6T7I: 40S ribosomal protein S0-A

Name: PDB 6T7I: Structure of yeast 80S ribosome stalled on the CGA-CGA 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-CGA inhibitory codon combination. Determined by electron microscopy at 3.2 Å resolution. Released 25 Dec 2019.

Method: Electron microscopy
Resolution: 3.2 Å
Organism: Saccharomyces cerevisiae
Chains: 81
Atoms: 202,973
Mol. weight: 3160.04 kDa
Released: 25 Dec 2019

Explore 6T7I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6T7I contains 428 α-helices and 514 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: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	42-48	7
β-strand	74	1	68
α-helix	84-92	9
β-strand	99-100	2	139
β-strand	101-103	3	69
α-helix	104-107	4
β-strand	111	1	70
β-strand	113	1	68
β-strand	124-127	4	69
β-strand	129	1	70
α-helix	132-141	10
β-strand	144-147	4	69

Chain LA: 5 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
α-helix	29-31	3
α-helix	35-38	4
β-strand	40-49	10	76
β-strand	58-63	6	76
β-strand	73-77	5	76
α-helix	78	1
β-strand	79	1	77
β-strand	83	1	78
β-strand	87-91	5	76
β-strand	103	1	79
β-strand	112-114	3	80
β-strand	134-140	7	80
β-strand	145-149	5	80
β-strand	155-159	5	80
β-strand	163	1	79
β-strand	165-166	2	80
β-strand	169	1	77
α-helix	182-189	8
β-strand	224-225	2	81
β-strand	237-238	2	81

Chain Lb: 2 helices, 0 β-strands

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

Chain LB: 7 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	43	1	84
β-strand	45-59	15	85
β-strand	71-80	10	85
β-strand	84-93	10	86
β-strand	100-105	6	86
α-helix	131-135	5
α-helix	142-153	12
β-strand	157-163	7	86
α-helix	166-168	3
β-strand	178-182	5	86
β-strand	183	1	84
α-helix	188-198	11
β-strand	201-203	3	86
β-strand	214-220	7	85
β-strand	223-227	5	87
α-helix	229-232	4
α-helix	236-238	3
β-strand	268-271	4	87
β-strand	274-286	13	85
β-strand	321-325	5	85
β-strand	335-340	6	85
β-strand	356-359	4	85
α-helix	373-380	8

Chain Lc: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	10-19	10
β-strand	22-25	4	88
α-helix	27-35	9
β-strand	41-44	4	88
α-helix	50-63	14
β-strand	66-69	4	88
α-helix	74-81	8
β-strand	89-94	6	88

Chain LC: 20 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	90
β-strand	9	1	91
β-strand	10	1	92
β-strand	13	1	92
β-strand	19-20	2	90
α-helix	32-42	11
β-strand	63	1	93
β-strand	76	1	93
β-strand	88	1	93
α-helix	98-99	2
α-helix	115-129	15
α-helix	132-138	7
β-strand	150-152	3	91
α-helix	154-158	5
α-helix	162-172	11
α-helix	175-183	9
β-strand	186-187	2	94
α-helix	191-195	5
β-strand	199-200	2	94
β-strand	206-209	4	91
α-helix	215-218	4
β-strand	226-229	4	91
α-helix	235-238	4
α-helix	240-242	3
β-strand	248-251	4	91
α-helix	252-262	11
β-strand	264	1	95
β-strand	267	1	95
α-helix	286-290	5
α-helix	294-298	5
α-helix	299-301	3
α-helix	321-327	7
α-helix	330-337	8
α-helix	339-341	3
α-helix	344-346	3
α-helix	353-360	8

Chain Ld: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	9-15	7	96
α-helix	25-27	3
α-helix	28-44	17
β-strand	49-50	2	96
α-helix	53-60	8
β-strand	70-79	10	96
β-strand	89-95	7	96
β-strand	107-109	3	96

Chain LD: 16 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	10-15	6
α-helix	22-25	4
α-helix	30-37	8
β-strand	50-55	6	98
β-strand	60-67	8	98
β-strand	72-79	8	98
α-helix	80-85	6
α-helix	95-113	19
α-helix	133-135	3
β-strand	143	1	99
β-strand	145-147	3	98
α-helix	158-169	12
β-strand	172	1	99
β-strand	184	1	100
β-strand	189	1	100
α-helix	192-199	8
α-helix	202-212	11
α-helix	216-221	6
α-helix	224-228	5
α-helix	236-249	14
α-helix	262-272	11
α-helix	276-278	3
α-helix	279-289	11
α-helix	290-294	5

