6SNT: Yeast 80S ribosome stalled on SDD1 mRNA
Yeast 80S ribosome stalled on SDD1 mRNA. Determined by electron microscopy at 2.8 Å resolution. Released 4 Mar 2020.
- Method
- Electron microscopy
- Resolution
- 2.8 Å
- Organism
- Saccharomyces cerevisiae
- Chains
- 81
- Atoms
- 201,787
- Mol. weight
- 3165.15 kDa
- Ligands
- ZN, MG
- Released
- 4 Mar 2020
Explore 6SNT in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6SNT contains 459 α-helices and 522 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 a: 3 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 21-22 | 2 | 7 |
| β-strand | 29-30 | 2 | 7 |
| β-strand | 38-43 | 6 | 8 |
| α-helix | 50-56 | 7 | |
| β-strand | 57 | 1 | 113 |
| β-strand | 66-71 | 6 | 8 |
| α-helix | 75-80 | 6 | |
| α-helix | 91-93 | 3 | |
Chain A: 9 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-10 | 2 | |
| α-helix | 11-19 | 9 | |
| β-strand | 24-27 | 4 | 4 |
| β-strand | 37 | 1 | 5 |
| β-strand | 45-47 | 3 | 4 |
| β-strand | 48 | 1 | 5 |
| α-helix | 50-65 | 16 | |
| α-helix | 70-72 | 3 | |
| β-strand | 74-77 | 4 | 6 |
| α-helix | 80-82 | 3 | |
| α-helix | 83-92 | 10 | |
| β-strand | 96-99 | 4 | 6 |
| β-strand | 121-123 | 3 | 6 |
| α-helix | 130-138 | 9 | |
| β-strand | 143-147 | 5 | 6 |
| β-strand | 159-161 | 3 | 6 |
| α-helix | 167-185 | 19 | |
| α-helix | 200-202 | 3 | |
Chain aa: 3 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-12 | 4 | |
| α-helix | 20-33 | 14 | |
| β-strand | 37-38 | 2 | 78 |
| β-strand | 45-51 | 7 | 78 |
| β-strand | 54-57 | 4 | 78 |
| β-strand | 63-65 | 3 | 78 |
| α-helix | 74-90 | 17 | |
Chain ab: 3 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3 | 1 | 158 |
| β-strand | 7-12 | 6 | 159 |
| β-strand | 19-27 | 9 | 159 |
| α-helix | 28-29 | 2 | |
| α-helix | 32-34 | 3 | |
| α-helix | 38-47 | 10 | |
| β-strand | 66-74 | 9 | 159 |
| β-strand | 80-88 | 9 | 159 |
| β-strand | 92 | 1 | 158 |
Chain AB: 3 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 17-18 | 2 | 25 |
| β-strand | 22-25 | 4 | 26 |
| β-strand | 27 | 1 | 27 |
| β-strand | 31 | 1 | 28 |
| β-strand | 33-39 | 7 | 26 |
| α-helix | 48-50 | 3 | |
| β-strand | 51-52 | 2 | 25 |
| β-strand | 57-62 | 6 | 26 |
| β-strand | 65 | 1 | 28 |
| β-strand | 73-80 | 8 | 26 |
| β-strand | 85-86 | 2 | 29 |
| β-strand | 92-95 | 4 | 29 |
| β-strand | 99-102 | 4 | 26 |
| β-strand | 103 | 1 | 30 |
| β-strand | 109 | 1 | 30 |
| β-strand | 114 | 1 | 27 |
| β-strand | 118 | 1 | 31 |
| α-helix | 120-123 | 4 | |
| α-helix | 127-131 | 5 | |
| β-strand | 136 | 1 | 31 |
Chain ac: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-22 | 20 | |
Chain ad: 2 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 80-90 | 11 | |
| β-strand | 94-96 | 3 | 146 |
| β-strand | 103 | 1 | 146 |
| β-strand | 121-123 | 3 | 146 |
| α-helix | 124-127 | 4 | |
Chain ae: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-19 | 13 | |
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 |
|---|
| Saccharomyces cerevisiae S288C 18S ribosomal RNA (RDN18-1), rRNA | 2 | RNA | 1800 | Saccharomyces cerevisiae | |
| 40S ribosomal protein S0-A | A | protein | 252 | Saccharomyces cerevisiae | P32905 (AlphaFold model) |
| 40S ribosomal protein S1-A | B | protein | 255 | Saccharomyces cerevisiae | P33442 (AlphaFold model) |
| 40S ribosomal protein S15 | P | protein | 142 | Saccharomyces cerevisiae | Q01855 (AlphaFold model) |
| 40S ribosomal protein S2 | C | protein | 254 | Saccharomyces cerevisiae | P25443 (AlphaFold model) |
| 40S ribosomal protein S3 | D | protein | 240 | Saccharomyces cerevisiae | P05750 |
| 40S ribosomal protein S4-A | E | protein | 261 | Saccharomyces cerevisiae | P0CX35 |
| 40S ribosomal protein S5 | F | protein | 225 | Saccharomyces cerevisiae | P26783 |
| 40S ribosomal protein S6-A | G | protein | 236 | Saccharomyces cerevisiae | P0CX37 |
| 40S ribosomal protein S7-A | H | protein | 190 | Saccharomyces cerevisiae | P26786 |
| 40S ribosomal protein S8-A | I | protein | 200 | Saccharomyces cerevisiae | P0CX39 |
| 40S ribosomal protein S9-A | J | protein | 197 | Saccharomyces cerevisiae | O13516 |
69 more molecules are not listed.
