6T7T: Yeast 80S ribosome stalled on poly(A) tract
Structure of yeast 80S ribosome stalled on poly(A) tract. Determined by electron microscopy at 3.1 Å resolution. Released 25 Dec 2019.
- Method
- Electron microscopy
- Resolution
- 3.1 Å
- Organism
- Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
- Chains
- 82
- Atoms
- 202,869
- Mol. weight
- 3000.04 kDa
- Released
- 25 Dec 2019
Explore 6T7T in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6T7T contains 438 α-helices and 499 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: 5 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-11 | 5 | |
| α-helix | 42-47 | 6 | |
| β-strand | 72-74 | 3 | 70 |
| α-helix | 84-92 | 9 | |
| β-strand | 99-100 | 2 | 128 |
| β-strand | 101-103 | 3 | 71 |
| α-helix | 104-107 | 4 | |
| β-strand | 111-113 | 3 | 70 |
| β-strand | 124-127 | 4 | 71 |
| α-helix | 132-141 | 10 | |
| β-strand | 144-147 | 4 | 71 |
Chain LA: 9 helices, 16 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-5 | 3 | |
| α-helix | 6-12 | 7 | |
| α-helix | 29-31 | 3 | |
| α-helix | 35-38 | 4 | |
| β-strand | 40-49 | 10 | 1 |
| α-helix | 50-51 | 2 | |
| β-strand | 58-62 | 5 | 1 |
| β-strand | 73-77 | 5 | 1 |
| α-helix | 78 | 1 | |
| β-strand | 79 | 1 | 2 |
| β-strand | 83 | 1 | 3 |
| β-strand | 86-91 | 6 | 1 |
| β-strand | 103 | 1 | 4 |
| β-strand | 112-114 | 3 | 5 |
| β-strand | 134-140 | 7 | 5 |
| β-strand | 145-150 | 6 | 5 |
| β-strand | 154-159 | 6 | 5 |
| β-strand | 163 | 1 | 4 |
| β-strand | 165-166 | 2 | 5 |
| β-strand | 169 | 1 | 2 |
| α-helix | 174-176 | 3 | |
| α-helix | 182-192 | 11 | |
| α-helix | 201-203 | 3 | |
| β-strand | 224-225 | 2 | 6 |
| β-strand | 237-238 | 2 | 6 |
Chain Lb: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-18 | 7 | |
| α-helix | 37-57 | 21 | |
Chain LB: 11 helices, 19 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 33-35 | 3 | |
| β-strand | 43 | 1 | 17 |
| β-strand | 45-59 | 15 | 18 |
| β-strand | 71-80 | 10 | 18 |
| β-strand | 84-93 | 10 | 19 |
| β-strand | 100-105 | 6 | 19 |
| α-helix | 114-117 | 4 | |
| α-helix | 131-136 | 6 | |
| α-helix | 142-153 | 12 | |
| β-strand | 157-163 | 7 | 19 |
| β-strand | 178-182 | 5 | 19 |
| β-strand | 183 | 1 | 17 |
| α-helix | 188-197 | 10 | |
| β-strand | 201-203 | 3 | 19 |
| α-helix | 205-208 | 4 | |
| β-strand | 215-221 | 7 | 18 |
| α-helix | 222-223 | 2 | |
| β-strand | 225-227 | 3 | 20 |
| α-helix | 229 | 1 | |
| α-helix | 230-234 | 5 | |
| α-helix | 235-238 | 4 | |
| β-strand | 268-270 | 3 | 20 |
| β-strand | 273-278 | 6 | 18 |
| β-strand | 282-286 | 5 | 18 |
| β-strand | 311 | 1 | 21 |
| β-strand | 315 | 1 | 21 |
| β-strand | 321-325 | 5 | 18 |
| β-strand | 335-340 | 6 | 18 |
| β-strand | 356-359 | 4 | 18 |
| α-helix | 373-380 | 8 | |
Chain Lc: 4 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-20 | 11 | |
| β-strand | 22-25 | 4 | 79 |
| α-helix | 27-35 | 9 | |
| β-strand | 41-45 | 5 | 79 |
| α-helix | 50-63 | 14 | |
| β-strand | 66-70 | 5 | 79 |
| α-helix | 74-81 | 8 | |
| β-strand | 89-94 | 6 | 79 |
