6FYX: 40S ribosomal protein S0
Structure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain (model C1). Determined by electron microscopy at 3.5 Å resolution. Released 5 Dec 2018.
- Method
- Electron microscopy
- Resolution
- 3.5 Å
- Organisms
- Saccharomyces cerevisiae, Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37), Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
- Chains
- 47
- Atoms
- 104,404
- Mol. weight
- 1762.33 kDa
- Ligands
- GCP, MET, ZN, MG
- Released
- 5 Dec 2018
Explore 6FYX in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6FYX contains 338 α-helices and 397 β-strands across 44 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: 5 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 19 | 1 | |
| β-strand | 20-22 | 3 | 8 |
| α-helix | 23 | 1 | |
| β-strand | 29-31 | 3 | 8 |
| β-strand | 36-39 | 4 | 9 |
| β-strand | 42-43 | 2 | 10 |
| α-helix | 50-54 | 5 | |
| β-strand | 57 | 1 | 78 |
| β-strand | 66-67 | 2 | 10 |
| β-strand | 70-73 | 4 | 9 |
| α-helix | 75-80 | 6 | |
| α-helix | 86-88 | 3 | |
Chain A: 12 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-7 | 3 | |
| α-helix | 11-20 | 10 | |
| β-strand | 24 | 1 | 5 |
| β-strand | 37-40 | 4 | 6 |
| α-helix | 45 | 1 | |
| β-strand | 46-48 | 3 | 6 |
| α-helix | 50-66 | 17 | |
| α-helix | 70-72 | 3 | |
| β-strand | 73-77 | 5 | 7 |
| α-helix | 80-82 | 3 | |
| α-helix | 83-92 | 10 | |
| α-helix | 95 | 1 | |
| β-strand | 96-99 | 4 | 7 |
| β-strand | 120-123 | 4 | 7 |
| α-helix | 130-138 | 9 | |
| β-strand | 143-147 | 5 | 7 |
| β-strand | 159-161 | 3 | 7 |
| α-helix | 168-185 | 18 | |
| α-helix | 199-201 | 3 | |
| α-helix | 208-219 | 12 | |
Chain b: 4 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-17 | 6 | |
| α-helix | 19 | 1 | |
| β-strand | 32-36 | 5 | 13 |
| α-helix | 37 | 1 | |
| β-strand | 43-47 | 5 | 13 |
| β-strand | 54 | 1 | 14 |
| β-strand | 64-65 | 2 | 14 |
| α-helix | 71 | 1 | |
| β-strand | 72-73 | 2 | 14 |
| β-strand | 78 | 1 | 13 |
| β-strand | 81 | 1 | 13 |
Chain B: 11 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 27-33 | 7 | 11 |
| β-strand | 42-49 | 8 | 11 |
| α-helix | 57-61 | 5 | |
| β-strand | 65-69 | 5 | 11 |
| α-helix | 71-74 | 4 | |
| α-helix | 77-79 | 3 | |
| β-strand | 82-91 | 10 | 11 |
| β-strand | 95-105 | 11 | 11 |
| α-helix | 107-113 | 7 | |
| β-strand | 118 | 1 | 12 |
| α-helix | 119 | 1 | |
| β-strand | 120-128 | 9 | 11 |
| β-strand | 134-142 | 9 | 11 |
| α-helix | 144-146 | 3 | |
| β-strand | 154 | 1 | 12 |
| α-helix | 155-157 | 3 | |
| α-helix | 158-178 | 21 | |
| α-helix | 181-188 | 8 | |
| α-helix | 192-201 | 10 | |
| β-strand | 208-219 | 12 | 11 |
| α-helix | 225-231 | 7 | |
Chain c: 0 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 8-18 | 11 | 18 |
| β-strand | 25-32 | 8 | 18 |
| β-strand | 39-45 | 7 | 18 |
| β-strand | 53-56 | 4 | 18 |
Chain C: 11 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-43 | 3 | |
