAERVQDRGLSAVAQAESMKFKLLNGLAIRRAAYGVV
RYVMESGAKGCEVVVSGKLRAARAKAMKFADGFLIHSGQPVNDFIDTATRHVLMRQGVLG
IKVKIMRDPAKSRTGPKALPDAVTIIEPKEEEPILAPSVKDY

Sequence of entity 8 (S), FASTA

>6TB3_8 40S ribosomal protein S4-A (chains S)
ARGPKKHLKRLAAPHHWLLDKLSGCYAPRPSAGPHKLRESLPLIVFLRNRLKYALNGREV
KAILMQRHVKVDGKVRTDTTYPAGFMDVITLDATNENFRLVYDVKGRFAVHRITDEEASY
KLGKVKKVQLGKKGVPYVVTHDGRTIRYPDPNIKVNDTVKIDLASGKITDFIKFDAGKLV
YVTGGRNLGRIGTIVHKERHDGGFDLVHIKDSLDNTFVTRLNNVFVIGEQGKPYISLPKG
KGIKLSIAEERDRRRAQQ

Sequence of entity 9 (B), FASTA

>6TB3_9 40S ribosomal protein S5 (chains B)
FTPVVLATPIPEEVQQAQTEIKLFNKWSFEEVEVKDASLVDYVQVRQPIFVAHTAGRYAN
KRFRKAQCPIIERLTNSLMMNGRNNGKKLKAVRIIKHTLDIINVLTDQNPIQVVVDAITN
TGPREDTTRVGGGGAARRQAVDVSPLRRVNQAIALLTIGAREAAFRNIKTIAETLAEELI
NAAKGSSTSYAIKKKDELERVAKSNR

Sequence of entity 10 (T), FASTA

>6TB3_10 40S ribosomal protein S6-A (chains T)
MKLNISYPVNGSQKTFEIDDEHRIRVFFDKRIGQEVDGEAVGDEFKGYVFKISGGNDKQG
FPMKQGVLLPTRIKLLLTKNVSCYRPRRDGERKRKSVRGAIVGPDLAVLALVIVKKGEQE
LEGLTDTTVPKRLGPKRANNIRKFFGLSKEDDVRDFVIRREVTKGEKTYTKAPKIQRLVT
PQRLQRKRHQRALKVRNAQAQREAAAEYAQLLAKRLSERKAEKAEIRK

Sequence of entity 11 (U), FASTA

>6TB3_11 40S ribosomal protein S7-A (chains U)
PQAKILSQAPTELELQVAQAFVELENSSPELKAELRPLQFKSIREIDVAGGKKALAIFVP
VPSLAGFHKVQTKLTRELEKKFQDRHVIFLAERRILPKPSRTSRQVQKRPRSRTLTAVHD
KILEDLVFPTEIVGKRVRYLVGGNKIQKVLLDSKDVQQIDYKLESFQAVYNKLTGKQIVF
EIPS

Sequence of entity 12 (V), FASTA

>6TB3_12 40S ribosomal protein S8 (chains V)
GISRDSRHKRSATGAKRAQFRKKRKFELGRQPANTKIGAKRIHSVRTRGGNKKYRALRIE
TGNFSWASEGISKKTRIAGVVYHPSNNELVRTNTLTKAAIVQIDATPFRQWFEAHYGQTL
GKKSKNAERKWAARAASAKIESSVESQFSAGRLYACISSRPGQSGRCDGYILEGEELAFY
LRRLTAK

Ligands and cofactors

ID	Name	Formula	Copies
SPD	Spermidine	C7 H19 N3	1
ZN	Zinc ion	Zn	7
MG	Magnesium ion	Mg	327

Primary citation

The Ccr4-Not complex monitors the translating ribosome for codon optimality. Buschauer, R., Matsuo, Y., Sugiyama, T. et al. Science (2020) 368. DOI 10.1126/science.aay6912 · 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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