Chain LC: 22 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6-7 | 2 | 85 |
| α-helix | 8-9 | 2 | |
| β-strand | 19-20 | 2 | 85 |
| α-helix | 32-44 | 13 | |
| α-helix | 48-50 | 3 | |
| β-strand | 63 | 1 | 86 |
| β-strand | 76 | 1 | 86 |
| β-strand | 88 | 1 | 86 |
| α-helix | 98-99 | 2 | |
| α-helix | 102-104 | 3 | |
| α-helix | 115-130 | 16 | |
| α-helix | 133-136 | 4 | |
| β-strand | 150-152 | 3 | 87 |
| α-helix | 154-158 | 5 | |
| α-helix | 162-172 | 11 | |
| α-helix | 175-184 | 10 | |
| β-strand | 186-187 | 2 | 88 |
| α-helix | 193-195 | 3 | |
| β-strand | 199-200 | 2 | 88 |
| β-strand | 206-209 | 4 | 87 |
| α-helix | 215-218 | 4 | |
| β-strand | 226-229 | 4 | 87 |
| α-helix | 235-238 | 4 | |
| α-helix | 240-242 | 3 | |
| β-strand | 248-251 | 4 | 87 |
| α-helix | 252-262 | 11 | |
| 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 | 353-360 | 8 | |
Chain Ld: 3 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 9-15 | 7 | 89 |
| α-helix | 16-20 | 5 | |
| α-helix | 28-44 | 17 | |
| β-strand | 49-51 | 3 | 89 |
| α-helix | 53-59 | 7 | |
| β-strand | 70-79 | 10 | 89 |
| β-strand | 89-95 | 7 | 89 |
| β-strand | 107-109 | 3 | 89 |
Chain LD: 14 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-15 | 6 | |
| α-helix | 16-19 | 4 | |
| α-helix | 30-37 | 8 | |
| β-strand | 50-55 | 6 | 92 |
| β-strand | 60-66 | 7 | 92 |
| β-strand | 73-79 | 7 | 92 |
| α-helix | 83-85 | 3 | |
| α-helix | 95-113 | 19 | |
| α-helix | 134-135 | 2 | |
| β-strand | 143 | 1 | 93 |
| β-strand | 145-147 | 3 | 92 |
| α-helix | 158-169 | 12 | |
| β-strand | 172 | 1 | 93 |
| α-helix | 192-199 | 8 | |
| α-helix | 202-214 | 13 | |
| α-helix | 216-221 | 6 | |
| α-helix | 224-228 | 5 | |
| α-helix | 233-249 | 17 | |
| 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 |
|---|
| 60S ribosomal protein L2-A | LA | protein | 251 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P0CX45 (AlphaFold model) |
| 40S ribosomal protein S0-A | SA | protein | 206 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P32905 (AlphaFold model) |
| 60S ribosomal protein L3 | LB | protein | 386 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P14126 (AlphaFold model) |
| 40S ribosomal protein S1-A | SB | protein | 232 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P33442 (AlphaFold model) |
| 18S rRNA | C2 | RNA | 1771 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | |
| 40S ribosomal protein S15 | SP | protein | 117 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | Q01855 |
| 40S ribosomal protein S2 | SC | protein | 216 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P25443 |
| 40S ribosomal protein S3 | SD | protein | 222 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P05750 |
| 40S ribosomal protein S4-A | SE | protein | 258 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P0CX35 |
| Rps5p | SF | protein | 206 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P26783 |
| 40S ribosomal protein S6-A | SG | protein | 228 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P0CX37 |