| α-helix | 45-52 | 8 | |
| α-helix | 58-63 | 6 | |
| α-helix | 72-77 | 6 | |
| β-strand | 82-94 | 13 | 15 |
| β-strand | 99-110 | 12 | 15 |
| β-strand | 115-123 | 9 | 15 |
| α-helix | 126-140 | 15 | |
| β-strand | 142-143 | 2 | 15 |
| β-strand | 146-147 | 2 | 16 |
| β-strand | 158-159 | 2 | 16 |
| β-strand | 163-167 | 5 | 17 |
| β-strand | 170-176 | 7 | 17 |
| β-strand | 183-184 | 2 | 17 |
| α-helix | 187-196 | 10 | |
| β-strand | 201-203 | 3 | 17 |
| β-strand | 206 | 1 | 17 |
| α-helix | 212-225 | 14 | |
| α-helix | 232-234 | 3 | |
| α-helix | 237-238 | 2 | |
| α-helix | 241-243 | 3 | |
| α-helix | 244-247 | 4 | |
Chain d: 2 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 30 | 1 | 23 |
| α-helix | 33-35 | 3 | |
| β-strand | 39 | 1 | 23 |
| α-helix | 40-50 | 11 | |
| β-strand | 53-54 | 2 | 116 |
Chain D: 8 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-28 | 22 | |
| β-strand | 34-41 | 8 | 19 |
| β-strand | 46-52 | 7 | 19 |
| α-helix | 55-59 | 5 | |
| α-helix | 65-76 | 12 | |
| α-helix | 79-80 | 2 | |
| β-strand | 84-90 | 7 | 19 |
| α-helix | 98-111 | 14 | |
| α-helix | 115-129 | 15 | |
| β-strand | 133-140 | 8 | 20 |
| β-strand | 148-155 | 8 | 20 |
| α-helix | 163-166 | 4 | |
| β-strand | 168-176 | 9 | 20 |
| β-strand | 181-189 | 9 | 20 |
| β-strand | 206-208 | 3 | 21 |
| α-helix | 209-211 | 3 | |
| β-strand | 223 | 1 | 22 |
36 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 |
|---|
| tRNAi | 1 | RNA | 75 | Saccharomyces cerevisiae | |
| 18S ribosomal RNA | 2 | RNA | 1798 | Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) | |
| mRNA (31-mer) | 3 | RNA | 49 | Saccharomyces cerevisiae | |
| 40S ribosomal protein S0 | A | protein | 254 | Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) | Q6CN12 (AlphaFold model) |
| 40S ribosomal protein S1 | B | protein | 255 | Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) | Q6CWD0 (AlphaFold model) |
| KLLA0F09812p | C | protein | 259 | Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) | Q6CKL3 (AlphaFold model) |
| KLLA0D08305p | D | protein | 237 | Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) | Q6CRK7 (AlphaFold model) |
| 40S ribosomal protein S4 | E | protein | 261 | Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) | Q6CWJ2 |
| KLLA0D10659p | F | protein | 227 | Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) | Q6CRA3 |
| 40S ribosomal protein S6 | G | protein | 236 | Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) | Q6CM04 |
| 40S ribosomal protein S7 | H | protein | 190 | Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) | Q6CTD6 |
| 40S ribosomal protein S8 | I | protein | 201 | Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) | Q6CMG3 |
35 more molecules are not listed.
Sequence of entity 1 (1), FASTA
>6FYX_1 tRNAi (chains 1)
AGCGCCGUGGCGCAGUGGAAGCGCGCAGGGCUCAUAACCCUGAUGUCCUCGGAUCGAAAC
