8IP9: Wheat 40S ribosome
Wheat 40S ribosome in complex with a tRNAi. Determined by electron microscopy at 3.0 Å resolution. Released 21 Feb 2024.
- Method
- Electron microscopy
- Resolution
- 3.0 Å
- Organisms
- Triticum aestivum, Oryza sativa
- Chains
- 35
- Atoms
- 73,028
- Mol. weight
- 1210.39 kDa
- Ligands
- MG, ZN
- Released
- 21 Feb 2024
Explore 8IP9 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8IP9 contains 187 α-helices and 217 β-strands across 32 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 ba: 4 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 11 | 1 | 3 |
| β-strand | 14-20 | 7 | 4 |
| β-strand | 25-30 | 6 | 4 |
| β-strand | 33 | 1 | 3 |
| α-helix | 42-53 | 12 | |
| β-strand | 61-64 | 4 | 4 |
| β-strand | 77-82 | 6 | 4 |
| α-helix | 85-90 | 6 | |
| α-helix | 94-100 | 7 | |
| α-helix | 116-119 | 4 | |
Chain bb: 9 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 27-33 | 7 | 63 |
| β-strand | 44-49 | 6 | 63 |
| α-helix | 58-61 | 4 | |
| β-strand | 65-68 | 4 | 63 |
| α-helix | 71-74 | 4 | |
| α-helix | 77-79 | 3 | |
| β-strand | 84-91 | 8 | 63 |
| β-strand | 95-103 | 9 | 63 |
| α-helix | 107-113 | 7 | |
| β-strand | 118 | 1 | 64 |
| β-strand | 120-128 | 9 | 63 |
| β-strand | 134-142 | 9 | 63 |
| α-helix | 145-146 | 2 | |
| β-strand | 154 | 1 | 64 |
| α-helix | 160-175 | 16 | |
| α-helix | 181-188 | 8 | |
| α-helix | 192-200 | 9 | |
| β-strand | 208-219 | 12 | 63 |
| α-helix | 225-231 | 7 | |
Chain ca: 10 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4 | 1 | 6 |
| α-helix | 11-12 | 2 | |
| α-helix | 23-25 | 3 | |
| α-helix | 26-28 | 3 | |
| β-strand | 29 | 1 | 6 |
| β-strand | 37-38 | 2 | 7 |
| β-strand | 43-48 | 6 | 7 |
| α-helix | 50-52 | 3 | |
| β-strand | 54-61 | 8 | 7 |
| β-strand | 63-68 | 6 | 8 |
| β-strand | 73-84 | 12 | 8 |
| α-helix | 89-93 | 5 | |
| β-strand | 96 | 1 | 7 |
| β-strand | 102-105 | 4 | 8 |
| α-helix | 108-115 | 8 | |
| α-helix | 156-162 | 7 | |
| α-helix | 173-181 | 9 | |
| β-strand | 184-188 | 5 | 8 |
| α-helix | 192-195 | 4 | |
| β-strand | 199-202 | 4 | 8 |
| α-helix | 205-215 | 11 | |
Chain cb: 4 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2 | 1 | 65 |
| β-strand | 8 | 1 | 65 |
| α-helix | 13-15 | 3 | |
| β-strand | 16 | 1 | 66 |
| β-strand | 23 | 1 | 66 |
| β-strand | 32-37 | 6 | 67 |
| α-helix | 38-39 | 2 | |
| β-strand | 49-54 | 6 | 67 |
| α-helix | 56-61 | 6 | |
| α-helix | 64-72 | 9 | |
Chain da: 3 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-17 | 13 | |
| β-strand | 20-22 | 3 | 13 |
| α-helix | 40-51 | 12 | |
| β-strand | 55-58 | 4 | 13 |
| β-strand | 65-68 | 4 | 13 |
| α-helix | 70-77 | 8 | |
Chain db: 4 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 20-22 | 3 | 1 |
| β-strand | 29-31 | 3 | 1 |
