8IPA: 40S ribosomal protein eS24
Wheat 80S ribosome stalled on AUG-Stop boron dependently 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
- 80
- Atoms
- 201,166
- Mol. weight
- 3243.45 kDa
- Ligands
- 3HE, ZN, MG
- Released
- 21 Feb 2024
Explore 8IPA in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8IPA contains 483 α-helices and 526 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 AA: 15 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 49 | 1 | 48 |
| α-helix | 52-66 | 15 | |
| α-helix | 71-74 | 4 | |
| α-helix | 79-81 | 3 | |
| α-helix | 82-94 | 13 | |
| α-helix | 100-112 | 13 | |
| α-helix | 113-117 | 5 | |
| α-helix | 122-125 | 4 | |
| β-strand | 129-130 | 2 | 49 |
| α-helix | 132-141 | 10 | |
| β-strand | 146-150 | 5 | 49 |
| α-helix | 156-158 | 3 | |
| α-helix | 162-168 | 7 | |
| β-strand | 173-176 | 4 | 49 |
| α-helix | 179-186 | 8 | |
| β-strand | 193-196 | 4 | 49 |
| α-helix | 201-203 | 3 | |
| α-helix | 204-218 | 15 | |
| α-helix | 222-225 | 4 | |
| α-helix | 236-249 | 14 | |
Chain AB: 6 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-7 | 3 | |
| β-strand | 22 | 1 | 50 |
| α-helix | 24-28 | 5 | |
| α-helix | 38-51 | 14 | |
| α-helix | 55-66 | 12 | |
| α-helix | 69-80 | 12 | |
| α-helix | 83-101 | 19 | |
Chain ba: 4 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 14-20 | 7 | 9 |
| β-strand | 25-30 | 6 | 9 |
| β-strand | 33 | 1 | 10 |
| α-helix | 42-53 | 12 | |
| β-strand | 61-64 | 4 | 9 |
| β-strand | 74 | 1 | 10 |
| β-strand | 77-82 | 6 | 9 |
| α-helix | 85-90 | 6 | |
| α-helix | 94-99 | 6 | |
| α-helix | 116-118 | 3 | |
Chain BA: 7 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-18 | 2 | |
| α-helix | 28-31 | 4 | |
| β-strand | 39-42 | 4 | 57 |
| α-helix | 52-54 | 3 | |
| α-helix | 55-57 | 3 | |
| β-strand | 60-68 | 9 | 57 |
| β-strand | 71-80 | 10 | 57 |
| β-strand | 83-92 | 10 | 57 |
| α-helix | 93-95 | 3 | |
| β-strand | 96-98 | 3 | 57 |
| α-helix | 103-121 | 19 | |
| β-strand | 139-141 | 3 | 58 |
| β-strand | 146-148 | 3 | 32 |
| α-helix | 151-153 | 3 | |
Chain bb: 6 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 27-32 | 6 | 159 |
| β-strand | 44-49 | 6 | 159 |
| α-helix | 57-61 | 5 | |
| β-strand | 65-69 | 5 | 160 |
| β-strand | 83-87 | 5 | 160 |
| β-strand | 91 | 1 | 159 |
| β-strand | 96 | 1 | 159 |
| β-strand | 99-104 | 6 | 160 |
| α-helix | 107-113 | 7 | |
| β-strand | 120-129 | 10 | 160 |
| β-strand | 133-142 | 10 | 160 |
| α-helix | 160-175 | 16 | |
| α-helix | 181-188 | 8 | |
| α-helix | 192-198 | 7 | |
| β-strand | 208-219 | 12 | 160 |
| 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 | 47-74 | 28 | |
| α-helix | 90-94 | 5 | |
| α-helix | 96-97 | 2 | |
