6TNU: Yeast 80S ribosome
Yeast 80S ribosome in complex with eIF5A and decoding A-site and P-site tRNAs. Determined by electron microscopy at 3.1 Å resolution. Released 22 Apr 2020.
- Method
- Electron microscopy
- Resolution
- 3.1 Å
- Organism
- Saccharomyces cerevisiae
- Chains
- 83
- Atoms
- 204,962
- Mol. weight
- 3038.61 kDa
- Ligands
- ZN, SPD, 3HE
- Released
- 22 Apr 2020
Explore 6TNU in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6TNU contains 434 α-helices and 526 β-strands across 76 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: 2 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3 | 1 | 160 |
| β-strand | 6 | 1 | 160 |
| β-strand | 16 | 1 | 161 |
| β-strand | 23 | 1 | 161 |
| β-strand | 32-39 | 8 | 162 |
| β-strand | 45-55 | 11 | 162 |
| α-helix | 57-62 | 6 | |
| α-helix | 65-76 | 12 | |
Chain A: 10 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-28 | 22 | |
| α-helix | 30-32 | 3 | |
| β-strand | 34-42 | 9 | 47 |
| β-strand | 45-52 | 8 | 47 |
| α-helix | 55-59 | 5 | |
| α-helix | 61-63 | 3 | |
| α-helix | 64-77 | 14 | |
| α-helix | 79-80 | 2 | |
| β-strand | 84-86 | 3 | 47 |
| β-strand | 89-90 | 2 | 47 |
| α-helix | 98-111 | 14 | |
| α-helix | 115-129 | 15 | |
| β-strand | 133-141 | 9 | 48 |
| β-strand | 147-155 | 9 | 48 |
| α-helix | 162-166 | 5 | |
| β-strand | 168-177 | 10 | 48 |
| β-strand | 180-189 | 10 | 48 |
| α-helix | 209-213 | 5 | |
| β-strand | 221-224 | 4 | 49 |
Chain AA: 12 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 47-49 | 3 | |
| α-helix | 54-68 | 15 | |
| α-helix | 81-83 | 3 | |
| α-helix | 84-96 | 13 | |
| α-helix | 102-118 | 17 | |
| α-helix | 136-144 | 9 | |
| β-strand | 150-154 | 5 | 139 |
| α-helix | 160-162 | 3 | |
| α-helix | 166-172 | 7 | |
| β-strand | 177-180 | 4 | 139 |
| α-helix | 183-189 | 7 | |
| β-strand | 197-200 | 4 | 139 |
| α-helix | 208-221 | 14 | |
| α-helix | 226-231 | 6 | |
| α-helix | 240-254 | 15 | |
Chain AB: 2 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 17-18 | 2 | 69 |
| β-strand | 22-25 | 4 | 70 |
| β-strand | 27 | 1 | 71 |
| β-strand | 33-39 | 7 | 70 |
| β-strand | 51-52 | 2 | 69 |
| β-strand | 57-61 | 5 | 70 |
| β-strand | 74-80 | 7 | 70 |
| β-strand | 85-86 | 2 | 72 |
| β-strand | 92-95 | 4 | 72 |
| β-strand | 99-102 | 4 | 70 |
| β-strand | 114 | 1 | 71 |
| β-strand | 117 | 1 | 73 |
| α-helix | 120-125 | 6 | |
| α-helix | 127-131 | 5 | |
| β-strand | 135 | 1 | 73 |
Chain AC: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7 | 1 | 147 |
| β-strand | 14 | 1 | 147 |
| α-helix | 33-34 | 2 | |
| α-helix | 35-48 | 14 | |
| α-helix | 52-63 | 12 | |
| α-helix | 66-76 | 11 | |
| α-helix | 80-99 | 20 | |
Chain AD: 3 helices, 15 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3 | 1 | 142 |