Sequence of entity 1 (2), FASTA
>6SNT_1 Saccharomyces cerevisiae S288C 18S ribosomal RNA (RDN18-1), rRNA (chains 2)
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 (A), FASTA
>6SNT_2 40S ribosomal protein S0-A (chains A)
MSLPATFDLTPEDAQLLLAANTHLGARNVQVHQEPYVFNARPDGVHVINVGKTWEKLVLA
ARIIAAIPNPEDVVAISSRTFGQRAVLKFAAHTGATPIAGRFTPGSFTNYITRSFKEPRL
VIVTDPRSDAQAIKEASYVNIPVIALTDLDSPSEFVDVAIPCNNRGKHSIGLIWYLLARE
VLRLRGALVDRTQPWSIMPDLYFYRDPEEVEQQVAEEATTEEAGEEEAKEEVTEEQAEAT
EWAEENADNVEW
Sequence of entity 3 (B), FASTA
>6SNT_3 40S ribosomal protein S1-A (chains B)
MAVGKNKRLSKGKKGQKKRVVDPFTRKEWFDIKAPSTFENRNVGKTLVNKSTGLKSASDA
LKGRVVEVCLADLQGSEDHSFRKIKLRVDEVQGKNLLTNFHGMDFTTDKLRSMVRKWQTL
IEANVTVKTSDDYVLRIFAIAFTRKQANQVKRHSYAQSSHIRAIRKVISEILTKEVQGST
LAQLTSKLIPEVINKEIENATKDIFPLQNIHVRKVKLLKQPKFDVGALMALHGEGSGEEK
GKKVTGFKDEVLETV
Sequence of entity 4 (P), FASTA
>6SNT_4 40S ribosomal protein S15 (chains P)
MSQAVNAKKRVFKTHSYRGVDLEKLLEMSTEDFVKLAPARVRRRFARGMTSKPAGFMKKL
RAAKLAAPENEKPAPVRTHMRNMIIVPEMIGSVVGIYNGKAFNQVEIRPEMLGHYLGEFS
ITYTPVRHGRAGATTSRFIPLK
Sequence of entity 5 (C), FASTA
>6SNT_5 40S ribosomal protein S2 (chains C)
MSAPEAQQQKRGGFGGRNRGRPNRRGPRNTEEKGWVPVTKLGRLVKAGKITTIEEIFLHS
LPVKEFQIIDTLLPGLQDEVMNIKPVQKQTRAGQRTRFKAVVVVGDSNGHVGLGIKTAKE
VAGAIRAGIIIAKLSVIPIRRGYWGTNLGQPHSLATKTTGKCGSVTVRLIPAPRGSGIVA
SPAVKKLLQLAGVEDVYTQSNGKTRTLENTLKAAFVAIGNTYGFLTPNLWAEQPLPVSPL
DIYSDEASAQKKRF
Sequence of entity 6 (D), FASTA
>6SNT_6 40S ribosomal protein S3 (chains D)
MVALISKKRKLVADGVFYAELNEFFTRELAEEGYSGVEVRVTPTKTEVIIRATRTQDVLG
ENGRRINELTLLVQKRFKYAPGTIVLYAERVQDRGLSAVAQAESMKFKLLNGLAIRRAAY
GVVRYVMESGAKGCEVVVSGKLRAARAKAMKFADGFLIHSGQPVNDFIDTATRHVLMRQG
VLGIKVKIMRDPAKSRTGPKALPDAVTIIEPKEEEPILAPSVKDYRPAEETEAQAEPVEA
Sequence of entity 7 (E), FASTA
>6SNT_7 40S ribosomal protein S4-A (chains E)
MARGPKKHLKRLAAPHHWLLDKLSGCYAPRPSAGPHKLRESLPLIVFLRNRLKYALNGRE
VKAILMQRHVKVDGKVRTDTTYPAGFMDVITLDATNENFRLVYDVKGRFAVHRITDEEAS
YKLGKVKKVQLGKKGVPYVVTHDGRTIRYPDPNIKVNDTVKIDLASGKITDFIKFDAGKL
VYVTGGRNLGRIGTIVHKERHDGGFDLVHIKDSLDNTFVTRLNNVFVIGEQGKPYISLPK