| 40S ribosomal protein S7-A | SH | protein | 184 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P26786 |
69 more molecules are not listed.
Sequence of entity 1 (LA), FASTA
>6T7T_1 60S ribosomal protein L2-A (chains LA)
GRVIRNQRKGAGSIFTSHTRLRQGAAKLRTLDYAERHGYIRGIVKQIVHDSGRGAPLAKV
VFRDPYKYRLREEIFIANEGVHTGQFIYAGKKASLNVGNVLPLGSVPEGTIVSNVEEKPG
DRGALARASGNYVIIIGHNPDENKTRVRLPSGAKKVISSDARGVIGVIAGGGRVDKPLLK
AGRAFHKYRLKRNSWPKTRGVAMNPVDHPHGGGNHQHIGKASTISRGAVSGQKAGLIAAR
RTGLLRGSQKT
Sequence of entity 2 (SA), FASTA
>6T7T_2 40S ribosomal protein S0-A (chains SA)
SLPATFDLTPEDAQLLLAANTHLGARNVQVHQEPYVFNARPDGVHVINVGKTWEKLVLAA
RIIAAIPNPEDVVAISSRTFGQRAVLKFAAHTGATPIAGRFTPGSFTNYITRSFKEPRLV
IVTDPRSDAQAIKEASYVNIPVIALTDLDSPSEFVDVAIPCNNRGKHSIGLIWYLLAREV
LRLRGALVDRTQPWSIMPDLYFYRDP
Sequence of entity 3 (LB), FASTA
>6T7T_3 60S ribosomal protein L3 (chains LB)
SHRKYEAPRHGHLGFLPRKRAASIRARVKAFPKDDRSKPVALTSFLGYKAGMTTIVRDLD
RPGSKFHKREVVEAVTVVDTPPVVVVGVVGYVETPRGLRSLTTVWAEHLSDEVKRRFYKN
WYKSKKKAFTKYSAKYAQDGAGIERELARIKKYASVVRVLVHTQIRKTPLAQKKAHLAEI
QLNGGSISEKVDWAREHFEKTVAVDSVFEQNEMIDAIAVTKGHGFEGVTHRWGTKKLPRK
THRGLRKVACIGAWHPAHVMWSVARAGQRGYHSRTSINHKIYRVGKGDDEANGATSFDRT
KKTITPMGGFVHYGEIKNDFIMVKGCIPGNRKRIVTLRKSLYTNTSRKALEEVSLKWIDT
ASKFGKGRFQTPAEKHAFMGTLKKDL
Sequence of entity 4 (SB), FASTA
>6T7T_4 40S ribosomal protein S1-A (chains SB)
AVGKNKRLSKGKKGQKKRVVDPFTRKEWFDIKAPSTFENRNVGKTLVNKSTGLKSASDAL
KGRVVEVCLADLQGSEDHSFRKIKLRVDEVQGKNLLTNFHGMDFTTDKLRSMVRKWQTLI
EANVTVKTSDDYVLRIFAIAFTRKQANQVKRHSYAQSSHIRAIRKVISEILTKEVQGSTL
AQLTSKLIPEVINKEIENATKDIFPLQNIHVRKVKLLKQPKFDVGALMALHG
Sequence of entity 5 (C2), FASTA
>6T7T_5 18S rRNA (chains C2)
UAUCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCU
AAGUAUAAGCAAUUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUCGUUUAU
UUGAUAGUUCCUUUACUACAUGGUAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCUUAA
AAUCUCGACCCUUUGGAAGAGAUGUAUUUAUUAGAUAAAAAAUCAAUGUCUUCGGACUCU
UUGAUGAUUCAUAAUAACUUUUCGAAUCGCAUGGCCUUGUGCUGGCGAUGGUUCAUUCAA
AUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUUUCAACGGGUAA
CGGGGAAUAAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGA
AGGCAGCAGGCGCGCAAAUUACCCAAUCCUAAUUCAGGGAGGUAGUGACAAUAAAUAACG
AUACAGGGCCCAUUCGGGUCUUGUAAUUGGAAUGAGUACAAUGUAAAUACCUUAACGAGG
AACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAU
AUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAACUUUGGGCCCGGUUGGCCGGUCGG
AUUUCCAACGGGGCCUUUCCUUCUGGCUAACCUUGAGCUUGGCGAACCAGGACUUUUACU
UUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUAUUGCUCGAAUAUAUUAGCAUGGAAUAAU
AGAAUAGGACGUUUGGUUCUAUUUUGUUGGUUUCUAGGACCAUCGUAAUGAUUAAUAGGG
ACGGUCGGGGGCAUCAGUAUUCAAUUGUCAGAGGUGAAAUUCUUGGAUUUAUUGAAGACU
AACUACUGCGAAAGCAUUUGCCAAGGACGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGA
UCGAAGAUGAUCAGAUACCGUCGUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGG
UGGUGUUUUUUUAAUGACCCACUCGGCACCUUACGAGAAAUCAAAGUCUUUGGGUUCUGG
GGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGU
GGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCCAGACACAAUAAG
GAUUGACAGAUUGAGAGCUCUUUCUUGAUUUUGUGGGUGGUGGUGCAUGGCCGUUCUUAG
UUGGUGGAGUGAUUUGUCUGCUUAAUUGCGAUAACGAACGAGACCUUAACCUACUAAAUA