| α-helix | 98-101 | 4 | |
| α-helix | 106-113 | 8 | |
| β-strand | 120-122 | 3 | 59 |
Chain bl: 13 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-24 | 16 | |
| β-strand | 33-38 | 6 | 4 |
| α-helix | 44-58 | 15 | |
| α-helix | 66-82 | 17 | |
| β-strand | 92-99 | 8 | 4 |
| β-strand | 107-113 | 7 | 4 |
| β-strand | 123-127 | 5 | 4 |
| α-helix | 134-140 | 7 | |
| β-strand | 145-151 | 7 | 5 |
| β-strand | 154-160 | 7 | 5 |
| β-strand | 166-172 | 7 | 5 |
| α-helix | 175-178 | 4 | |
| α-helix | 183-185 | 3 | |
| α-helix | 186-211 | 26 | |
| β-strand | 213 | 1 | 6 |
| β-strand | 220 | 1 | 6 |
| β-strand | 224-229 | 6 | 5 |
| α-helix | 234-239 | 6 | |
| α-helix | 245-248 | 4 | |
| β-strand | 251-256 | 6 | 5 |
| α-helix | 261-292 | 32 | |
| β-strand | 302-304 | 3 | 7 |
| α-helix | 306-312 | 7 | |
| β-strand | 318-324 | 7 | 7 |
| β-strand | 330-335 | 6 | 8 |
| β-strand | 342-347 | 6 | 8 |
| β-strand | 372 | 1 | 8 |
| α-helix | 375-381 | 7 | |
| β-strand | 390-393 | 4 | 7 |
| α-helix | 398-405 | 8 | |
| β-strand | 410-414 | 5 | 7 |
Chain ca: 9 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4 | 1 | 13 |
| α-helix | 11-12 | 2 | |
| α-helix | 23-25 | 3 | |
| α-helix | 26-28 | 3 | |
| β-strand | 29 | 1 | 13 |
| β-strand | 37-38 | 2 | 14 |
| β-strand | 43-48 | 6 | 14 |
| β-strand | 54-61 | 8 | 14 |
| β-strand | 63-68 | 6 | 15 |
| β-strand | 73-85 | 13 | 15 |
| α-helix | 89-94 | 6 | |
| β-strand | 96 | 1 | 14 |
| β-strand | 101-105 | 5 | 15 |
| α-helix | 108-115 | 8 | |
| α-helix | 156-162 | 7 | |
| α-helix | 173-181 | 9 | |
| β-strand | 184-188 | 5 | 15 |
| α-helix | 192-195 | 4 | |
| β-strand | 199-202 | 4 | 15 |
| α-helix | 206-215 | 10 | |
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 |
|---|
| 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 |
68 more molecules are not listed.
Sequence of entity 1 (aa), FASTA
>8IPA_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
>8IPA_2 40S ribosomal protein eS24 (chains ba)
MADAKTAPAVTLRTRKFMTNRLLSRKQFVLEVIHPGRANVSKADLKERLAKIYEVKDSNC
IFVFKFRTHFGGGKSTGFGLIYDNLEAAKKFEPKYRLIRNGLATKVEKSRKQIKERKNRT
KKIRGVKKTKAGDAKKK
Sequence of entity 3 (ca), FASTA
>8IPA_3 40S ribosomal protein eS8 (chains ca)
MGISRDSMHKRRATGGKQKAWRKKRKYELGRQPANTKLSSNKTVRRVRVRGGNVKWRALR
LDTGNFSWGSEAVTRKTRLLDVVYNSSNNELVRTQTLVKNAIVQVDAAPFKQWYLTHYGV
EIGRKKKAAAAAKKEPAEGQEAEVAAAATEEAKKSNNVQRKLEKRQQGRTLDSHIEEQFS
GGRLLACISSRPGQCGRADGYILEGKELEFYMRKLQKKKGKGATA
Sequence of entity 4 (da), FASTA
>8IPA_4 40S ribosomal protein eS10 (chains da)
MIISKKNRNEICKYLFQEGVLYAKKDYNLAKHPQIDVPNLQVIKLMQSFKSKEYVRETFS
WQHYYWYLTNDGIEFLRNFLNLPSEIVPATLKKSARPPGRPLGSGPPGDRPRGPPRFEGD
RPRYGDRDGYRGGPRGAPGDFGGEKGGAPAEFQPSFRSSGGGGFGRGGGGGFGRGGGGGG
