6T4Q: 40S ribosomal protein S1-A

Name: PDB 6T4Q: Structure of yeast 80S ribosome stalled on the CGA-CCG inhibitory codon combination.
Published: 2019-12-25
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: translation

Structure of yeast 80S ribosome stalled on the CGA-CCG inhibitory codon combination. Determined by electron microscopy at 2.6 Å resolution. Released 25 Dec 2019.

Method: Electron microscopy
Resolution: 2.6 Å
Organism: Saccharomyces cerevisiae
Chains: 82
Atoms: 203,581
Mol. weight: 3023.4 kDa
Ligands: ZN, MG
Released: 25 Dec 2019

Explore 6T4Q in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6T4Q contains 473 α-helices and 513 β-strands across 74 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 La: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	7-11	5
α-helix	42-47	6
β-strand	72-74	3	61
α-helix	84-92	9
β-strand	99-100	2	133
β-strand	101-103	3	62
α-helix	104-107	4
β-strand	111-113	3	61
β-strand	124-127	4	62
β-strand	129	1	61
α-helix	132-141	10
β-strand	144-147	4	62

Chain LA: 9 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	6-9	4
α-helix	29-31	3
α-helix	35-38	4
β-strand	40-49	10	68
β-strand	58-63	6	68
β-strand	73-77	5	68
α-helix	78	1
β-strand	79	1	69
β-strand	83	1	70
α-helix	86	1
β-strand	87-91	5	68
β-strand	103	1	71
β-strand	112-114	3	72
β-strand	134-140	7	72
β-strand	145-149	5	72
β-strand	155-159	5	72
β-strand	163	1	71
β-strand	165-166	2	72
β-strand	169	1	69
α-helix	174-176	3
α-helix	182-190	9
α-helix	201-203	3
β-strand	224-225	2	73
β-strand	237-238	2	73

Chain Lb: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	12-18	7
α-helix	37-58	22

Chain LB: 16 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	14-16	3
α-helix	27-29	3
α-helix	33-35	3
α-helix	40-41	2
β-strand	43	1	75
β-strand	45-59	15	76
β-strand	63	1	77
β-strand	65	1	77
β-strand	71-80	10	76
α-helix	82-83	2
β-strand	84-95	12	78
β-strand	98-105	8	78
α-helix	112-115	4
α-helix	116-118	3
α-helix	142-153	12
β-strand	157-163	7	78
α-helix	166-168	3
β-strand	178-182	5	78
β-strand	183	1	75
α-helix	188-198	11
β-strand	201-203	3	78
α-helix	205-207	3
β-strand	214-220	7	76
α-helix	221-223	3
β-strand	226-227	2	79
α-helix	229-233	5
α-helix	235-238	4
β-strand	268-269	2	79
β-strand	274-286	13	76
α-helix	307	1
β-strand	311	1	80
β-strand	315	1	80
β-strand	321-325	5	76
β-strand	335-340	6	76
β-strand	356-359	4	76
α-helix	373-380	8

Chain Lc: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	10-20	11
β-strand	23-25	3	81
α-helix	27-35	9
β-strand	41-44	4	81
α-helix	50-63	14
β-strand	66-69	4	81
α-helix	74-80	7
β-strand	89-92	4	81

Chain LC: 22 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	83
β-strand	8-9	2	84
β-strand	10	1	85
β-strand	13	1	85
β-strand	19-20	2	83
α-helix	32-42	11
β-strand	63	1	86
β-strand	76	1	86
β-strand	88	1	86
α-helix	115-127	13
α-helix	128-130	3
α-helix	132-137	6
β-strand	150-152	3	84
α-helix	154-158	5
α-helix	162-172	11
α-helix	175-183	9
β-strand	186-187	2	87
α-helix	193-195	3
β-strand	199-200	2	87
β-strand	206-209	4	84
α-helix	215-218	4
β-strand	226-229	4	84
α-helix	235-238	4
α-helix	240-242	3
β-strand	248-251	4	84
α-helix	252-262	11
α-helix	276-279	4
α-helix	287-290	4
α-helix	294-298	5
α-helix	299-301	3
α-helix	307-309	3
α-helix	315-316	2
α-helix	321-327	7
α-helix	331-337	7
α-helix	339-341	3
α-helix	353-360	8

Chain Ld: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	9-15	7	88
α-helix	25-27	3
α-helix	28-44	17
β-strand	49-51	3	88
α-helix	53-59	7
β-strand	70-79	10	88
β-strand	89-95	7	88
β-strand	107-109	3	88