CGAGCGGCGCUACCA
Sequence of entity 2 (2), FASTA
>6FYX_2 18S ribosomal RNA (chains 2)
UAUCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCU
AAGUAUAAGCAAUUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUCGUUUAU
UUGAUAGUUCCUUUACUACAUGGAUAUCUGUGGUAAUUCUAGAGCUAAUACAUGCUUAAA
AUCUCGACCCUUUGGAAGAGAUGUAUUUAUUAGAUAAAAAAUCAAUGUCUUCGGACUCCU
UGAUGAUUCAUAAUAACUUUUCGAAUCGCAUGGCCUUGUGCUGGCGAUGGUUCAUUCAAA
UUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUUUCAACGGGUAAC
GGGGAAUAAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAA
GGCAGCAGGCGCGCAAAUUACCCAAUCCUAAUUCAGGGAGGUAGUGACAAUAAAUAACGA
UACAGGGCCCAUUCGGGUCUUGUAAUUGGAAUGAGUACAAUGUAAAUACCUUAACGAGGA
ACAACUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAGUAGCGUAUA
UUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAACUUUGGGUCUGGUUGUCCGGUCCGA
CUUUAUGUCGCGCACGGUUUUUCAACCGGAUCUUUCCUUCUGGCUAACCUGUACUCCUUG
UGGGUGCAGGCGAACCAGGACUUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCGAA
AGCUCGAAUAUAUUAGCAUGGAAUAAUGGAAUAGGACGUUUGGUUCUAUUUUGUUGGUUU
CUAGGACCAUCGUAAUGAUUAAUAGGGACGGUCGGGGGCAUCAGUAUUCAAUUGUCAGAG
GUGAAAUUCUUGGAUUUAUUGAAGACUAACUACUGCGAAAGCAUUUGCCAAGGACGUUUU
CAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUCAGAUACCGUCGUAGUCUUAAC
CAUAAACUAUGCCGACUAGGGAUCGGGUGGUGUUUUUCUUAUGACCCACUCGGCACCUUA
CGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGG
AAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACXCAACACGGGG
AAACUCACCAGGUCCAGACACAAUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUUUG
UGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGCUUAAUUGCGAUA
ACGAACGAGACCUUAACCUACUAAAUAGGGUUGCUGGCACUUGCCGGUUGACUCUUCUUA
GAGGGACUAUCGGUUUCAAGCCGAUGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCU
UAGACGUUCUGGGCCGCACGCGCGCUACACUGACGGAGCCAGCGAGUACAACCUUGGCCG
AGAGGUCUGGGUAAUCUUGUGAAACUCCGUCGUGCUGGGGAUAGAGCAUUGUAAUUAUUG
CUCUUCAACGAGGAAUUCCUAGUAAGCGCAAGUCAUCAGCUUGCGUUGAUUACGUCCCUG
CCCUUUGUACACACCGCCCGUCGCUAGUACCGAUUGAAUGGCUUAGUGAGGCCUCAGGAU
UUGCUUAGAGAAGGGGGCAACUCCAUCUCAGAGCGAAGAAUCUGGUCAAACUUGGUCAUU
UAGAGGAACUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA
Sequence of entity 3 (3), FASTA
>6FYX_3 mRNA (31-MER) (chains 3)
GGGCUCUCUUCUCUCUCUAACUAUAAAAAUGUCUCUUCUCUCUCUCGAU
Sequence of entity 4 (A), FASTA
>6FYX_4 40S ribosomal protein S0 (chains A)
MSLPSTFDLTSEDAQLLLAARVHLGAKNVQVHQEPYVYKARPDGVNVINVGKTWEKIVLA
ARIIAAIPNPEDVVAISSRTYGQRAVLKYAAHTGATPIAGRFTPGSFTNYITRSFKEPRL
VIVTDPRSDAQAIKESSYVNIPVIALTDLDSPSEYVDVAIPCNNRGKHSIGLIWYLLARE
VLRLRGALPDRTQPWAIMPDLYFYRNPEEIEQQTAEEEAVASGEQTEEAVDATEEQTEAA
EWAEEGQAQEEEWN
Sequence of entity 5 (B), FASTA
>6FYX_5 40S ribosomal protein S1 (chains B)
MAVGKNKRLSKGKKGLKKRVVDPFTRKEWYDIKAPSTFENRNVGKTLVNKSVGLKNASDS
LKGRVVEVCLADLQGSEDHSFRKVKLRVDEVQGKNLLTNFHGMDFTTDKLRSMVRKWQTL
IEANVTVKTSDDYVLRIFAIAFTRKQANQVKRTSYAQSSHIRQIRKVISEILTREVQNST
LAQLTSKLIPEVINKEIENATKDIFPLQNVHIRKVKLLKQPKFDLGSLLSLHGEASAEEK
GKKVAGFKDEILETV