GFGASPME
Sequence of entity 5 (ga), FASTA
>8IPA_5 40S ribosomal protein uS12 (chains ga)
MGKTRGMGAGRKLKTHRRNQRWADKAYKKSHLGNEWKKPFAGSSHAKGIVLEKIGIEAKQ
PNSAIRKCARVQLVKNGKKIAAFVPNDGCLNFIEENDEVLIAGFGRKGHAVGDIPGVRFK
VVKVSGVSLLALFKEKKEKPRS
Sequence of entity 6 (ha), FASTA
>8IPA_6 RACK1 (chains ha)
MAGAQESLVYAGVMRGHNDVVTAIATPIDNSPFIVSSSRDKSLLVWDLTNPIQATQDSSS
EYGVPFRRLTGHGHFVQDVVLSSDGQFALSGSWDGELRLWDLSTGVTTRRFVGHEKDVLS
VAFSIDNRQIVSASRDRTIKLWNTLGECKYTIGGDLGGGEGHTGWVSCVRFSPNNFAPTI
VSGSWDRSVKVWNLTNCKLRCTLDGHGGYVSAVAVSPDGSLCASGGKDGVTLLWDLTEGK
RLYSLDAGSIINSLCFSPNRYWLCAATQDSIKIWDLESKHIVQDLRPEVPVSTKQMLYCT
CLSWSADGSTLYAGYTDGTIRIYKISGFSYSS
Sequence of entity 7 (ia), FASTA
>8IPA_7 40S ribosomal protein uS3 (chains ia)
MATQISKKKKFVSDGVFYAELNEMLTRELAEDGYSGVEVRVTPMRTEIIIRATRTQNVLG
EKGRRIRELTSVVQKRFNFLENGVELYAEKVVNRGLCAIAQAESLRYKLLGGLAVRRACY
GVLRFVMESGAKGCEVIVSGKLRAQRAKSMKFKDGYMISSGQPVNEYIDAAVRHVLLRQG
VLGIKVKIMLDWDPKGKLGPTTPLPDLVTIHPPKEENELRPPALVEV
Sequence of entity 8 (ja), FASTA
>8IPA_8 40S ribosomal protein eS4 (chains ja)
MARGLKKHLKRLNAPSHWMLDKLGGAFAPKPSSGPHKARECLPLILILRNRLKYALTYRE
VQSILMQRHIMVDGKVRTDKTYPAGFMDIISIPKTGENYRLLYDTKGRFRLHSVRDEDAK
FKLCKVRSVQFGQKGIPYLNTYDGRTIRYPDPLIKANDTIKLDLETNKIVDFIKFDVGNV
VMVTGGRNTGRVGVIKNREKHKGTFETIHVEDAQGHQFATRLGNVFTIGKGTKPWVSLPK
GKGIKLTIIEEQRKRDAAAQAAAKA
Sequence of entity 9 (ka), FASTA
>8IPA_9 40S ribosomal protein uS7 (chains ka)
MAVVEPVPGGDVKLFNRWTFEDVQVSDISLNDYLAVTSMKHYTFLPHSAGRYSAKRFRKA
QCPIIERLTNSLMMHGRNNGKKIMAVRIIKHTMEIIHLLTDANPIQIIVDAIINSGPRED
ATRIGSAGVVRRQAVDISPLRRVNQAIYLLTTGARESAFRNVKTIAECLADELINAAKGS
SNSYAIKKKDEIERVAKANR
Sequence of entity 10 (la), FASTA
>8IPA_10 40S ribosomal protein uS9 (chains la)
MAAVLTRPTPGTVQCFGRKKTAVAVAYCKPGRGLIKVNGAPIELIRPEMLRLKAFEPILL
AGRSRFKDIDMRIRVRGGGKTSQIYSIRQAIAKSLVAYYQKYVDEAAKKEVKEIFARYDR
TLLVADPRRCEPKKFGGRGARARFQKSYR
Sequence of entity 11 (ma), FASTA
>8IPA_11 40S ribosomal protein uS10 (chains ma)
MATELAYAPPMKSGKLGFEGTQEVQHRIRITLSSKSVKNLEKVCSDLVKGAKEKQLKVKG
PVRMPTKVLNITTRKSPCGEGTNTWDRFEMRVHKRVIDLVSSPDVVKQITSITIEPGVEV
EVTISDQ
Sequence of entity 12 (na), FASTA
>8IPA_12 40S ribosomal protein uS11 (chains na)
MSSKRKTREPKEENVTLGPAVREGEHVFGVAHIFASFNDTFIHVTDLSGRETLVRITGGM
KVKADRDESSPYAAMLASQDVATRCKELGITALHIKLRATGGNKTKTPGPGAQSALRALA
RSGMKIGRIEDVTPVPTDSTRRKGGRRGRRL
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| 3HE | 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2… | C15 H23 N O4 | 1 |
| ZN | Zinc ion | Zn | 4 |
| MG | Magnesium ion | Mg | 284 |
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
- 8IPB 3.4 Å, Wheat 80S ribosome pausing on AUG-Stop with cycloheximide
Browse structure collections
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