Chain LD: 16 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	10-15	6
α-helix	16-19	4
α-helix	30-37	8
α-helix	46-48	3
β-strand	50-56	7	90
β-strand	59-66	8	90
β-strand	73-79	7	90
α-helix	83-85	3
α-helix	95-113	19
α-helix	133-135	3
β-strand	143	1	91
β-strand	145-147	3	90
α-helix	159-169	11
β-strand	172	1	91
β-strand	183	1	92
β-strand	190	1	92
α-helix	192-200	9
α-helix	202-212	11
α-helix	216-221	6
α-helix	224-228	5
α-helix	233-235	3
α-helix	236-249	14
α-helix	262-272	11
α-helix	279-293	15

66 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	C2	RNA	1798	Saccharomyces cerevisiae
40S ribosomal protein S1-A	SB	protein	232	Saccharomyces cerevisiae	P33442 (AlphaFold model)
40S ribosomal protein S15	SP	protein	117	Saccharomyces cerevisiae	Q01855 (AlphaFold model)
40S ribosomal protein S2	SC	protein	216	Saccharomyces cerevisiae	P25443 (AlphaFold model)
40S ribosomal protein S3	SD	protein	222	Saccharomyces cerevisiae	P05750 (AlphaFold model)
40S ribosomal protein S4-A	SE	protein	258	Saccharomyces cerevisiae	P0CX35
Rps5p	SF	protein	206	Saccharomyces cerevisiae	A0A1L4AA68
40S ribosomal protein S6-A	SG	protein	228	Saccharomyces cerevisiae	P0CX37
40S ribosomal protein S7-A	SH	protein	184	Saccharomyces cerevisiae	P26786
40S ribosomal protein S8-A	SI	protein	198	Saccharomyces cerevisiae	P0CX39
40S ribosomal protein S9-A	SJ	protein	184	Saccharomyces cerevisiae	O13516
40S ribosomal protein S10-A	SK	protein	92	Saccharomyces cerevisiae	Q08745

70 more molecules are not listed.

Sequence of entity 1 (C2), FASTA

>6T4Q_1 18S rRNA (chains C2)
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 (SB), FASTA

>6T4Q_2 40S ribosomal protein S1-A (chains SB)
AVGKNKRLSKGKKGQKKRVVDPFTRKEWFDIKAPSTFENRNVGKTLVNKSTGLKSASDAL
KGRVVEVCLADLQGSEDHSFRKIKLRVDEVQGKNLLTNFHGMDFTTDKLRSMVRKWQTLI
EANVTVKTSDDYVLRIFAIAFTRKQANQVKRHSYAQSSHIRAIRKVISEILTKEVQGSTL
AQLTSKLIPEVINKEIENATKDIFPLQNIHVRKVKLLKQPKFDVGALMALHG

Sequence of entity 3 (SP), FASTA

>6T4Q_3 40S ribosomal protein S15 (chains SP)
KTHSYRGVDLEKLLEMSTEDFVKLAPARVRRRFARGMTSKPAGFMKKLRAAKLAAPENEK
PAPVRTHMRNMIIVPEMIGSVVGIYNGKAFNQVEIRPEMLGHYLGEFSITYTPVRHG

Sequence of entity 4 (SC), FASTA

>6T4Q_4 40S ribosomal protein S2 (chains SC)
GWVPVTKLGRLVKAGKITTIEEIFLHSLPVKEFQIIDTLLPGLQDEVMNIKPVQKQTRAG
QRTRFKAVVVVGDSNGHVGLGIKTAKEVAGAIRAGIIIAKLSVIPIRRGYWGTNLGQPHS
LATKTTGKCGSVTVRLIPAPRGSGIVASPAVKKLLQLAGVEDVYTQSNGKTRTLENTLKA
AFVAIGNTYGFLTPNLWAEQPLPVSPLDIYSDEASA

Sequence of entity 5 (SD), FASTA

>6T4Q_5 40S ribosomal protein S3 (chains SD)
LISKKRKLVADGVFYAELNEFFTRELAEEGYSGVEVRVTPTKTEVIIRATRTQDVLGENG
RRINELTLLVQKRFKYAPGTIVLYAERVQDRGLSAVAQAESMKFKLLNGLAIRRAAYGVV
RYVMESGAKGCEVVVSGKLRAARAKAMKFADGFLIHSGQPVNDFIDTATRHVLMRQGVLG
IKVKIMRDPAKSRTGPKALPDAVTIIEPKEEEPILAPSVKDY