| β-strand | 6-11 | 6 | 143 |
| β-strand | 17-20 | 4 | 144 |
| β-strand | 24-28 | 5 | 144 |
| β-strand | 33-37 | 5 | 144 |
| β-strand | 44-47 | 4 | 143 |
| β-strand | 52-57 | 6 | 143 |
| β-strand | 60 | 1 | 142 |
| α-helix | 62-83 | 22 | |
| β-strand | 86-93 | 8 | 145 |
| β-strand | 100-103 | 4 | 146 |
| β-strand | 112-115 | 4 | 146 |
| α-helix | 117-119 | 3 | |
| β-strand | 126 | 1 | 146 |
| β-strand | 133-135 | 3 | 145 |
| β-strand | 143-148 | 6 | 145 |
| α-helix | 151-164 | 14 | |
| β-strand | 178-186 | 9 | 145 |
Chain AE: 4 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 5 | 1 | 80 |
| β-strand | 12 | 1 | 80 |
| β-strand | 19-22 | 4 | 72 |
| β-strand | 28-31 | 4 | 72 |
| α-helix | 34-41 | 8 | |
| α-helix | 53-58 | 6 | |
| α-helix | 87-96 | 10 | |
| α-helix | 101-125 | 25 | |
Chain AF: 3 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-10 | 6 | |
| β-strand | 16-17 | 2 | 155 |
| β-strand | 27-28 | 2 | 155 |
| β-strand | 33-34 | 2 | 155 |
| α-helix | 51-56 | 6 | |
| α-helix | 67-76 | 10 | |
68 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 | 1798 | Saccharomyces cerevisiae | |
| mRNA | l | RNA | 6 | Saccharomyces cerevisiae | |
| 40S ribosomal protein S0-A | P | protein | 206 | Saccharomyces cerevisiae | P32905 (AlphaFold model) |
| 40S ribosomal protein S1-A | Q | protein | 232 | Saccharomyces cerevisiae | P33442 (AlphaFold model) |
| 40S ribosomal protein S15 | E | protein | 117 | Saccharomyces cerevisiae | Q01855 (AlphaFold model) |
| 40S ribosomal protein S2 | R | protein | 216 | Saccharomyces cerevisiae | P25443 (AlphaFold model) |
| 40S ribosomal protein S3 | A | protein | 222 | Saccharomyces cerevisiae | P05750 |
| 40S ribosomal protein S4-A | S | protein | 258 | Saccharomyces cerevisiae | P0CX35 |
| Rps5p | B | protein | 206 | Saccharomyces cerevisiae | P26783 |
| 40S ribosomal protein S6-A | T | protein | 228 | Saccharomyces cerevisiae | P0CX37 |
| 40S ribosomal protein S7-A | U | protein | 184 | Saccharomyces cerevisiae | P26786 |
| 40S ribosomal protein S8 | V | protein | 187 | Saccharomyces cerevisiae | P0CX39 |
71 more molecules are not listed.
Sequence of entity 1 (2), FASTA
>6TNU_1 18S 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
>6TNU_2 mRNA (chains l)
AUGAAA
Sequence of entity 3 (P), FASTA
>6TNU_3 40S ribosomal protein S0-A (chains P)
SLPATFDLTPEDAQLLLAANTHLGARNVQVHQEPYVFNARPDGVHVINVGKTWEKLVLAA
RIIAAIPNPEDVVAISSRTFGQRAVLKFAAHTGATPIAGRFTPGSFTNYITRSFKEPRLV
IVTDPRSDAQAIKEASYVNIPVIALTDLDSPSEFVDVAIPCNNRGKHSIGLIWYLLAREV
LRLRGALVDRTQPWSIMPDLYFYRDP
Sequence of entity 4 (Q), FASTA
>6TNU_4 40S ribosomal protein S1-A (chains Q)
AVGKNKRLSKGKKGQKKRVVDPFTRKEWFDIKAPSTFENRNVGKTLVNKSTGLKSASDAL
