8I7J: 40S ribosomal protein S0
Yeast 40S-eIF4B - partially open conformation of the 40S head. Determined by electron microscopy at 4.6 Å resolution. Released 7 Feb 2024.
- Method
- Electron microscopy
- Resolution
- 4.6 Å
- Organisms
- Kluyveromyces lactis NRRL Y-1140, Saccharomyces cerevisiae S288C
- Chains
- 35
- Atoms
- 76,299
- Mol. weight
- 1176.98 kDa
- Ligands
- MG, ZN
- Released
- 7 Feb 2024
Explore 8I7J in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8I7J contains 175 α-helices and 249 β-strands across 34 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: 4 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 20-22 | 3 | 4 |
| β-strand | 29-31 | 3 | 4 |
| β-strand | 36-43 | 8 | 5 |
| α-helix | 50-55 | 6 | |
| β-strand | 57 | 1 | 68 |
| β-strand | 66-73 | 8 | 5 |
| α-helix | 75-80 | 6 | |
| α-helix | 85-86 | 2 | |
| α-helix | 89-92 | 4 | |
Chain A: 6 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 11-19 | 9 | |
| β-strand | 41 | 1 | 2 |
| β-strand | 45 | 1 | 2 |
| α-helix | 50-66 | 17 | |
| α-helix | 70-72 | 3 | |
| β-strand | 73-76 | 4 | 3 |
| α-helix | 80-92 | 13 | |
| β-strand | 95-98 | 4 | 3 |
| β-strand | 122-123 | 2 | 3 |
| α-helix | 130-138 | 9 | |
| β-strand | 144-146 | 3 | 3 |
| β-strand | 158-160 | 3 | 3 |
| α-helix | 170-185 | 16 | |
Chain b: 1 helix, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-16 | 5 | |
| β-strand | 32-36 | 5 | 9 |
| β-strand | 43-47 | 5 | 9 |
| β-strand | 64 | 1 | 10 |
| β-strand | 73 | 1 | 10 |
| β-strand | 78-81 | 4 | 9 |
Chain B: 7 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 27-33 | 7 | 6 |
| β-strand | 45-49 | 5 | 6 |
| β-strand | 65-69 | 5 | 7 |
| α-helix | 70-74 | 5 | |
| β-strand | 82-87 | 6 | 7 |
| β-strand | 91 | 1 | 6 |
| β-strand | 95-97 | 3 | 6 |
| α-helix | 98 | 1 | |
| β-strand | 99-105 | 7 | 7 |
| α-helix | 107-113 | 7 | |
| β-strand | 120-127 | 8 | 8 |
| β-strand | 134-142 | 9 | 8 |
| α-helix | 158-175 | 18 | |
| α-helix | 181-188 | 8 | |
| α-helix | 192-201 | 10 | |
| β-strand | 211-219 | 9 | 8 |
| α-helix | 225-230 | 6 | |
Chain c: 1 helix, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 8-11 | 4 | 15 |
| β-strand | 19 | 1 | 16 |
| β-strand | 25 | 1 | 16 |
| β-strand | 31-32 | 2 | 15 |
| α-helix | 33-35 | 3 | |
| β-strand | 54-56 | 3 | 15 |
Chain C: 8 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 46-52 | 7 | |
| α-helix | 58-63 | 6 | |
| α-helix | 72-77 | 6 | |
| β-strand | 83-94 | 12 | 11 |
| β-strand | 99-109 | 11 | 11 |
| β-strand | 116 | 1 | 12 |
| β-strand | 117-123 | 7 | 11 |
| α-helix | 126-139 | 14 | |
| β-strand | 142 | 1 | 12 |
| β-strand | 147 | 1 | 13 |
| β-strand | 158 | 1 | 13 |
| β-strand | 163-167 | 5 | 14 |
| β-strand | 170-175 | 6 | 14 |
| β-strand | 183-184 | 2 | 14 |
| α-helix | 187-196 | 10 | |
| β-strand | 201-203 | 3 | 14 |
| β-strand | 206 | 1 | 14 |
| α-helix | 212-225 | 14 | |
| α-helix | 241-243 | 3 | |
| α-helix | 244-247 | 4 | |
Chain d: 3 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 15-18 | 4 | |