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 ribosomal RNA	C2	RNA	1800	Saccharomyces cerevisiae
40S ribosomal protein S0-A	SA	protein	252	Saccharomyces cerevisiae	P32905 (AlphaFold model)
40S ribosomal protein S1-A	SB	protein	255	Saccharomyces cerevisiae	P33442 (AlphaFold model)
40S ribosomal protein S15	SP	protein	142	Saccharomyces cerevisiae	Q01855 (AlphaFold model)
40S ribosomal protein S2	SC	protein	254	Saccharomyces cerevisiae	P25443 (AlphaFold model)
40S ribosomal protein S3	SD	protein	240	Saccharomyces cerevisiae	P05750
40S ribosomal protein S4-A	SE	protein	261	Saccharomyces cerevisiae	P0CX35
Rps5p	SF	protein	225	Saccharomyces cerevisiae	A0A1L4AA68
40S ribosomal protein S6-A	SG	protein	236	Saccharomyces cerevisiae	P0CX37
40S ribosomal protein S7-A	SH	protein	190	Saccharomyces cerevisiae	P26786
40S ribosomal protein S8-A	SI	protein	200	Saccharomyces cerevisiae	P0CX39
40S ribosomal protein S9-A	SJ	protein	197	Saccharomyces cerevisiae	O13516

69 more molecules are not listed.

Sequence of entity 1 (C2), FASTA

>6T7I_1 18S ribosomal RNA (chains C2)
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 (SA), FASTA

>6T7I_2 40S ribosomal protein S0-A (chains SA)
MSLPATFDLTPEDAQLLLAANTHLGARNVQVHQEPYVFNARPDGVHVINVGKTWEKLVLA
ARIIAAIPNPEDVVAISSRTFGQRAVLKFAAHTGATPIAGRFTPGSFTNYITRSFKEPRL
VIVTDPRSDAQAIKEASYVNIPVIALTDLDSPSEFVDVAIPCNNRGKHSIGLIWYLLARE
VLRLRGALVDRTQPWSIMPDLYFYRDPEEVEQQVAEEATTEEAGEEEAKEEVTEEQAEAT
EWAEENADNVEW

Sequence of entity 3 (SB), FASTA

>6T7I_3 40S ribosomal protein S1-A (chains SB)
MAVGKNKRLSKGKKGQKKRVVDPFTRKEWFDIKAPSTFENRNVGKTLVNKSTGLKSASDA
LKGRVVEVCLADLQGSEDHSFRKIKLRVDEVQGKNLLTNFHGMDFTTDKLRSMVRKWQTL
IEANVTVKTSDDYVLRIFAIAFTRKQANQVKRHSYAQSSHIRAIRKVISEILTKEVQGST
LAQLTSKLIPEVINKEIENATKDIFPLQNIHVRKVKLLKQPKFDVGALMALHGEGSGEEK
GKKVTGFKDEVLETV

Sequence of entity 4 (SP), FASTA

>6T7I_4 40S ribosomal protein S15 (chains SP)
MSQAVNAKKRVFKTHSYRGVDLEKLLEMSTEDFVKLAPARVRRRFARGMTSKPAGFMKKL
RAAKLAAPENEKPAPVRTHMRNMIIVPEMIGSVVGIYNGKAFNQVEIRPEMLGHYLGEFS
ITYTPVRHGRAGATTSRFIPLK

Sequence of entity 5 (SC), FASTA

>6T7I_5 40S ribosomal protein S2 (chains SC)
MSAPEAQQQKRGGFGGRNRGRPNRRGPRNTEEKGWVPVTKLGRLVKAGKITTIEEIFLHS
LPVKEFQIIDTLLPGLQDEVMNIKPVQKQTRAGQRTRFKAVVVVGDSNGHVGLGIKTAKE
VAGAIRAGIIIAKLSVIPIRRGYWGTNLGQPHSLATKTTGKCGSVTVRLIPAPRGSGIVA
SPAVKKLLQLAGVEDVYTQSNGKTRTLENTLKAAFVAIGNTYGFLTPNLWAEQPLPVSPL
DIYSDEASAQKKRF

