8IPB: 40S ribosomal protein eS24
Wheat 80S ribosome pausing on AUG-Stop with cycloheximide. Determined by electron microscopy at 3.4 Å resolution. Released 21 Feb 2024.
- Method
- Electron microscopy
- Resolution
- 3.4 Å
- Organisms
- Triticum aestivum, Oryza sativa
- Chains
- 79
- Atoms
- 197,701
- Mol. weight
- 3193.94 kDa
- Ligands
- MG, ZN, 3HE
- Released
- 21 Feb 2024
Explore 8IPB in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8IPB contains 490 α-helices and 500 β-strands across 73 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 AA: 16 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-39 | 2 | |
| β-strand | 49 | 1 | 41 |
| α-helix | 52-66 | 15 | |
| α-helix | 71-74 | 4 | |
| α-helix | 79-81 | 3 | |
| α-helix | 82-94 | 13 | |
| α-helix | 101-109 | 9 | |
| α-helix | 111-112 | 2 | |
| α-helix | 113-117 | 5 | |
| β-strand | 129-130 | 2 | 42 |
| α-helix | 132-140 | 9 | |
| β-strand | 146-150 | 5 | 42 |
| α-helix | 157-160 | 4 | |
| α-helix | 162-168 | 7 | |
| β-strand | 173-176 | 4 | 42 |
| α-helix | 179-186 | 8 | |
| β-strand | 193-196 | 4 | 42 |
| α-helix | 204-214 | 11 | |
| α-helix | 215-219 | 5 | |
| α-helix | 222-225 | 4 | |
| α-helix | 236-249 | 14 | |
Chain AB: 5 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| β-strand | 22 | 1 | 43 |
| α-helix | 24-27 | 4 | |
| α-helix | 38-51 | 14 | |
| α-helix | 55-66 | 12 | |
| α-helix | 69-80 | 12 | |
| α-helix | 83-101 | 19 | |
Chain ba: 3 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 11 | 1 | 4 |
| β-strand | 14-20 | 7 | 4 |
| β-strand | 25-33 | 9 | 4 |
| α-helix | 42-53 | 12 | |
| β-strand | 63-64 | 2 | 4 |
| β-strand | 74-82 | 9 | 4 |
| α-helix | 85-90 | 6 | |
| α-helix | 94-99 | 6 | |
Chain BA: 9 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-18 | 2 | |
| α-helix | 24-26 | 3 | |
| α-helix | 28-31 | 4 | |
| β-strand | 39-42 | 4 | 50 |
| α-helix | 52-54 | 3 | |
| β-strand | 60-68 | 9 | 50 |
| β-strand | 71-80 | 10 | 50 |
| β-strand | 83-92 | 10 | 50 |
| α-helix | 93-95 | 3 | |
| β-strand | 96-98 | 3 | 50 |
| α-helix | 103-121 | 19 | |
| α-helix | 130-132 | 3 | |
| α-helix | 135-138 | 4 | |
| β-strand | 139-141 | 3 | 51 |
| β-strand | 146-148 | 3 | 23 |
| α-helix | 151-155 | 5 | |
Chain bb: 7 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 27-32 | 6 | 147 |
| β-strand | 44-49 | 6 | 147 |
| α-helix | 57-60 | 4 | |
| β-strand | 65-69 | 5 | 147 |
| α-helix | 71-74 | 4 | |
| β-strand | 83-91 | 9 | 147 |
| β-strand | 96-104 | 9 | 147 |
| α-helix | 107-113 | 7 | |
| β-strand | 118 | 1 | 148 |