| β-strand | 30-31 | 2 | 26 |
| α-helix | 33-35 | 3 | |
| β-strand | 38-39 | 2 | 26 |
| α-helix | 40-44 | 5 | |
| β-strand | 54 | 1 | 81 |
Chain D: 9 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-25 | 19 | |
| α-helix | 30-33 | 4 | |
| β-strand | 37 | 1 | 17 |
| β-strand | 46 | 1 | 18 |
| β-strand | 50 | 1 | 17 |
| α-helix | 56-59 | 4 | |
| α-helix | 66-77 | 12 | |
| β-strand | 84 | 1 | 18 |
| α-helix | 94-96 | 3 | |
| α-helix | 100-109 | 10 | |
| α-helix | 115-129 | 15 | |
| β-strand | 135-136 | 2 | 19 |
| β-strand | 137 | 1 | 20 |
| β-strand | 139 | 1 | 21 |
| β-strand | 140 | 1 | 22 |
| β-strand | 148 | 1 | 22 |
| β-strand | 151 | 1 | 20 |
| α-helix | 164-167 | 4 | |
| β-strand | 168-172 | 5 | 19 |
| β-strand | 176 | 1 | 23 |
| β-strand | 181 | 1 | 23 |
| β-strand | 183 | 1 | 21 |
| β-strand | 185-189 | 5 | 19 |
| α-helix | 193-195 | 3 | |
| β-strand | 208 | 1 | 24 |
| β-strand | 223 | 1 | 25 |
26 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 |
|---|
| RNA (1780-mer) | 2 | RNA | 1799 | Kluyveromyces lactis NRRL Y-1140 | |
| 40S ribosomal protein S0 | A | protein | 254 | Kluyveromyces lactis NRRL Y-1140 | Q6CN12 (AlphaFold model) |
| 40S ribosomal protein S1 | B | protein | 255 | Kluyveromyces lactis NRRL Y-1140 | Q6CWD0 (AlphaFold model) |
| KLLA0F09812p | C | protein | 259 | Kluyveromyces lactis NRRL Y-1140 | Q6CKL3 (AlphaFold model) |
| KLLA0D08305p | D | protein | 237 | Kluyveromyces lactis NRRL Y-1140 | Q6CRK7 (AlphaFold model) |
| 40S ribosomal protein S4 | E | protein | 261 | Kluyveromyces lactis NRRL Y-1140 | Q6CWJ2 |
| KLLA0D10659p | F | protein | 227 | Kluyveromyces lactis NRRL Y-1140 | Q6CRA3 |
| 40S ribosomal protein S6 | G | protein | 236 | Kluyveromyces lactis NRRL Y-1140 | Q6CM04 |
| 40S ribosomal protein S7 | H | protein | 190 | Kluyveromyces lactis NRRL Y-1140 | Q6CTD6 |
| 40S ribosomal protein S8 | I | protein | 201 | Kluyveromyces lactis NRRL Y-1140 | Q6CMG3 |
| KLLA0E23673p | J | protein | 188 | Kluyveromyces lactis NRRL Y-1140 | Q6CM18 |
| KLLA0B08173p | K | protein | 106 | Kluyveromyces lactis NRRL Y-1140 | Q6CVZ5 |
23 more molecules are not listed.
Sequence of entity 1 (2), FASTA
>8I7J_1 RNA (1780-MER) (chains 2)
UAUCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCU
AAGUAUAAGCAAUUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUCGUUUAU
UUGAUAGUUCCUUUACUACAUGGAUAUCUGUGGUAAUUCUAGAGCUAAUACAUGCUUAAA
AUCUCGACCCUUUGGAAGAGAUGUAUUUAUUAGAUAAAAAAUCAAUGUCUUCGGACUCCU
UGAUGAUUCAUAAUAACUUUUCGAAUCGCAUGGCCUUGUGCUGGCGAUGGUUCAUUCAAA
UUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUUUCAACGGGUAAC
GGGGAAUAAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAA
GGCAGCAGGCGCGCAAAUUACCCAAUCCUAAUUCAGGGAGGUAGUGACAAUAAAUAACGA
UACAGGGCCCAUUCGGGUCUUGUAAUUGGAAUGAGUACAAUGUAAAUACCUUAACGAGGA
ACAACUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAGUAGCGUAUA
UUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAACUUUGGGUCUGGUUGUCCGGUCCGA