Sequence of entity 6 (SD), FASTA

>6T7I_6 40S ribosomal protein S3 (chains SD)
MVALISKKRKLVADGVFYAELNEFFTRELAEEGYSGVEVRVTPTKTEVIIRATRTQDVLG
ENGRRINELTLLVQKRFKYAPGTIVLYAERVQDRGLSAVAQAESMKFKLLNGLAIRRAAY
GVVRYVMESGAKGCEVVVSGKLRAARAKAMKFADGFLIHSGQPVNDFIDTATRHVLMRQG
VLGIKVKIMRDPAKSRTGPKALPDAVTIIEPKEEEPILAPSVKDYRPAEETEAQAEPVEA

Sequence of entity 7 (SE), FASTA

>6T7I_7 40S ribosomal protein S4-A (chains SE)
MARGPKKHLKRLAAPHHWLLDKLSGCYAPRPSAGPHKLRESLPLIVFLRNRLKYALNGRE
VKAILMQRHVKVDGKVRTDTTYPAGFMDVITLDATNENFRLVYDVKGRFAVHRITDEEAS
YKLGKVKKVQLGKKGVPYVVTHDGRTIRYPDPNIKVNDTVKIDLASGKITDFIKFDAGKL
VYVTGGRNLGRIGTIVHKERHDGGFDLVHIKDSLDNTFVTRLNNVFVIGEQGKPYISLPK
GKGIKLSIAEERDRRRAQQGL

Sequence of entity 8 (SF), FASTA

>6T7I_8 Rps5p (chains SF)
MSDTEAPVEVQEDFEVVEEFTPVVLATPIPEEVQQAQTEIKLFNKWSFEEVEVKDASLVD
YVQVRQPIFVAHTAGRYANKRFRKAQCPIIERLTNSLMMNGRNNGKKLKAVRIIKHTLDI
INVLTDQNPIQVVVDAITNTGPREDTTRVGGGGAARRQAVDVSPLRRVNQAIALLTIGAR
EAAFRNIKTIAETLAEELINAAKGSSTSYAIKKKDELERVAKSNR

Sequence of entity 9 (SG), FASTA

>6T7I_9 40S ribosomal protein S6-A (chains SG)
MKLNISYPVNGSQKTFEIDDEHRIRVFFDKRIGQEVDGEAVGDEFKGYVFKISGGNDKQG
FPMKQGVLLPTRIKLLLTKNVSCYRPRRDGERKRKSVRGAIVGPDLAVLALVIVKKGEQE
LEGLTDTTVPKRLGPKRANNIRKFFGLSKEDDVRDFVIRREVTKGEKTYTKAPKIQRLVT
PQRLQRKRHQRALKVRNAQAQREAAAEYAQLLAKRLSERKAEKAEIRKRRASSLKA

Sequence of entity 10 (SH), FASTA

>6T7I_10 40S ribosomal protein S7-A (chains SH)
MSAPQAKILSQAPTELELQVAQAFVELENSSPELKAELRPLQFKSIREIDVAGGKKALAI
FVPVPSLAGFHKVQTKLTRELEKKFQDRHVIFLAERRILPKPSRTSRQVQKRPRSRTLTA
VHDKILEDLVFPTEIVGKRVRYLVGGNKIQKVLLDSKDVQQIDYKLESFQAVYNKLTGKQ
IVFEIPSETH

Sequence of entity 11 (SI), FASTA

>6T7I_11 40S ribosomal protein S8-A (chains SI)
MGISRDSRHKRSATGAKRAQFRKKRKFELGRQPANTKIGAKRIHSVRTRGGNKKYRALRI
ETGNFSWASEGISKKTRIAGVVYHPSNNELVRTNTLTKAAIVQIDATPFRQWFEAHYGQT
LGKKKNVKEEETVAKSKNAERKWAARAASAKIESSVESQFSAGRLYACISSRPGQSGRCD
GYILEGEELAFYLRRLTAKK

Sequence of entity 12 (SJ), FASTA

>6T7I_12 40S ribosomal protein S9-A (chains SJ)
MPRAPRTYSKTYSTPKRPYESSRLDAELKLAGEFGLKNKKEIYRISFQLSKIRRAARDLL
TRDEKDPKRLFEGNALIRRLVRVGVLSEDKKKLDYVLALKVEDFLERRLQTQVYKLGLAK
SVHHARVLITQRHIAVGKQIVNIPSFMVRLDSEKHIDFAPTSPFGGARPGRVARRNAARK
AEASGEAADEADEADEE

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 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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