| β-strand | 120-129 | 10 | 147 |
| β-strand | 133-142 | 10 | 147 |
| β-strand | 154 | 1 | 148 |
| α-helix | 160-175 | 16 | |
| α-helix | 181-188 | 8 | |
| α-helix | 192-198 | 7 | |
| β-strand | 208-219 | 12 | 147 |
| α-helix | 225-231 | 7 | |
Chain BB: 7 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 8-11 | 4 | |
| α-helix | 16-39 | 24 | |
| α-helix | 44-46 | 3 | |
| α-helix | 47-74 | 28 | |
| α-helix | 90-93 | 4 | |
| α-helix | 98-102 | 5 | |
| α-helix | 106-113 | 8 | |
| β-strand | 120-122 | 3 | 52 |
Chain ca: 9 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4 | 1 | 6 |
| α-helix | 23-25 | 3 | |
| α-helix | 26-28 | 3 | |
| β-strand | 29 | 1 | 6 |
| β-strand | 36-38 | 3 | 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 | 73-85 | 13 | 8 |
| α-helix | 89-94 | 6 | |
| β-strand | 96-97 | 2 | 7 |
| β-strand | 101-105 | 5 | 8 |
| α-helix | 108-115 | 8 | |
| α-helix | 156-164 | 9 | |
| 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 CA: 6 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 9-13 | 5 | 56 |
| β-strand | 22-29 | 8 | 56 |
| β-strand | 40-48 | 9 | 56 |
| α-helix | 49-53 | 5 | |
| α-helix | 59-65 | 7 | |
| β-strand | 69-76 | 8 | 56 |
| α-helix | 77-79 | 3 | |
| β-strand | 80-86 | 7 | 56 |
| α-helix | 105-125 | 21 | |
| α-helix | 129-132 | 4 | |
| α-helix | 134-135 | 2 | |
65 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 uS12 | 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 |
67 more molecules are not listed.
Sequence of entity 1 (aa), FASTA
>8IPB_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
>8IPB_2 40S ribosomal protein eS24 (chains ba)
MADAKTAPAVTLRTRKFMTNRLLSRKQFVLEVIHPGRANVSKADLKERLAKIYEVKDSNC
IFVFKFRTHFGGGKSTGFGLIYDNLEAAKKFEPKYRLIRNGLATKVEKSRKQIKERKNRT
KKIRGVKKTKAGDAKKK
Sequence of entity 3 (ca), FASTA
>8IPB_3 40S ribosomal protein eS8 (chains ca)
MGISRDSMHKRRATGGKQKAWRKKRKYELGRQPANTKLSSNKTVRRVRVRGGNVKWRALR
LDTGNFSWGSEAVTRKTRLLDVVYNSSNNELVRTQTLVKNAIVQVDAAPFKQWYLTHYGV
EIGRKKKAAAAAKKEPAEGQEAEVAAAATEEAKKSNNVQRKLEKRQQGRTLDSHIEEQFS
GGRLLACISSRPGQCGRADGYILEGKELEFYMRKLQKKKGKGATA
Sequence of entity 4 (da), FASTA
>8IPB_4 40S ribosomal protein eS10 (chains da)
MIISKKNRNEICKYLFQEGVLYAKKDYNLAKHPQIDVPNLQVIKLMQSFKSKEYVRETFS
WQHYYWYLTNDGIEFLRNFLNLPSEIVPATLKKSARPPGRPLGSGPPGDRPRGPPRFEGD
RPRYGDRDGYRGGPRGAPGDFGGEKGGAPAEFQPSFRSSGGGGFGRGGGGGFGRGGGGGG
GFGASPME
Sequence of entity 5 (ga), FASTA
>8IPB_5 40S ribosomal protein uS12 (chains ga)
MGKTRGMGAGRKLKTHRRNQRWADKAYKKSHLGNEWKKPFAGSSHAKGIVLEKIGIEAKQ
PNSAIRKCARVQLVKNGKKIAAFVPNDGCLNFIEENDEVLIAGFGRKGHAVGDIPGVRFK