CUUUAUGUCGCGCACUGGUUUUUCAACCGGAUCUUUCCUUCUGGCUAACCUGUACUCCUU
GUGGGUGCAGGCGAACCAGGACUUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCGA
AAGCUCGAAUAUAUUAGCAUGGAAUAAUGGAAUAGGACGUUUGGUUCUAUUUUGUUGGUU
UCUAGGACCAUCGUAAUGAUUAAUAGGGACGGUCGGGGGCAUCAGUAUUCAAUUGUCAGA
GGUGAAAUUCUUGGAUUUAUUGAAGACUAACUACUGCGAAAGCAUUUGCCAAGGACGUUU
UCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUCAGAUACCGUCGUAGUCUUAA
CCAUAAACUAUGCCGACUAGGGAUCGGGUGGUGUUUUUCUUAUGACCCACUCGGCACCUU
ACGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAG
GAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGG
GAAACUCACCAGGUCCAGACACAAUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUUU
GUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGCUUAAUUGCGAU
AACGAACGAGACCUUAACCUACUAAAUAGGGUUGCUGGCACUUGCCGGUUGACUCUUCUU
AGAGGGACUAUCGGUUUCAAGCCGAUGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCC
UUAGACGUUCUGGGCCGCACGCGCGCUACACUGACGGAGCCAGCGAGUACAACCUUGGCC
GAGAGGUCUGGGUAAUCUUGUGAAACUCCGUCGUGCUGGGGAUAGAGCAUUGUAAUUAUU
GCUCUUCAACGAGGAAUUCCUAGUAAGCGCAAGUCAUCAGCUUGCGUUGAUUACGUCCCU
GCCCUUUGUACACACCGCCCGUCGCUAGUACCGAUUGAAUGGCUUAGUGAGGCCUCAGGA
UUUGCUUAGAGAAGGGGGCAACUCCAUCUCAGAGCGAAGAAUCUGGUCAAACUUGGUCAU
UUAGAGGAACUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA
Sequence of entity 2 (A), FASTA
>8I7J_2 40S ribosomal protein S0 (chains A)
MSLPSTFDLTSEDAQLLLAARVHLGAKNVQVHQEPYVYKARPDGVNVINVGKTWEKIVLA
ARIIAAIPNPEDVVAISSRTYGQRAVLKYAAHTGATPIAGRFTPGSFTNYITRSFKEPRL
VIVTDPRSDAQAIKESSYVNIPVIALTDLDSPSEYVDVAIPCNNRGKHSIGLIWYLLARE
VLRLRGALPDRTQPWAIMPDLYFYRNPEEIEQQTAEEEAVASGEQTEEAVDATEEQTEAA
EWAEEGQAQEEEWN
Sequence of entity 3 (B), FASTA
>8I7J_3 40S ribosomal protein S1 (chains B)
MAVGKNKRLSKGKKGLKKRVVDPFTRKEWYDIKAPSTFENRNVGKTLVNKSVGLKNASDS
LKGRVVEVCLADLQGSEDHSFRKVKLRVDEVQGKNLLTNFHGMDFTTDKLRSMVRKWQTL
IEANVTVKTSDDYVLRIFAIAFTRKQANQVKRTSYAQSSHIRQIRKVISEILTREVQNST
LAQLTSKLIPEVINKEIENATKDIFPLQNVHIRKVKLLKQPKFDLGSLLSLHGEASAEEK
GKKVAGFKDEILETV
Sequence of entity 4 (C), FASTA
>8I7J_4 KLLA0F09812p (chains C)
MSAPQAQGQQAPRRGGFGGANRGGRGGRRGGRRDQEEKGWVPVTKLGRLVKAGKISSIEE
IFLHSLPVKEFQIIDQLLPNLKDEVMNIKPVQKQTRAGQRTRFKAVVVVGDSNGHVGLGI
KTAKEVAGAIRAGIIIAKLSVIPIRRGYWGTNLGQPHSLATKTSGKCGSVSVRLIPAPRG
SGIVASPAVKKLMQLAGVEDVYTSSTGSTRTLENTLKAAFVAIGNTYGFLTPNLWEVQAL
TPSPMDVYADYATASKKKL
Sequence of entity 5 (D), FASTA
>8I7J_5 KLLA0D08305p (chains D)
MVAIISKKRKLVADGVFYAELNEFFTRELAEEGYSGVEVRVTPTKTEIIIRATKVQDVVG
ENGRRINELTLLIEKRFKYKRGTIALYAERVHDRGLSAVAQAESMKFKLLNGLAIRRAAY
GVVRYVMESGAKGCEVVISGKLRAARAKSMKFADGFLIHSGQPVNDFIETATRHVLLRQG
VLGIKVKIMKDPSRNTSGPKALPDAVTIIEPKEEEPVLEPSVKDYRPTEPVEAAESA
Sequence of entity 6 (E), FASTA
>8I7J_6 40S ribosomal protein S4 (chains E)
MARGPKKHLKRLAAPHHWMLDKLSGCYAPRPSAGPHKLRESLPLIVFLRNRLKYALNGRE
VKAILMQRHVKVDGKVRTDTTFPAGFMDVITLEATNENFRLVYDVKGRFAVHRITDEEAS
YKLAKVKKVQLGKKGIPYVVTHDGRTIRYPDPNIKVNDTVKVDLATGTITDFIKFDTGKL
VYVTGGRNLGRVGTIVHRERHEGGFDLVHIKDSLENTFVTRLNNVFVIGEPGRPWISLPK
GKGIKLTISEERDRRRAQHGL
Sequence of entity 7 (F), FASTA
>8I7J_7 KLLA0D10659p (chains F)