Sequence of entity 6 (SE), FASTA

>6T4Q_6 40S ribosomal protein S4-A (chains SE)
ARGPKKHLKRLAAPHHWLLDKLSGCYAPRPSAGPHKLRESLPLIVFLRNRLKYALNGREV
KAILMQRHVKVDGKVRTDTTYPAGFMDVITLDATNENFRLVYDVKGRFAVHRITDEEASY
KLGKVKKVQLGKKGVPYVVTHDGRTIRYPDPNIKVNDTVKIDLASGKITDFIKFDAGKLV
YVTGGRNLGRIGTIVHKERHDGGFDLVHIKDSLDNTFVTRLNNVFVIGEQGKPYISLPKG
KGIKLSIAEERDRRRAQQ

Sequence of entity 7 (SF), FASTA

>6T4Q_7 Rps5p (chains SF)
FTPVVLATPIPEEVQQAQTEIKLFNKWSFEEVEVKDASLVDYVQVRQPIFVAHTAGRYAN
KRFRKAQCPIIERLTNSLMMNGRNNGKKLKAVRIIKHTLDIINVLTDQNPIQVVVDAITN
TGPREDTTRVGGGGAARRQAVDVSPLRRVNQAIALLTIGAREAAFRNIKTIAETLAEELI
NAAKGSSTSYAIKKKDELERVAKSNR

Sequence of entity 8 (SG), FASTA

>6T4Q_8 40S ribosomal protein S6-A (chains SG)
MKLNISYPVNGSQKTFEIDDEHRIRVFFDKRIGQEVDGEAVGDEFKGYVFKISGGNDKQG
FPMKQGVLLPTRIKLLLTKNVSCYRPRRDGERKRKSVRGAIVGPDLAVLALVIVKKGEQE
LEGLTDTTVPKRLGPKRANNIRKFFGLSKEDDVRDFVIRREVTKGEKTYTKAPKIQRLVT
PQRLQRKRHQRALKVRNAQAQREAAAEYAQLLAKRLSERKAEKAEIRK

Sequence of entity 9 (SH), FASTA

>6T4Q_9 40S ribosomal protein S7-A (chains SH)
PQAKILSQAPTELELQVAQAFVELENSSPELKAELRPLQFKSIREIDVAGGKKALAIFVP
VPSLAGFHKVQTKLTRELEKKFQDRHVIFLAERRILPKPSRTSRQVQKRPRSRTLTAVHD
KILEDLVFPTEIVGKRVRYLVGGNKIQKVLLDSKDVQQIDYKLESFQAVYNKLTGKQIVF
EIPS

Sequence of entity 10 (SI), FASTA

>6T4Q_10 40S ribosomal protein S8-A (chains SI)
GISRDSRHKRSATGAKRAQFRKKRKFELGRQPANTKIGAKRIHSVRTRGGNKKYRALRIE
TGNFSWASEGISKKTRIAGVVYHPSNNELVRTNTLTKAAIVQIDATPFRQWFEAHYGQTL
GKKKNVKEEETVAKSKNAERKWAARAASAKIESSVESQFSAGRLYACISSRPGQSGRCDG
YILEGEELAFYLRRLTAK

Sequence of entity 11 (SJ), FASTA

>6T4Q_11 40S ribosomal protein S9-A (chains SJ)
PRAPRTYSKTYSTPKRPYESSRLDAELKLAGEFGLKNKKEIYRISFQLSKIRRAARDLLT
RDEKDPKRLFEGNALIRRLVRVGVLSEDKKKLDYVLALKVEDFLERRLQTQVYKLGLAKS
VHHARVLITQRHIAVGKQIVNIPSFMVRLDSEKHIDFAPTSPFGGARPGRVARRNAARKA
EASG

Sequence of entity 12 (SK), FASTA

>6T4Q_12 40S ribosomal protein S10-A (chains SK)
MLMPKEDRNKIHQYLFQEGVVVAKKDFNQAKHEEIDTKNLYVIKALQSLTSKGYVKTQFS
WQYYYYTLTEEGVEYLREYLNLPEHIVPGTYI

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	7
MG	Magnesium ion	Mg	291

Primary citation

Molecular mechanism of translational stalling by inhibitory codon combinations and poly(A) tracts. Tesina, P., Lessen, L.N., Buschauer, R. et al. EMBO J (2020) 39:e103365-e103365. DOI 10.15252/embj.2019103365 · PubMed

Other PDB entries of the same protein (UniProt P33442 (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…
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
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…

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