GKGIKLSIAEERDRRRAQQGL
Sequence of entity 8 (F), FASTA
>6SNT_8 40S ribosomal protein S5 (chains F)
MSDTEAPVEVQEDFEVVEEFTPVVLATPIPEEVQQAQTEIKLFNKWSFEEVEVKDASLVD
YVQVRQPIFVAHTAGRYANKRFRKAQCPIIERLTNSLMMNGRNNGKKLKAVRIIKHTLDI
INVLTDQNPIQVVVDAITNTGPREDTTRVGGGGAARRQAVDVSPLRRVNQAIALLTIGAR
EAAFRNIKTIAETLAEELINAAKGSSTSYAIKKKDELERVAKSNR
Sequence of entity 9 (G), FASTA
>6SNT_9 40S ribosomal protein S6-A (chains G)
MKLNISYPVNGSQKTFEIDDEHRIRVFFDKRIGQEVDGEAVGDEFKGYVFKISGGNDKQG
FPMKQGVLLPTRIKLLLTKNVSCYRPRRDGERKRKSVRGAIVGPDLAVLALVIVKKGEQE
LEGLTDTTVPKRLGPKRANNIRKFFGLSKEDDVRDFVIRREVTKGEKTYTKAPKIQRLVT
PQRLQRKRHQRALKVRNAQAQREAAAEYAQLLAKRLSERKAEKAEIRKRRASSLKA
Sequence of entity 10 (H), FASTA
>6SNT_10 40S ribosomal protein S7-A (chains H)
MSAPQAKILSQAPTELELQVAQAFVELENSSPELKAELRPLQFKSIREIDVAGGKKALAI
FVPVPSLAGFHKVQTKLTRELEKKFQDRHVIFLAERRILPKPSRTSRQVQKRPRSRTLTA
VHDKILEDLVFPTEIVGKRVRYLVGGNKIQKVLLDSKDVQQIDYKLESFQAVYNKLTGKQ
IVFEIPSETH
Sequence of entity 11 (I), FASTA
>6SNT_11 40S ribosomal protein S8-A (chains I)
MGISRDSRHKRSATGAKRAQFRKKRKFELGRQPANTKIGAKRIHSVRTRGGNKKYRALRI
ETGNFSWASEGISKKTRIAGVVYHPSNNELVRTNTLTKAAIVQIDATPFRQWFEAHYGQT
LGKKKNVKEEETVAKSKNAERKWAARAASAKIESSVESQFSAGRLYACISSRPGQSGRCD
GYILEGEELAFYLRRLTAKK
Sequence of entity 12 (J), FASTA
>6SNT_12 40S ribosomal protein S9-A (chains J)
MPRAPRTYSKTYSTPKRPYESSRLDAELKLAGEFGLKNKKEIYRISFQLSKIRRAARDLL
TRDEKDPKRLFEGNALIRRLVRVGVLSEDKKKLDYVLALKVEDFLERRLQTQVYKLGLAK
SVHHARVLITQRHIAVGKQIVNIPSFMVRLDSEKHIDFAPTSPFGGARPGRVARRNAARK
AEASGEAADEADEADEE
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 7 |
| MG | Magnesium ion | Mg | 87 |
Primary citation
RQT complex dissociates ribosomes collided on endogenous RQC substrate SDD1. Matsuo, Y., Tesina, P., Nakajima, S. et al. Nat Struct Mol Biol (2020) 27:323-332. DOI 10.1038/s41594-020-0393-9 · 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
Browse structure collections
About this viewer
MolViewer shows 6SNT directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.