Sequence of entity 6 (C), FASTA
>6FYX_6 KLLA0F09812p (chains C)
MSAPQAQGQQAPRRGGFGGANRGGRGGRRGGRRDQEEKGWVPVTKLGRLVKAGKISSIEE
IFLHSLPVKEFQIIDQLLPNLKDEVMNIKPVQKQTRAGQRTRFKAVVVVGDSNGHVGLGI
KTAKEVAGAIRAGIIIAKLSVIPIRRGYWGTNLGQPHSLATKTSGKCGSVSVRLIPAPRG
SGIVASPAVKKLMQLAGVEDVYTSSTGSTRTLENTLKAAFVAIGNTYGFLTPNLWEVQAL
TPSPMDVYADYATASKKKL
Sequence of entity 7 (D), FASTA
>6FYX_7 KLLA0D08305p (chains D)
MVAIISKKRKLVADGVFYAELNEFFTRELAEEGYSGVEVRVTPTKTEIIIRATKVQDVVG
ENGRRINELTLLIEKRFKYKRGTIALYAERVHDRGLSAVAQAESMKFKLLNGLAIRRAAY
GVVRYVMESGAKGCEVVISGKLRAARAKSMKFADGFLIHSGQPVNDFIETATRHVLLRQG
VLGIKVKIMKDPSRNTSGPKALPDAVTIIEPKEEEPVLEPSVKDYRPTEPVEAAESA
Sequence of entity 8 (E), FASTA
>6FYX_8 40S ribosomal protein S4 (chains E)
MARGPKKHLKRLAAPHHWMLDKLSGCYAPRPSAGPHKLRESLPLIVFLRNRLKYALNGRE
VKAILMQRHVKVDGKVRTDTTFPAGFMDVITLEATNENFRLVYDVKGRFAVHRITDEEAS
YKLAKVKKVQLGKKGIPYVVTHDGRTIRYPDPNIKVNDTVKVDLATGTITDFIKFDTGKL
VYVTGGRNLGRVGTIVHRERHEGGFDLVHIKDSLENTFVTRLNNVFVIGEPGRPWISLPK
GKGIKLTISEERDRRRAQHGL
Sequence of entity 9 (F), FASTA
>6FYX_9 KLLA0D10659p (chains F)
MSEHEAQVEVEVQEDFEVVQEFVPVELATTIPVEIQQAQQEIKLFNKWSFEDVEVKDASL
VDYIQISKPIYVAHTAGRYANKRFRKAQCPIVERLTNSLMMNGRNNGKKLKAVRIVKHTL
EIINVLTDQNPLQVVVDAIINSGPREDTTRVGGGGAARRQAVDVSPLRRVNQSIALLTIG
AREAAFRNIKTIAETLAEELINAAKGSSTSYAIKKKDELERVAKSNR
Sequence of entity 10 (G), FASTA
>6FYX_10 40S ribosomal protein S6 (chains G)
MKLNISYPINGTQKCIEIDDEHRVRVFYDKRIGQEVDGESVGDEFKGYVFKIAGGNDKQG
FPMKQGVLLPTRVKLLLAKGHSCYRPRRNGERKRKSVRGAIVGPDLAVLALIITKKGEQE
IEGITNDTVPKRLGPKRANNIRKFFGLTKEDDVRDYVIRREVTKGDKSYTKAPKIQRLVT
PQRLQRKRQQKSLKIKNAQAQREAAAEYAQLLAKRLSERKAEKAEVRKRRASSLKA
Sequence of entity 11 (H), FASTA
>6FYX_11 40S ribosomal protein S7 (chains H)
MSDPQAKILSQAPTELELQVAQAFIDLENNSPELKADLRALQFKSIREIEVAGGKKALAV
FVPVPSLAAYHKVQIKLTRELEKKFQDRHVIFLAERRILPKPSRKSRQTQKRPRSRTLTA
VHDKILEDLVFPTEIVGKRVRYLVGGNKIQKILLNSKDVQHIDNKLESFQAVYNKLTGKQ
IVFEIPSETH
Sequence of entity 12 (I), FASTA
>6FYX_12 40S ribosomal protein S8 (chains I)
MGISRDSRHKRAATGAKRAQFRKKRKFELGRQAANTKIGTKRIHPVRTRGGNQKFRALRI
ETGNFSWASEGVARKTRITGVVYHPSNNELVRTNTLTKAAIVQIDATPFRQWYESHYGQS
LGKKKNTKAEEETATTSKNTERKWAARAAEAKIEHAVDSQFGAGRLYAAISSRPGQSGRC
DGYILEGEELAFYLRRLTAKK
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| GCP | Phosphomethylphosphonic acid guanylate ester | C11 H18 N5 O13 P3 | 1 |
| MET | Methionine | C5 H11 N O2 S | 1 |
| ZN | Zinc ion | Zn | 5 |
| MG | Magnesium ion | Mg | 117 |
Primary citation
Translational initiation factor eIF5 replaces eIF1 on the 40S ribosomal subunit to promote start-codon recognition. Llacer, J.L., Hussain, T., Saini, A.K. et al. Elife (2018) 7. DOI 10.7554/eLife.39273 · 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
- 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
- 8S8G 4.0 Å, Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model…
Browse structure collections
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