| β-strand | 36-43 | 8 | 2 |
| α-helix | 47-49 | 3 | |
| α-helix | 51-54 | 4 | |
| β-strand | 57 | 1 | 44 |
| β-strand | 66-73 | 8 | 2 |
| α-helix | 75-80 | 6 | |
| α-helix | 91-93 | 3 | |
Chain eb: 8 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 23-35 | 13 | |
| α-helix | 41-63 | 23 | |
| α-helix | 69-84 | 16 | |
| α-helix | 103-107 | 5 | |
| α-helix | 111-117 | 7 | |
| α-helix | 124-131 | 8 | |
| β-strand | 136-137 | 2 | 5 |
| β-strand | 142 | 1 | 5 |
| α-helix | 153-155 | 3 | |
| β-strand | 159-160 | 2 | 5 |
| α-helix | 173-182 | 10 | |
Chain fb: 10 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 50-56 | 7 | |
| α-helix | 64-67 | 4 | |
| α-helix | 77-82 | 6 | |
| β-strand | 88-99 | 12 | 9 |
| β-strand | 104-114 | 11 | 9 |
| β-strand | 120-121 | 2 | 10 |
| β-strand | 122-128 | 7 | 9 |
| α-helix | 131-144 | 14 | |
| β-strand | 147-148 | 2 | 10 |
| β-strand | 152 | 1 | 11 |
| β-strand | 163 | 1 | 11 |
| β-strand | 168-172 | 5 | 12 |
| β-strand | 175-181 | 7 | 12 |
| β-strand | 188-189 | 2 | 12 |
| α-helix | 192-201 | 10 | |
| β-strand | 206-211 | 6 | 12 |
| α-helix | 217-229 | 13 | |
| α-helix | 230-232 | 3 | |
| α-helix | 237-239 | 3 | |
| α-helix | 242-243 | 2 | |
| α-helix | 249-252 | 4 | |
24 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 | aa | RNA | 1810 | Triticum aestivum | |
| 40S ribosomal protein eS24 | ba | protein | 137 | Triticum aestivum | A0A3B6PK86 (AlphaFold model) |
| 40S ribosomal protein eS8 | ca | protein | 225 | Triticum aestivum | A0A3B6AYT7 (AlphaFold model) |
| 40S ribosomal protein eS10 | da | protein | 188 | Triticum aestivum | W5AUH7 (AlphaFold model) |
| 40S ribosomal protein S23 | ga | protein | 142 | Triticum aestivum | W5FV77 (AlphaFold model) |
| RACK1 | ha | protein | 332 | Triticum aestivum | W5D4F5 |
| 40S ribosomal protein uS3 | ia | protein | 227 | Triticum aestivum | Q8L804 |
| 40S ribosomal protein eS4 | ja | protein | 265 | Triticum aestivum | A0A1D5SLI4 |
| 40S ribosomal protein uS7 | ka | protein | 200 | Triticum aestivum | A0A9R1JSD6 |
| 40S ribosomal protein uS9 | la | protein | 149 | Triticum aestivum | A0A3B6HX49 |
| 40S ribosomal protein uS10 | ma | protein | 127 | Triticum aestivum | U5HTD8 |
| 40S ribosomal protein uS11 | na | protein | 151 | Triticum aestivum | A0A3B6SS17 |
23 more molecules are not listed.
Sequence of entity 1 (aa), FASTA
>8IP9_1 18S ribosomal RNA (chains aa)
UACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUGC
AAGUAUGAACCAAUUUGAACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUG
UUUGAUGGUACGUGCUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCAACAAA
CCCCGACUUCUGGGAGGGGCGCAUUUAUUAGAUAAAAGGCUGACGCGGGCUCUGCUCGCU
GAUCCGAUGAUUCAUGAUAACUCGACGGAUCGCACGGCCUUCGUGCCGGCGACGCAUCAU
UCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGGGGCCUACCAUGGUGGUGACGG
GUGACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCA
AGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACGGGGAGGUAGUGACAAUAAAU
AACAAUACCGGGCGCAUUAGUGUCUGGUAAUUGGAAUGAGUACAAUCUAAAUCCCUUAAC
GAGGAUCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGC
GUAUAUUUAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGACCUUGGGCCGGGUCGGCCGG
UCCGCCUCACGGCGAGCACCGACCUACUCGACCCUUCGGCCGGCAUCGCGCUCCUAGCCU
UAAUUGGCCGGGUCGUGUUUCCGGCAUCGUUACUUUGAAGAAAUUAGAGUGCUCAAAGCA
AGCCAUCGCUCUGGAUACAUUAGCAUGGGAUAACAUCAUAGGAUUCCGGUCCUAUUGUGU
UGGCCUUCGGGAUCGGAGUAAUGAUUAAUAGGGACAGUCGGGGGCAUUCGUAUUUCAUAG
UCAGAGGUGAAAUUCUUGGAUUUAUGAAAGACGAACAACUGCGAAAGCAUUUGCCAAGGA
UGUUUUCAUUAAUCAAGAACGAAAGUUGGGGGCUCGAAGACGAUCAGAUACCGUCCUAGU
CUCAACCAUAAACGAUGCCGACCAGGGAUCGGCGGAUGUUGCUUAUAGGACUCCGCCGGC
ACCUUAUGAGAAAUCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACU
UAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGCUUAAUUUGACUCAACA
CGGGGAAACUUACCAGGUCCAGACAUAGCAAGGAUUGACAGACUGAGAGCUCUUUCUUGA
UUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUC
CGUUAACGAACGAGACCUCAGCCUGCUAACUAGCUAUGCGGAGCCAUCCCUCCGCAGCUA
GCUUCUUAGAGGGACUAUGGCCGUUUAGGCCACGGAAGUUUGAGGCAAUAACAGGUCUGU
CAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUGUAUUCAACGAGUAUAUA
GCCUUGGCCGACAGGCCCGGGUAAUCUUGGGAAAUUUCAUCGUGAUGGGGAUAGAUCAUU
GCAAUUGUUGGUCUUCAACGAGGAAUGCCUAGUAAGCGCGAGUCAUCAGCUCGCGUUGAC
UACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUGGUCCGGUGAA
GUGUUCGGAUCGCGGCGACGGGGGCGGUUCGCCGCCCCCGACGUCGCGAGAAGUCCAUUG
AACCUUAUCAUUUAGAGGAAGCAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGA
AGGAUCAUUG
Sequence of entity 2 (ba), FASTA
>8IP9_2 40S ribosomal protein eS24 (chains ba)
MADAKTAPAVTLRTRKFMTNRLLSRKQFVLEVIHPGRANVSKADLKERLAKIYEVKDSNC
IFVFKFRTHFGGGKSTGFGLIYDNLEAAKKFEPKYRLIRNGLATKVEKSRKQIKERKNRT
KKIRGVKKTKAGDAKKK
Sequence of entity 3 (ca), FASTA
>8IP9_3 40S ribosomal protein eS8 (chains ca)
MGISRDSMHKRRATGGKQKAWRKKRKYELGRQPANTKLSSNKTVRRVRVRGGNVKWRALR
LDTGNFSWGSEAVTRKTRLLDVVYNSSNNELVRTQTLVKNAIVQVDAAPFKQWYLTHYGV
EIGRKKKAAAAAKKEPAEGQEAEVAAAATEEAKKSNNVQRKLEKRQQGRTLDSHIEEQFS
GGRLLACISSRPGQCGRADGYILEGKELEFYMRKLQKKKGKGATA
Sequence of entity 4 (da), FASTA
>8IP9_4 40S ribosomal protein eS10 (chains da)
MIISKKNRNEICKYLFQEGVLYAKKDYNLAKHPQIDVPNLQVIKLMQSFKSKEYVRETFS
WQHYYWYLTNDGIEFLRNFLNLPSEIVPATLKKSARPPGRPLGSGPPGDRPRGPPRFEGD
RPRYGDRDGYRGGPRGAPGDFGGEKGGAPAEFQPSFRSSGGGGFGRGGGGGFGRGGGGGG
GFGASPME
Sequence of entity 5 (ga), FASTA
>8IP9_5 40S ribosomal protein S23 (chains ga)
MGKTRGMGAGRKLKTHRRNQRWADKAYKKSHLGNEWKKPFAGSSHAKGIVLEKIGIEAKQ
PNSAIRKCARVQLVKNGKKIAAFVPNDGCLNFIEENDEVLIAGFGRKGHAVGDIPGVRFK
VVKVSGVSLLALFKEKKEKPRS
Sequence of entity 6 (ha), FASTA
>8IP9_6 RACK1 (chains ha)
MAGAQESLVYAGVMRGHNDVVTAIATPIDNSPFIVSSSRDKSLLVWDLTNPIQATQDSSS