VVKVSGVSLLALFKEKKEKPRS
Sequence of entity 6 (ha), FASTA
>8IPB_6 RACK1 (chains ha)
MAGAQESLVYAGVMRGHNDVVTAIATPIDNSPFIVSSSRDKSLLVWDLTNPIQATQDSSS
EYGVPFRRLTGHGHFVQDVVLSSDGQFALSGSWDGELRLWDLSTGVTTRRFVGHEKDVLS
VAFSIDNRQIVSASRDRTIKLWNTLGECKYTIGGDLGGGEGHTGWVSCVRFSPNNFAPTI
VSGSWDRSVKVWNLTNCKLRCTLDGHGGYVSAVAVSPDGSLCASGGKDGVTLLWDLTEGK
RLYSLDAGSIINSLCFSPNRYWLCAATQDSIKIWDLESKHIVQDLRPEVPVSTKQMLYCT
CLSWSADGSTLYAGYTDGTIRIYKISGFSYSS
Sequence of entity 7 (ia), FASTA
>8IPB_7 40S ribosomal protein uS3 (chains ia)
MATQISKKKKFVSDGVFYAELNEMLTRELAEDGYSGVEVRVTPMRTEIIIRATRTQNVLG
EKGRRIRELTSVVQKRFNFLENGVELYAEKVVNRGLCAIAQAESLRYKLLGGLAVRRACY
GVLRFVMESGAKGCEVIVSGKLRAQRAKSMKFKDGYMISSGQPVNEYIDAAVRHVLLRQG
VLGIKVKIMLDWDPKGKLGPTTPLPDLVTIHPPKEENELRPPALVEV
Sequence of entity 8 (ja), FASTA
>8IPB_8 40S ribosomal protein eS4 (chains ja)
MARGLKKHLKRLNAPSHWMLDKLGGAFAPKPSSGPHKARECLPLILILRNRLKYALTYRE
VQSILMQRHIMVDGKVRTDKTYPAGFMDIISIPKTGENYRLLYDTKGRFRLHSVRDEDAK
FKLCKVRSVQFGQKGIPYLNTYDGRTIRYPDPLIKANDTIKLDLETNKIVDFIKFDVGNV
VMVTGGRNTGRVGVIKNREKHKGTFETIHVEDAQGHQFATRLGNVFTIGKGTKPWVSLPK
GKGIKLTIIEEQRKRDAAAQAAAKA
Sequence of entity 9 (ka), FASTA
>8IPB_9 40S ribosomal protein uS7 (chains ka)
MAVVEPVPGGDVKLFNRWTFEDVQVSDISLNDYLAVTSMKHYTFLPHSAGRYSAKRFRKA
QCPIIERLTNSLMMHGRNNGKKIMAVRIIKHTMEIIHLLTDANPIQIIVDAIINSGPRED
ATRIGSAGVVRRQAVDISPLRRVNQAIYLLTTGARESAFRNVKTIAECLADELINAAKGS
SNSYAIKKKDEIERVAKANR
Sequence of entity 10 (la), FASTA
>8IPB_10 40S ribosomal protein uS9 (chains la)
MAAVLTRPTPGTVQCFGRKKTAVAVAYCKPGRGLIKVNGAPIELIRPEMLRLKAFEPILL
AGRSRFKDIDMRIRVRGGGKTSQIYSIRQAIAKSLVAYYQKYVDEAAKKEVKEIFARYDR
TLLVADPRRCEPKKFGGRGARARFQKSYR
Sequence of entity 11 (ma), FASTA
>8IPB_11 40S ribosomal protein uS10 (chains ma)
MATELAYAPPMKSGKLGFEGTQEVQHRIRITLSSKSVKNLEKVCSDLVKGAKEKQLKVKG
PVRMPTKVLNITTRKSPCGEGTNTWDRFEMRVHKRVIDLVSSPDVVKQITSITIEPGVEV
EVTISDQ
Sequence of entity 12 (na), FASTA
>8IPB_12 40S ribosomal protein uS11 (chains na)
MSSKRKTREPKEENVTLGPAVREGEHVFGVAHIFASFNDTFIHVTDLSGRETLVRITGGM
KVKADRDESSPYAAMLASQDVATRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALA
RSGMKIGRIEDVTPVPTDSTRRKGGRRGRRL
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 265 |
| ZN | Zinc ion | Zn | 4 |
| 3HE | 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2… | C15 H23 N O4 | 1 |
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
- 8IP9 3.0 Å, Wheat 40S ribosome in complex with a tRNAi
- 8IPA 3.4 Å, Wheat 80S ribosome stalled on AUG-Stop boron dependently with cycloheximide
Browse structure collections
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