KGRVVEVCLADLQGSEDHSFRKIKLRVDEVQGKNLLTNFHGMDFTTDKLRSMVRKWQTLI
EANVTVKTSDDYVLRIFAIAFTRKQANQVKRHSYAQSSHIRAIRKVISEILTKEVQGSTL
AQLTSKLIPEVINKEIENATKDIFPLQNIHVRKVKLLKQPKFDVGALMALHG
Sequence of entity 5 (E), FASTA
>6TNU_5 40S ribosomal protein S15 (chains E)
KTHSYRGVDLEKLLEMSTEDFVKLAPARVRRRFARGMTSKPAGFMKKLRAAKLAAPENEK
PAPVRTHMRNMIIVPEMIGSVVGIYNGKAFNQVEIRPEMLGHYLGEFSITYTPVRHG
Sequence of entity 6 (R), FASTA
>6TNU_6 40S ribosomal protein S2 (chains R)
GWVPVTKLGRLVKAGKITTIEEIFLHSLPVKEFQIIDTLLPGLQDEVMNIKPVQKQTRAG
QRTRFKAVVVVGDSNGHVGLGIKTAKEVAGAIRAGIIIAKLSVIPIRRGYWGTNLGQPHS
LATKTTGKCGSVTVRLIPAPRGSGIVASPAVKKLLQLAGVEDVYTQSNGKTRTLENTLKA
AFVAIGNTYGFLTPNLWAEQPLPVSPLDIYSDEASA
Sequence of entity 7 (A), FASTA
>6TNU_7 40S ribosomal protein S3 (chains A)
LISKKRKLVADGVFYAELNEFFTRELAEEGYSGVEVRVTPTKTEVIIRATRTQDVLGENG
RRINELTLLVQKRFKYAPGTIVLYAERVQDRGLSAVAQAESMKFKLLNGLAIRRAAYGVV
RYVMESGAKGCEVVVSGKLRAARAKAMKFADGFLIHSGQPVNDFIDTATRHVLMRQGVLG
IKVKIMRDPAKSRTGPKALPDAVTIIEPKEEEPILAPSVKDY
Sequence of entity 8 (S), FASTA
>6TNU_8 40S ribosomal protein S4-A (chains S)
ARGPKKHLKRLAAPHHWLLDKLSGCYAPRPSAGPHKLRESLPLIVFLRNRLKYALNGREV
KAILMQRHVKVDGKVRTDTTYPAGFMDVITLDATNENFRLVYDVKGRFAVHRITDEEASY
KLGKVKKVQLGKKGVPYVVTHDGRTIRYPDPNIKVNDTVKIDLASGKITDFIKFDAGKLV
YVTGGRNLGRIGTIVHKERHDGGFDLVHIKDSLDNTFVTRLNNVFVIGEQGKPYISLPKG
KGIKLSIAEERDRRRAQQ
Sequence of entity 9 (B), FASTA
>6TNU_9 Rps5p (chains B)
FTPVVLATPIPEEVQQAQTEIKLFNKWSFEEVEVKDASLVDYVQVRQPIFVAHTAGRYAN
KRFRKAQCPIIERLTNSLMMNGRNNGKKLKAVRIIKHTLDIINVLTDQNPIQVVVDAITN
TGPREDTTRVGGGGAARRQAVDVSPLRRVNQAIALLTIGAREAAFRNIKTIAETLAEELI
NAAKGSSTSYAIKKKDELERVAKSNR
Sequence of entity 10 (T), FASTA
>6TNU_10 40S ribosomal protein S6-A (chains T)
MKLNISYPVNGSQKTFEIDDEHRIRVFFDKRIGQEVDGEAVGDEFKGYVFKISGGNDKQG
FPMKQGVLLPTRIKLLLTKNVSCYRPRRDGERKRKSVRGAIVGPDLAVLALVIVKKGEQE
LEGLTDTTVPKRLGPKRANNIRKFFGLSKEDDVRDFVIRREVTKGEKTYTKAPKIQRLVT
PQRLQRKRHQRALKVRNAQAQREAAAEYAQLLAKRLSERKAEKAEIRK
Sequence of entity 11 (U), FASTA
>6TNU_11 40S ribosomal protein S7-A (chains U)
PQAKILSQAPTELELQVAQAFVELENSSPELKAELRPLQFKSIREIDVAGGKKALAIFVP
VPSLAGFHKVQTKLTRELEKKFQDRHVIFLAERRILPKPSRTSRQVQKRPRSRTLTAVHD
KILEDLVFPTEIVGKRVRYLVGGNKIQKVLLDSKDVQQIDYKLESFQAVYNKLTGKQIVF
EIPS
Sequence of entity 12 (V), FASTA
>6TNU_12 40S ribosomal protein S8 (chains V)
GISRDSRHKRSATGAKRAQFRKKRKFELGRQPANTKIGAKRIHSVRTRGGNKKYRALRIE
TGNFSWASEGISKKTRIAGVVYHPSNNELVRTNTLTKAAIVQIDATPFRQWFEAHYGQTL
GKKSKNAERKWAARAASAKIESSVESQFSAGRLYACISSRPGQSGRCDGYILEGEELAFY
LRRLTAK
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 7 |
| SPD | Spermidine | C7 H19 N3 | 1 |
| 3HE | 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2… | C15 H23 N O4 | 1 |
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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