EYGVPFRRLTGHGHFVQDVVLSSDGQFALSGSWDGELRLWDLSTGVTTRRFVGHEKDVLS
VAFSIDNRQIVSASRDRTIKLWNTLGECKYTIGGDLGGGEGHTGWVSCVRFSPNNFAPTI
VSGSWDRSVKVWNLTNCKLRCTLDGHGGYVSAVAVSPDGSLCASGGKDGVTLLWDLTEGK
RLYSLDAGSIINSLCFSPNRYWLCAATQDSIKIWDLESKHIVQDLRPEVPVSTKQMLYCT
CLSWSADGSTLYAGYTDGTIRIYKISGFSYSS
Sequence of entity 7 (ia), FASTA
>8IP9_7 40S ribosomal protein uS3 (chains ia)
MATQISKKKKFVSDGVFYAELNEMLTRELAEDGYSGVEVRVTPMRTEIIIRATRTQNVLG
EKGRRIRELTSVVQKRFNFLENGVELYAEKVVNRGLCAIAQAESLRYKLLGGLAVRRACY
GVLRFVMESGAKGCEVIVSGKLRAQRAKSMKFKDGYMISSGQPVNEYIDAAVRHVLLRQG
VLGIKVKIMLDWDPKGKLGPTTPLPDLVTIHPPKEENELRPPALVEV
Sequence of entity 8 (ja), FASTA
>8IP9_8 40S ribosomal protein eS4 (chains ja)
MARGLKKHLKRLNAPSHWMLDKLGGAFAPKPSSGPHKARECLPLILILRNRLKYALTYRE
VQSILMQRHIMVDGKVRTDKTYPAGFMDIISIPKTGENYRLLYDTKGRFRLHSVRDEDAK
FKLCKVRSVQFGQKGIPYLNTYDGRTIRYPDPLIKANDTIKLDLETNKIVDFIKFDVGNV
VMVTGGRNTGRVGVIKNREKHKGTFETIHVEDAQGHQFATRLGNVFTIGKGTKPWVSLPK
GKGIKLTIIEEQRKRDAAAQAAAKA
Sequence of entity 9 (ka), FASTA
>8IP9_9 40S ribosomal protein uS7 (chains ka)
MAVVEPVPGGDVKLFNRWTFEDVQVSDISLNDYLAVTSMKHYTFLPHSAGRYSAKRFRKA
QCPIIERLTNSLMMHGRNNGKKIMAVRIIKHTMEIIHLLTDANPIQIIVDAIINSGPRED
ATRIGSAGVVRRQAVDISPLRRVNQAIYLLTTGARESAFRNVKTIAECLADELINAAKGS
SNSYAIKKKDEIERVAKANR
Sequence of entity 10 (la), FASTA
>8IP9_10 40S ribosomal protein uS9 (chains la)
MAAVLTRPTPGTVQCFGRKKTAVAVAYCKPGRGLIKVNGAPIELIRPEMLRLKAFEPILL
AGRSRFKDIDMRIRVRGGGKTSQIYSIRQAIAKSLVAYYQKYVDEAAKKEVKEIFARYDR
TLLVADPRRCEPKKFGGRGARARFQKSYR
Sequence of entity 11 (ma), FASTA
>8IP9_11 40S ribosomal protein uS10 (chains ma)
MATELAYAPPMKSGKLGFEGTQEVQHRIRITLSSKSVKNLEKVCSDLVKGAKEKQLKVKG
PVRMPTKVLNITTRKSPCGEGTNTWDRFEMRVHKRVIDLVSSPDVVKQITSITIEPGVEV
EVTISDQ
Sequence of entity 12 (na), FASTA
>8IP9_12 40S ribosomal protein uS11 (chains na)
MSSKRKTREPKEENVTLGPAVREGEHVFGVAHIFASFNDTFIHVTDLSGRETLVRITGGM
KVKADRDESSPYAAMLASQDVATRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALA
RSGMKIGRIEDVTPVPTDSTRRKGGRRGRRL
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 84 |
| ZN | Zinc ion | Zn | 2 |
Primary citation
Boric acid intercepts 80S ribosome migration from AUG-stop by stabilizing eRF1. Tanaka, M., Yokoyama, T., Saito, H. et al. Nat Chem Biol (2024) 20:605-614. DOI 10.1038/s41589-023-01513-0 · PubMed
Other PDB entries of the same protein (UniProt A0A3B6PK86 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 8JIW 2.88 Å, Atomic structure of wheat ribosome reveals unique features of the plant ribosomes
- 8IP8 2.9 Å, Wheat 80S ribosome stalled on AUG-Stop boron dependently
- 8IPA 3.4 Å, Wheat 80S ribosome stalled on AUG-Stop boron dependently with cycloheximide
- 8IPB 3.4 Å, Wheat 80S ribosome pausing on AUG-Stop with cycloheximide
Browse structure collections
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