MSEHEAQVEVEVQEDFEVVQEFVPVELATTIPVEIQQAQQEIKLFNKWSFEDVEVKDASL
VDYIQISKPIYVAHTAGRYANKRFRKAQCPIVERLTNSLMMNGRNNGKKLKAVRIVKHTL
EIINVLTDQNPLQVVVDAIINSGPREDTTRVGGGGAARRQAVDVSPLRRVNQSIALLTIG
AREAAFRNIKTIAETLAEELINAAKGSSTSYAIKKKDELERVAKSNR
Sequence of entity 8 (G), FASTA
>8I7J_8 40S ribosomal protein S6 (chains G)
MKLNISYPINGTQKCIEIDDEHRVRVFYDKRIGQEVDGESVGDEFKGYVFKIAGGNDKQG
FPMKQGVLLPTRVKLLLAKGHSCYRPRRNGERKRKSVRGAIVGPDLAVLALIITKKGEQE
IEGITNDTVPKRLGPKRANNIRKFFGLTKEDDVRDYVIRREVTKGDKSYTKAPKIQRLVT
PQRLQRKRQQKSLKIKNAQAQREAAAEYAQLLAKRLSERKAEKAEVRKRRASSLKA
Sequence of entity 9 (H), FASTA
>8I7J_9 40S ribosomal protein S7 (chains H)
MSDPQAKILSQAPTELELQVAQAFIDLENNSPELKADLRALQFKSIREIEVAGGKKALAV
FVPVPSLAAYHKVQIKLTRELEKKFQDRHVIFLAERRILPKPSRKSRQTQKRPRSRTLTA
VHDKILEDLVFPTEIVGKRVRYLVGGNKIQKILLNSKDVQHIDNKLESFQAVYNKLTGKQ
IVFEIPSETH
Sequence of entity 10 (I), FASTA
>8I7J_10 40S ribosomal protein S8 (chains I)
MGISRDSRHKRAATGAKRAQFRKKRKFELGRQAANTKIGTKRIHPVRTRGGNQKFRALRI
ETGNFSWASEGVARKTRITGVVYHPSNNELVRTNTLTKAAIVQIDATPFRQWYESHYGQS
LGKKKNTKAEEETATTSKNTERKWAARAAEAKIEHAVDSQFGAGRLYAAISSRPGQSGRC
DGYILEGEELAFYLRRLTAKK
Sequence of entity 11 (J), FASTA
>8I7J_11 KLLA0E23673p (chains J)
MPRAPRTYSKTYSTPKRPYESARLDAELKLAGEYGLKNKREIYRISFQLSKIRRAARDLL
TRDEKDPKRLFEGNALIRRLVRIGVLSEDKKKLDYVLALKVEDFLERRLQTQVYKLGLAK
SVHHARVLISQRHIAVGKQIVNIPSFMVRLESEKHIDFARTSPFGGARPGRVARKRAAAA
GGEEADEE
Sequence of entity 12 (K), FASTA
>8I7J_12 KLLA0B08173p (chains K)
MLIPKEDRKKIYQHLFQEGVLVAKKDFNQPKHEEIDTKNLFVIKALQSLTSKGFVKTQFS
WQYYYYTLTEEGVVYLREYLNLPEHIFPATYLAGQSGDQRPQGKKY
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 2 |
| ZN | Zinc ion | Zn | 3 |
Primary citation
Yeast Eukaryotic Initiation Factor 4B Remodels the MRNA Entry Site on the Small Ribosomal Subunit. Datey, A., Sharma, P., Khaja, F.T. et al. Biochemistry (2025). DOI 10.1021/acs.biochem.4c00489 · PubMed
Other PDB entries of the same protein (UniProt Q6CN12 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 6FYY 3.02 Å, Structure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain…
- 8RW1 3.35 Å, Structure of a yeast 48S-AUC preinitiation complex in closed conformation
- 8S8D 3.45 Å, Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model…
- 3JAM 3.46 Å, CryoEM structure of 40S-eIF1A-eIF1 complex from yeast
- 6FYX 3.5 Å, Structure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain…
- 5IT7 3.6 Å, Structure of the Kluyveromyces lactis 80S ribosome in complex with the cricket paralysis…
- 6UZ7 3.6 Å, K.lactis 80S ribosome with p/PE tRNA and eIF5B
- 3J80 3.75 Å, CryoEM structure of 40S-eIF1-eIF1A preinitiation complex
- 5IT9 3.8 Å, Structure of the yeast Kluyveromyces lactis small ribosomal subunit in complex with the…
- 8S8E 3.85 Å, Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model…
- 8S8F 3.95 Å, Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model…
- 3J81 4.0 Å, CryoEM structure of a partial yeast 48S preinitiation complex
Browse structure collections
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