GUGGUGCUAGCAUUUGCUGGUUAUCCACUUCUUAGAGGGACUAUCGGUUUCAAGCCGAUG
GAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGACGUUCUGGGCCGCACGCGCGCU
ACACUGACGGAGCCAGCGAGUCUAACCUUGGCCGAGAGGUCUUGGUAAUCUUGUGAAACU
CCGUCGUGCUGGGGAUAGAGCAUUGUAAUUAUUGCUCUUCAACGAGGAAUUCCUAGUAAG
CGCAAGUCAUCAGCUUGCGUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUA
GUACCGAUUGAAUGGCUUAGUGAGGCCUCAGGAUCUGCUUAGAGAAGGGGGCAACUCCAU
CUCAGAGCGGAGAAUUUGGACAAACUUGGUCAUUUAGAGGAACUAAAAGUCGUAACAAGG
UUUCCGUAGGUGAACCUGCGGAAGGAUCAUU
Sequence of entity 6 (SP), FASTA
>6T7T_6 40S ribosomal protein S15 (chains SP)
KTHSYRGVDLEKLLEMSTEDFVKLAPARVRRRFARGMTSKPAGFMKKLRAAKLAAPENEK
PAPVRTHMRNMIIVPEMIGSVVGIYNGKAFNQVEIRPEMLGHYLGEFSITYTPVRHG
Sequence of entity 7 (SC), FASTA
>6T7T_7 40S ribosomal protein S2 (chains SC)
GWVPVTKLGRLVKAGKITTIEEIFLHSLPVKEFQIIDTLLPGLQDEVMNIKPVQKQTRAG
QRTRFKAVVVVGDSNGHVGLGIKTAKEVAGAIRAGIIIAKLSVIPIRRGYWGTNLGQPHS
LATKTTGKCGSVTVRLIPAPRGSGIVASPAVKKLLQLAGVEDVYTQSNGKTRTLENTLKA
AFVAIGNTYGFLTPNLWAEQPLPVSPLDIYSDEASA
Sequence of entity 8 (SD), FASTA
>6T7T_8 40S ribosomal protein S3 (chains SD)
LISKKRKLVADGVFYAELNEFFTRELAEEGYSGVEVRVTPTKTEVIIRATRTQDVLGENG
RRINELTLLVQKRFKYAPGTIVLYAERVQDRGLSAVAQAESMKFKLLNGLAIRRAAYGVV
RYVMESGAKGCEVVVSGKLRAARAKAMKFADGFLIHSGQPVNDFIDTATRHVLMRQGVLG
IKVKIMRDPAKSRTGPKALPDAVTIIEPKEEEPILAPSVKDY
Sequence of entity 9 (SE), FASTA
>6T7T_9 40S ribosomal protein S4-A (chains SE)
ARGPKKHLKRLAAPHHWLLDKLSGCYAPRPSAGPHKLRESLPLIVFLRNRLKYALNGREV
KAILMQRHVKVDGKVRTDTTYPAGFMDVITLDATNENFRLVYDVKGRFAVHRITDEEASY
KLGKVKKVQLGKKGVPYVVTHDGRTIRYPDPNIKVNDTVKIDLASGKITDFIKFDAGKLV
YVTGGRNLGRIGTIVHKERHDGGFDLVHIKDSLDNTFVTRLNNVFVIGEQGKPYISLPKG
KGIKLSIAEERDRRRAQQ
Sequence of entity 10 (SF), FASTA
>6T7T_10 Rps5p (chains SF)
FTPVVLATPIPEEVQQAQTEIKLFNKWSFEEVEVKDASLVDYVQVRQPIFVAHTAGRYAN
KRFRKAQCPIIERLTNSLMMNGRNNGKKLKAVRIIKHTLDIINVLTDQNPIQVVVDAITN
TGPREDTTRVGGGGAARRQAVDVSPLRRVNQAIALLTIGAREAAFRNIKTIAETLAEELI
NAAKGSSTSYAIKKKDELERVAKSNR
Sequence of entity 11 (SG), FASTA
>6T7T_11 40S ribosomal protein S6-A (chains SG)
MKLNISYPVNGSQKTFEIDDEHRIRVFFDKRIGQEVDGEAVGDEFKGYVFKISGGNDKQG
FPMKQGVLLPTRIKLLLTKNVSCYRPRRDGERKRKSVRGAIVGPDLAVLALVIVKKGEQE
LEGLTDTTVPKRLGPKRANNIRKFFGLSKEDDVRDFVIRREVTKGEKTYTKAPKIQRLVT
PQRLQRKRHQRALKVRNAQAQREAAAEYAQLLAKRLSERKAEKAEIRK
Sequence of entity 12 (SH), FASTA
>6T7T_12 40S ribosomal protein S7-A (chains SH)
PQAKILSQAPTELELQVAQAFVELENSSPELKAELRPLQFKSIREIDVAGGKKALAIFVP
VPSLAGFHKVQTKLTRELEKKFQDRHVIFLAERRILPKPSRTSRQVQKRPRSRTLTAVHD
KILEDLVFPTEIVGKRVRYLVGGNKIQKVLLDSKDVQQIDYKLESFQAVYNKLTGKQIVF
EIPS
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 P0CX45 (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…
- 8P8N 2.15 Å, Mouse RPL39 integrated into the yeast 60S ribosomal subunit
- 8PFR 2.15 Å, Mouse RPL39L integrated into the yeast 60S ribosomal subunit
- 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,…
- 8P8U 2.23 Å, Yeast 60S ribosomal subunit
- 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
- 7UOO 2.34 Å, Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state
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